Protein structure prediction method based on mutual attraction relationship between residue side chain low-entropy hydration layers

Abstract

The invention discloses a protein structure prediction method based on a mutual attraction relation between residue side chain low-entropy hydration layers, and belongs to the technical field of structural biology. The problem that an existing prediction method of the protein folding structure is poor in prediction effect is solved. According to the protein structure prediction method based on the mutual attraction relation between the residue side chain low-entropy hydration layers, protein structure prediction is achieved through water entropy force; the prediction is to predict a secondary structure and a tertiary structure of the protein based on the primary structure of the protein; the water entropy force is an interaction attraction force between amino residue side chain low-entropy hydration layers; the interaction attraction force means that entropy increase of low-entropy water molecules of the low-entropy hydration layer drives lateral attachment between amino acid residue side chains; the lateral attachment means that the two residue side chains are in a nearly parallel state. The method is used for protein structure prediction.

Description

Technical Field

[0001] The invention belongs to the technical field of structural biology, and in particular relates to a protein structure prediction method. Background Art

[0002] Protein structure prediction is crucial for biological research. The function of a protein depends largely on its structure, so obtaining the three-dimensional structure of a protein is crucial for understanding its function, interaction, and pathological mechanisms. At present, protein structure prediction mainly uses methods such as deep learning, comparative models, and molecular dynamics simulation. Among them, deep learning, that is, artificial intelligence and machine learning technology, has played a key role in protein structure prediction, but the progress of this technical method can only be attributed to the progress in the field of artificial intelligence. Artificial intelligence methods do not yet directly derive protein folding rules and protein structure prediction methods based on clear physical and chemical mechanisms. In addition, using molecular dynamics simulation to try to simulate the folding process of proteins on computers is considered to be a way to solve the protein folding problem based on physical methods. This approach requires a large amount of high-performance computing resources to simulate the movement and interaction of polypeptide chain molecules over a certain period of time to infer the most stable protein structure, but the current protein folding dynamics simulation method still cannot accurately predict the molecular structure of proteins.

[0003] The popular view in the academic community today is that the physical driving forces of protein folding include hydrophobic interaction, hydrogen bonding, electrostatic force, van der Waals force, ionic bond force, etc. The effect of predicting protein folding structure based on this theoretical prediction method is not ideal. Accurate protein folding only occurs in an aqueous environment. In any other non-aqueous solvent, most proteins cannot fold correctly. It must be emphasized that water molecules have extremely strong electrical polarity, a very high dielectric constant, and an obvious electrostatic shielding effect. Therefore, it can be seen that the above prediction methods based on hydrogen bonding, electrostatic force, van der Waals force, ionic bond force, etc. cannot be well explained in theory. This also explains why the above prediction methods have poor prediction results, and also confirms that the above prediction methods have the problem of unsatisfactory prediction results in theory. At present, there is no method that is urgently needed to predict protein structure based only on the law of hydrophobic interaction between the side chains of amino acid residues. Summary of the invention

[0004] The present invention aims to solve the problem that the current prediction methods for protein folding structure have poor prediction effects.

[0005] A protein structure prediction method based on the mutual attraction relationship between low entropy hydration layers of residue side chains, the prediction method is to realize protein structure prediction by using water entropy force; the prediction is to predict the secondary structure and tertiary structure of the protein based on the primary structure of the protein; the water entropy force refers to the interaction attraction between the low entropy hydration layers of the amino residue side chains; the interaction attraction refers to the entropy increase of low entropy water molecules in the low entropy hydration layer driving the lateral adhesion between the amino acid residue side chains; the lateral adhesion refers to the state that the two residue side chains are in a nearly parallel state.

[0006] Furthermore, the process of using water entropy force to predict protein structure includes:

[0007] 1. Forecasting preparation:

[0008] Firstly, an entropy value is assigned to the side chains of amino acid residues in the primary structure of the protein, wherein the entropy value is a relative measure of the entropy increase potential of the low entropy hydration layer outside the side chains of the amino acid residues;

[0009] Then, the amino acid residue side chains in the primary structure of the protein after entropy assignment are divided into five residue forms:

[0010] Residues with micro-entropy increase potential: serine S, threonine T, aspartic acid D, asparagine N;

[0011] Hydrophilic residues: histidine H, arginine R, lysine K, glutamic acid E, glutamine Q, aspartic acid D, asparagine N, tyrosine Y, tryptophan W, serine S;

[0012] Turn residues: glycine G, proline P;

[0013] Hydrophobic residues: isoleucine I, valine V, leucine L, phenylalanine F, tyrosine Y, tryptophan W, alanine A, methionine M, cysteine ​​C, histidine H;

[0014] Residues with high entropy increase potential: isoleucine I, valine V, leucine L, lysine K, arginine R, phenylalanine F, tyrosine Y, tryptophan W, alanine A, methionine M, cysteine ​​C, glutamate E, glutamine Q, histidine H;

[0015] Finally, determine the preferred pairing between amino acid residue side chains

[0016] The preferred pairing between the side chains of amino acid residues is that the side chains of multiple pairs of amino acid residues are laterally fitted together, resulting in sufficient entropy increase of the low entropy hydration layers of the side chains of multiple pairs of amino acid residues. The pair relationship between the multiple pairs of amino acid residues is the preferred pairing between the side chains of amino acid residues.

[0017] The preferred pairing between the side chains of amino acid residues includes the preferred pairing between the side chains of amino acid residues in a 1-4 / 5 sequence position relationship, the preferred pairing between the side chains of amino acid residues in a 1-3 sequence position relationship, and the preferred pairing between the side chains of amino acid residues in a 1-2 sequence position relationship;

[0018] The 1-4 / 5 sequence position relationship refers to the relationship between the sequence positions of one residue side chain and another residue side chain in the amino acid residue sequence in the primary structure of the protein, which are separated by 2 or 3 amino acid residues;

[0019] The 1-3 sequence position relationship refers to the relationship between the sequence positions of one residue side chain and another residue side chain in the primary structure of the protein, which are separated by one amino acid residue;

[0020] The 1-2 sequence position relationship refers to the sequence position relationship between a residue side chain and another adjacent residue side chain in the amino acid residue sequence in the primary structure of the protein;

[0021] 2. Protein secondary structure prediction:

[0022] Based on the sequence position of the residue side chains in step 1, the classification and entropy value of the amino acid residues, and the preferred pairing between the residue side chains, the following process is used to predict the secondary structure of the protein:

[0023] S100, starting a new line below the amino acid sequence marked with entropy values, repeatedly listing the amino acid residues in the amino acid sequence that are high entropy increase potential residues as a high entropy increase potential residue connected segment; then, starting a new line, repeatedly listing the amino acid residues in the amino acid sequence that are low entropy residues and corner residues;

[0024] S200. List the unblocked connected segments of residues with high entropy increase potential, and assume the listed unblocked connected segments of residues with high entropy increase potential to be α-helices or β-folds in the secondary structure of the protein:

[0025] S201. Assuming that the connected segment of residues with high entropy increase potential forms an α-helix, if a residue side chain in the connected segment of residues with high entropy increase potential achieves preferred pairing between amino acid residue side chains, the amino acid residue in the connected segment of residues with high entropy increase potential is marked as * below;

[0026] S202, assuming that the high entropy increase potential residue connected segment forms a β-fold, if the high entropy increase potential residue connected segment is a preferred pairing between the side chains of the amino acid residues in the 1-3 sequence position relationship, then the amino acid residues in the high entropy increase potential residue connected segment are marked as &;

[0027] S203, analyze the marked * and &:

[0028] S2031. If none of the connected segments of residues with high entropy increase potential in the primary structure of the protein are marked as &-&, and more than 80% of the amino acid residues in the connected segment of residues with high entropy increase potential are marked as *, then it is predicted that the connected segment of residues with high entropy increase potential forms an α-helix;

[0029] S2032. If the connected segment of residues with high entropy increase potential in the primary structure of the protein is marked with &-&, it is predicted that the connected segment of residues with high entropy increase potential forms a β-fold; if the number of * marked in the connected segment of residues with high entropy increase potential in the primary structure of the protein is less than 50% of the number of amino acid residues in the connected segment of residues with high entropy increase potential, it is predicted that the connected segment of residues with high entropy increase potential forms a β-fold;

[0030] S300, searching the amino acid side chains on both sides of the connected segment of high entropy increase potential residues that have been predicted by S200 to form an α-helix, if the amino acid residues in the amino acid side chains on both sides have a preferred pairing between the amino acid residue side chains in a 1-4 / 5 sequence position relationship with the amino acid residues in the connected segment of high entropy increase potential residues, then it is predicted that the amino acid residue side chains in a 1-4 / 5 sequence position relationship preferably pair to form an α-helix;

[0031] S400, determine whether the S200 hypothesis predicts the formation of α-helix or β-fold in the protein secondary structure:

[0032] The entropy increments of the amino acid residues in the primary structure of the protein predicted to be α-helix and β-fold are respectively counted, and the entropy increments of the α-helix predicted to be β-fold are compared; when the value of the relatively larger entropy increment of the two is greater than the value of the other entropy increment by more than 20%, the prediction result of the relatively larger entropy value of the two is determined as the final prediction result; when the value of the relatively larger entropy increment of the two is less than 20% of the other entropy increment, the prediction of the formation of α-helix or β-fold in the secondary structure of the protein by S200 hypothesis is determined as a potential result;

[0033] Among them, the entropy value-added statistical method of β-folding: the side chains of amino acid residues with a 1-3 sequence position relationship in the primary structure of the protein are preferably paired, and the entropy value of the amino acid residues in the preferred pairing is used as the entropy value;

[0034] Statistical method for entropy increment of α-helix: the preferred pairing between the side chains of amino acid residues with a 1-4 / 5 sequence position relationship in the primary structure of the protein is used, and the entropy value of the amino acid residues in the preferred pairing is used as the entropy increment;

[0035] S500, if there are two consecutive amino acid residues with low entropy increase potential in the connected segment of high entropy increase potential residues that are not predicted to be α-helices in the primary structure of the protein, the two amino acid residues are predicted to form a turn and are marked as T;

[0036] A segment of 4 or more consecutive hydrophilic amino acid residues in the primary structure of a protein is named a "continuous hydrophilic residue segment"; if there is a segment with more than 7 amino acid residues in the high entropy increase potential residue connected segment that is not predicted to be an α-helix in the primary structure of a protein, and the number of residues with low entropy increase potential and / or corner residues and / or amino acid residue A and / or residues in the continuous hydrophilic residue segment accounts for more than or equal to 50% of the number of the segment with more than 7 amino acid residues, then the segment with more than 7 amino acid residues is predicted to form a random curl and is used as a potential prediction result;

[0037] S600. A fragment consisting of 5 or more consecutive hydrophilic amino acid residues in the primary structure of a protein, if the fragment has been predicted to be a connected fragment of residues with high entropy increase potential, then the fragment consisting of 5 or more consecutive hydrophilic amino acid residues is predicted to form a random curl, and used as a potential prediction result, thereby completing the protein structure prediction method based on the mutual attraction relationship between the low entropy hydration layers of the residue side chains.

[0038] Furthermore, preferred pairings between amino acid residue side chains include:

[0039] FF, QQ, KK, EE, TT, RR, AA, SS, MM;

[0040] MA, QE, TS, RE, KR, EK, FY, WY, WE, RW, RY, KY, HV, DE, NE, DQ, NQ;

[0041] QR / K, I / V / L / FI / V / L / F, I / V / L / F / YI / V / L / F / Y, I / V / LY, I / V / LK, I / V / LR, I / V / LA, I / V / LW, I / V / L / F / YW, I / V / LM, CM / Y, MI / V / L, A / TD / N.

[0042] Furthermore, the preferred pairing between amino acid residue side chains in step S201 refers to the preferred pairing between amino acid residue side chains with a 1-4 / 5 sequence position relationship; if there is a preferred pairing between amino acid residue side chains with a 1-2 sequence position relationship in the connected segment of residues with high entropy increase potential, or there is a sequence position relationship of I / V / L 1-4 / 5G / A1-4 / 5I / V / L / F in the connected segment of residues with high entropy increase potential, it is marked as * below the amino acid.

[0043] Furthermore, the preferred pairing between the side chains of the amino acid residues in the 1-3 sequence position relationship described in S202 is I / V / L / FI / V / L / F; if taking the amino acids in I / V / L / FI / V / L / F as the starting point, there is a preferred pairing between the side chains of the amino acid residues in the 1-4 / 5 sequence position relationship in the adjacent high entropy increase potential residue connected fragment, then the amino acids in the preferred pairing between the side chains of the amino acid residues in the 1-3 sequence position relationship are not marked as &.

[0044] Furthermore, as described in S2032, if a connected segment of residues with high entropy increase potential in the primary structure of a protein is marked with &-&, and more than 85% of the amino acid residues in the amino acid side chain region in the primary structure of the protein far away from the connected segment of residues with high entropy increase potential marked with &-& are marked with *, and there is a preferred pairing between the side chains of amino acid residues that has a 1-4 / 5 sequence position relationship of I / V / L / F / YI / V / L / F / Y with the irrelevant residues marked with &-&, then it is predicted that the connected segment of residues with high entropy increase potential marked with &-& forms an α-helix; wherein, the distance refers to a continuous interval of two low entropy residues or corner residues, or an interval of at least 3 hydrophilic residues, or an interval of one amino acid residue P; the irrelevant residues refer to other amino acid residues in the primary structure of the protein except those marked with &-&; the amino acid side chain region refers to a region composed of amino acid side chains with a number of amino acid residues greater than 5.

[0045] Further, the connected segment of residues with high entropy increase potential described in S2032 is predicted to form a β-fold, and there are two consecutive low entropy residues aspartic acid D or asparagine N in the connected segment of residues with high entropy increase potential, then the two consecutive low entropy residues aspartic acid D or asparagine N are predicted to form a turn as a prediction result.

[0046] Furthermore, in the entropy increment statistics of the β-fold described in S400, if the same amino acid residue in the primary structure of the protein realizes the preferred pairing between the side chains of two amino acid residues with a 1-3 sequence position relationship, the entropy increment of the amino acid residue is accumulated twice;

[0047] In the entropy increment statistics of α-helix, if the same amino acid residue in the primary structure of the protein realizes multiple preferred pairings between the side chains of amino acid residues with a 1-4 / 5 sequence position relationship, the entropy increment of the amino acid residue is accumulated twice.

[0048] Furthermore, in the entropy increase statistics of the α-helix described in S400, if there is a preferred pairing between the side chains of amino acid residues with a 1-2 sequence position relationship in the primary structure of the protein, and the preferred pairing is I / V / L / MI / V / L / M, then the two pairs of I / V / L / M are recorded as one entropy increase.

[0049] Furthermore, the amino acid residues in the two consecutive amino acid residues in S600 are one or two of S, T, N, D, and G.

[0050] Furthermore, the relative measurement value of the entropy increase potential of the low entropy hydration layer around the side chains of amino acid residues in the primary structure of the protein is a measurement indicator that takes the length of the hydrophobic portion on the side chains of amino acid residues in the primary structure of the protein as the relative measurement value.

[0051] Furthermore, the relative measure of the entropy increase potential of the low entropy hydration layer on the periphery of the amino acid residue side in the primary structure of the protein is to take the number of carbon-carbon bonds on the amino acid residue chain in the primary structure of the protein as 1 entropy value.

[0052] Furthermore, the entropy values ​​of the 20 amino acids are as follows:

[0053] Serine S=0.5, threonine T=0.5, aspartic acid D=0.5, asparagine N=0.5, glycine G=0, histidine H=3, arginine R=3, glutamic acid E=3, lysine K=4, tryptophan W=5, isoleucine I=6, valine V=6, leucine L=6, phenylalanine F=6, proline P=0, cysteine ​​C=4, glutamine Q=3, alanine A=1, methionine M=4, tyrosine Y=5.

[0054] Furthermore, the sufficient entropy increase described in step one means that when the side chains of two amino acid residues in the primary structure of the protein are similar, the two residue side chains are laterally fitted together, so that the low entropy hydration layer of the two side chains undergoes sufficient entropy increase; the similarity of the amino acid residue side chains means that the smaller the difference in entropy values ​​of the two hydrophilic amino acid residues is, the more similar the two hydrophilic residues are; and the smaller the difference in entropy values ​​of the two hydrophobic amino acid residues is, the more similar the two hydrophobic residues are.

[0055] Furthermore, in the process of determining the unblocked high entropy increase potential residue connected segment, first find the segment consisting of consecutive high entropy increase potential residues in the sequence, name the original "high entropy increase potential residue connected segment", then determine the non-high entropy increase potential residues that do not block the high entropy increase potential residue connected segment, and then determine the unblocked high entropy increase potential residue connected segment, specifically including:

[0056] (1) When there is only one amino acid residue S or T between two residues with high entropy increase potential, the S or T residue participates in forming an unblocked high entropy increase potential residue connected segment;

[0057] (2) When there is only one isolated N, D or G residue between two high entropy increase potential residues in the amino acid sequence, and there is a high entropy pairing between I, V, L, F, and Y with a 1-3 or 1-4 / 5 relationship across the D, N or G, then the D, N or G is considered to participate in the formation of an unblocked high entropy increase potential residue connected segment;

[0058] (3) When any one of the amino acid residues S, T, N, D, and G appears in the amino acid sequence of the polypeptide chain, and it is adjacent to any one of the amino acid residues S, T, N, D, and G, check the 1-4 / 5 sequence position relationship across the two adjacent amino acid residues. When the two amino acid residues at the 1-4 / 5 position are both I, V, L, F, and Y residues, and at least one of the amino acid residues is I, V, or L, it is predicted that the two adjacent amino acid residues participate in forming an unblocked high entropy increase potential residue connected segment;

[0059] (4) When a P residue appears in the amino acid sequence of a polypeptide chain, and the P residue is not in a 1-2 or 1-3 sequence position relationship with a D or N residue, and there is a 1-4 / 5 sequence position relationship across the P residue, and the amino acid residues on 1-4 / 5 are I, V, L, or F, then the predicted P residue participates in the formation of an unblocked high entropy increase potential residue connected segment;

[0060] (5) When a G or A residue appears in the amino acid sequence of a polypeptide chain, if an amino acid residue that forms a 1-4 / 5 sequence position relationship with the residue can be found on one side of the sequence where the G or A residue is located, and an amino acid residue that forms a 1-4 / 5 sequence position relationship with the G or A residue can also be found on the other side of the sequence where the G or A residue is located, and if there is a single D, N, G or P residue that is not adjacent to other microentropy residues or corner residues between the I, V, L residues, or there are two adjacent S, T, N, D residues, then it is predicted that these single D, N, G or P residues or two adjacent S, T, N, D, G residues participate in the formation of an unblocked high entropy increase potential residue connected segment.

[0061] Furthermore, the length of the unblocked connected segment of residues with high entropy increase potential is greater than or equal to 3 amino acid residues.

[0062] Furthermore, if there is a fragment of 5 or more amino acid residues in the sequence whose primary structure is not predicted to be an α-helix or β-turn, when the fragment is in the general initial thermodynamic metastable state of unfolded protein, if there is no hydrophilic atom of the side chain of a hydrophilic amino acid residue in the fragment whose value minus the height of the adjacent hydrophobic residue side chain is less than or equal to 1, then the fragment is predicted to be a β-fold; wherein the height of the residue side chain refers to the height of the residue side chain, in which the number of covalent bonds within the shortest path between the top atom of the side chain of the amino acid residue and the carbon atom of its main chain in the fragment is the number of covalent bonds.

[0063] A protein structure prediction method based on the mutual attraction relationship between low entropy hydration layers of residue side chains, wherein the prediction method uses water entropy force to achieve protein structure prediction; the prediction is based on the secondary structure of the protein predicted by the protein structure prediction method based on the mutual attraction relationship between low entropy hydration layers of residue side chains to predict the tertiary structure of the protein, including the following steps:

[0064] Definition of the similarity of amino acid residue side chains: The smaller the difference in the "entropy values" of the side chains of two hydrophilic residues, the more similar the two hydrophilic residues are; the smaller the difference in the "entropy values" of the side chains of two hydrophobic residues, the more similar the two hydrophobic residues are;

[0065] The amino acid residues that have achieved the preferred pairing between I / V / L / F in the predicted secondary structure are marked, and the hydrophobic surface of the hydrophobic side chain cluster that has achieved the lateral fit between the side chains of the I / V / L / F amino acid residues is marked and named as "cluster hydrophobic surface". The protein structure is predicted to be the one where the hydrophobic surface of an I / V / L / F cluster and the hydrophobic surface of another adjacent I / V / L / F cluster are fitted on the surface;

[0066] When there is no preferred pairing relationship between I / V / L / F in a β-sheet or α-helix secondary structure, the secondary structure is searched for a preferred pairing relationship between I / V / LY. If so, the hydrophobic surface of the hydrophobic side chain clusters that are laterally attached between the side chains of the I / V / LY amino acid residues is also marked as a "cluster hydrophobic surface"; it is predicted that a hydrophobic surface of an I / V / L / Y cluster and a hydrophobic surface of another adjacent cluster will be attached to form a protein structure;

[0067] When an α-helical structure has two clustered hydrophobic surfaces and the two clustered hydrophobic surfaces are not connected in the axial direction of the α-helix, it is predicted that one of the clustered hydrophobic surfaces with a smaller number of I / V / L / F / Y will not fit with the other I / V / LF / clustered hydrophobic surface in an adjacent β-sheet or α-helical secondary structure as a possible prediction result.

[0068] Furthermore, the protein structure prediction method based on the mutual attraction relationship between the low entropy hydration layers of the residue side chains further includes the following steps:

[0069] For the current prediction of β-fold, it is necessary to mark the strong hydrophobic residues of the 1-3 position relationship preferred pairing connected fragments in the β-fold, i.e., I / V / L / F / W / Y, and mark these hydrophobic fragments connected by the 1-3 position relationship at the same time, compare the lengths of adjacent β-folds in the sequence, and predict that α-helices of similar lengths will fold into a sheet structure, and then based on the distribution of the side chains of the strong hydrophobic residues of the two β-folds, the corresponding positions of the two are based on the most strong hydrophobic residues on one β-fold to achieve preferred pairing with the side chains of the amino acid residues on the other α-helix. The state of the two β-folds being attached is the predicted sheet folding structure.

[0070] The present invention has the following beneficial effects:

[0071] After research, the present invention believes that only the hydrophobic interaction between the side chains of amino acid residues is the core driving force of protein folding, and the effects of hydrogen bonding, electrostatic force, van der Waals force, ionic bonding force, etc. are byproducts of hydrophobic interaction, that is, the products of entropy enthalpy compensation. Furthermore, the present invention proposes a method for predicting protein structure based only on the law of hydrophobic interaction between the side chains of amino acid residues. The present invention can accurately analyze the folding dynamic mechanism and folding law of protein structure, so as to accurately predict the protein folding structure, and provide a method for predicting the secondary and tertiary structures of proteins based on the law. It helps scientists design new proteins and purposefully mutate existing protein structures for important biological applications. BRIEF DESCRIPTION OF THE DRAWINGS

[0072] Figure 1 Schematic diagram of amino acid residues in the low entropy hydration layer of 20 amino acids, the atoms in the dotted box are hydrophobic atoms;

[0073] Figure 2 It is a diagram of the lateral fitting state of two amino acid residues E and one amino acid residue K;

[0074] Figure 3 This is a diagram of the side chain alignment of adjacent amino acid residues in a typical strand structure.

[0075] Figure 4 A schematic diagram of the relationship between the sequence positions of an amino acid residue side chain and a certain amino acid residue side chain separated by 2 or 3 amino acid residues, i.e., a 1-4 / 5 sequence position relationship;

[0076] Figure 5 Schematic diagram of the positional relationship of 1-2 sequences;

[0077] Figure 6 There are three carbon-carbon bonds in the side chain of amino acid residue E;

[0078] Figure 7 It is the optimal entropy increase pairing diagram;

[0079] Figure 8 A schematic diagram of the fitting of the hydrophobic end of the side chain of an amino acid residue and the hydrophobic part of the side chain of another amino acid residue;

[0080] Fig. 9 Schematic diagram of the hydrophobic surface of the cluster;

[0081] Fig.10 This is a schematic diagram of the folding structure of the sheet;

[0082] Fig.11 This is a schematic diagram of the configuration of the "cluster hydrophobic surfaces" fully fitting together;

[0083] Fig.12 Schematic diagram of a helix structure;

[0084] Fig.13 Schematic diagram of the sheet structure (beta strand);

[0085] Fig.14 It is a schematic diagram of a corner structure (turn);

[0086] Fig.15 Schematic diagram of amorphous structure (random coil);

[0087] Fig.16 Schematic diagram of the protein structure in the state of surface adhesion. DETAILED DESCRIPTION

[0088] The main theory about the change of entropy and enthalpy in the process of protein folding that is currently popular believes that: during the process of protein folding: as the protein changes from the unfolded state to the folded state, the conformational freedom is greatly reduced and the entropy is reduced. That is to say, it is believed that the folding process of protein is accompanied by a decrease in entropy. At the same time, the current popular theory believes that during the process of protein folding: as the protein begins to fold, hydrogen bonds, hydrophobic interactions and van der Waals forces inside the molecule are gradually formed, and these interactions release energy, thereby leading to a decrease in enthalpy. Therefore, the current popular theory believes that: during the process of protein folding, entropy gradually decreases and enthalpy decreases during the folding process. In the relevant research of the present invention, it is believed that this is problematic because the entropy increase of the water solvent in the system is not considered in this process. Specifically, it is because protein folding only occurs in a water solvent environment, and proteins cannot be folded correctly in any other non-aqueous solvent environment. Therefore, the invention proposes a brand-new theory: it is believed that the protein folding process is a process of increasing entropy and enthalpy of the system. The new theory (the basis of the present invention) believes that: protein folding is driven by the entropy increase of the low-entropy hydration layer around the hydrophobic atoms on the surface of the side chains of the polypeptide chain residues. That is, the hydrophobic interaction between the hydrophobic atoms of the side chains of different residues causes the entropy increase of the low entropy hydration layer to the entropy increase process of free solvent water, which drives the folding of the protein. In addition, during the protein folding process, the polypeptide chain molecules need to get rid of the strong hydrogen bonds, electrostatic forces and van der Waals forces formed between the strong electric polar water molecules around them and the polypeptide chains before they can form weaker hydrogen bonds, electrostatic forces and van der Waals forces inside the protein molecules. Therefore, the folding process of protein is an enthalpy increase process, not an enthalpy decrease process. In other words, the new concept believes that the folding process of protein is a systematic entropy increase process that compensates for the enthalpy increase, which is usually achieved through the balance between entropy increase and enthalpy increase. Based on this theory, the present invention has carried out research and simulation verification, which can accurately predict the protein structure. Therefore, the method of the present invention belongs to an original technical invention, which proposes a new theory of the protein structure formation process, and proposes a prediction method based on the corresponding theory. The core technology of the present invention is: the present invention finds that the folding process of protein is dominated by the hydrophobic interaction between the side chains of amino acid residues, that is, it is believed that the hydrogen bonding force, electrostatic and van der Waals forces formed within the molecule during the folding process of protein do not dominate the folding process of protein. The method described in the present invention ignores physical forces such as hydrogen bonding, electrostatic and van der Waals, and only preferentially analyzes the hydrophobic interaction between the side chains of amino acid residues to predict the structure of protein, which is different from the existing methods for predicting the structure of protein. The method of the present invention believes that the protein folding process depends only on "water entropy force", that is, the hydrophobic interaction relationship between the low entropy hydration layers of the side chains of amino acid residues determines the precise folding law of protein, and the interaction attraction between the low entropy hydration layers of the side chains of amino acid residues is defined as "water entropy force" by the present invention.

[0089] The present invention believes that the folding process of protein is dominated by the mutual attraction between the low entropy hydration layers of the amino acid residue side chains. The carbon atoms and sulfur atoms in the amino acid residue side chains are hydrophobic, which causes the water molecules around these hydrophobic atoms to be in a low entropy state, that is, there is a low entropy hydration layer around the hydrophobic atoms. The entropy increase trend of the low entropy hydration layer will cause mutual attraction and collapse between such low entropy hydration layers, and at the same time avoid the low entropy hydration layer and the hydrophilic amino acid residues from getting close, thereby causing lateral attraction and lateral adhesion between specific amino acid residue side chains, becoming one of the core mechanical mechanisms that dominate protein folding. In the folding process of protein, hydrophobic interaction occurs between the side chains of hydrophobic amino acid residues, that is, spontaneous aggregation between the side chains of hydrophobic amino acid residues drives the folding of protein. The present invention points out that there is also a low entropy hydration layer around the hydrophobic atoms in the side chains of hydrophilic amino acid residues, and the water molecules therein also have an entropy increase effect, which can cause some hydrophilic amino acid residue side chains to laterally fit with adjacent hydrophilic amino acid residue side chains. This entropy increase effect is also an important driving force for protein folding, and it should be emphasized that this is the technical starting point of the present invention. Figure 2 As shown,

[0090] Driven by the entropy increase of water molecules in the environment, some hydrophilic amino acid residue side chains will spontaneously laterally fit with adjacent hydrophilic amino acid residue side chains (that is, the amino acid residue side chains are in a state of being parallel to each other), and in this state, a state of agglomeration of hydrophobic atoms in multiple hydrophilic amino acid residue side chains is formed, that is, the entropy increase of the low entropy hydration layer is achieved. The present invention believes that the main physical mechanism of protein folding is that the entropy increase of low entropy water molecules drives the lateral fit between amino acid residue side chains (lateral fit refers to the state that two amino acid residue side chains are in an approximately parallel state), and the method of the present invention mainly predicts which two amino acid residue side chains in the amino acid residue sequence will lateral fit. This state is commonly found in the secondary structure strand and helix of proteins, and the relative position relationship of the sequence position of the amino acid residue side chain is used to represent the sequence position of the amino acid residue side chain. That is, the entropy increase of the entropy hydration layer around the hydrophilic amino acid residue side chain causes the hydrophobic parts of some hydrophilic amino acid residue side chains to be close to each other, and also drives the hydrophilic top atoms of the amino acid residue side chains to be close to each other, which is a protein folding dynamic mechanism revealed by the present invention for the first time.

[0091] For example, in the secondary structure of a strand, the side chain of an amino acid residue is usually in an approximately parallel fit with the side chain of the adjacent amino acid residue. In the present invention, the sequence position relationship of the side chains of two amino acid residues separated by one amino acid residue in the amino acid residue sequence of the primary structure is named as the "1-3" sequence position relationship, such as Figure 3 shown.

[0092] Similarly, in the helix secondary structure, the side chains of two other amino acid residues separated by 2 and 3 amino acid residues in an amino acid residue side chain sequence are in an approximately parallel fit state, such as Figure 4 As shown, the present invention names the relationship between the sequence position of an amino acid residue side chain and a certain amino acid residue side chain in the primary structure amino acid residue sequence separated by 2 or 3 amino acid residues as a "1-4 / 5" sequence position relationship.

[0093] In addition, in the helix structure, the side chain of an amino acid residue is in a nearly parallel state with the side chain of an adjacent amino acid residue in the sequence. The present invention names the sequence position relationship of two adjacent amino acid residues in the amino acid residue sequence of the primary structure as the "1-2" sequence position relationship, such as Figure 5 shown.

[0094] from Figure 1 It can be seen that the side chains of many hydrophilic amino acid residues also contain hydrophobic carbon atoms and sulfur atoms. Therefore, it is believed that these hydrophobic carbon atoms and sulfur atoms lead to the existence of a low entropy hydration layer around them, that is, there is also a low entropy hydration layer outside the side chains of many hydrophilic amino acid residues. In addition, since the roots of almost all amino acid residue side chains are composed of hydrophobic carbon atoms (such as Figure 1 As shown), it is believed that these hydrophobic carbon atoms obscure the hydrophilicity of the main chain structure of the polypeptide chain. Therefore, the present invention regards the main chain structure of the polypeptide chain as hydrophobic, that is, in the process of predicting protein structure, the hydrophilicity of the carbonyl oxygen and amide hydrogen groups of the main chain is ignored. Specifically, the water molecules around the polypeptide chain must pass through the root of the branch chain to approach the main chain. Since the root of the branch chain is hydrophobic and the water molecules around the hydrophobic root are low entropy, most of the water molecules that interact hydrophilically with the main chain of the polypeptide chain are these low entropy water molecules, which leads to the fact that the hydrophilicity of the main chain cannot be fully expressed, that is, there are not a large number of free water molecules that can frequently generate and break hydrogen bonds with the main chain. Therefore, when predicting protein folding, the hydrophilicity of the main chain is ignored. It should be pointed out that the side chains of amino acid residues such as E, Q, R, K, and H have relatively long hydrophobic roots, see Figure 1 Therefore, it is believed that there is also a low-entropy hydration layer outside the side chains of residues such as E, Q, R, K, and H.

[0095] In order to make the objectives, technical solutions and advantages of the embodiments of the present invention more clearly understood, the spirit of the contents disclosed by the present invention will be described in detail below. After understanding the embodiments of the contents of the present invention, any technician in the relevant technical field can change and modify them according to the techniques taught by the contents of the present invention without departing from the spirit and scope of the contents of the present invention.

[0096] The exemplary embodiments and descriptions of the present invention are used to explain the present invention, but are not intended to limit the present invention. The present invention will be further described below in conjunction with specific implementation methods. Specific implementation method one:

[0098] The present embodiment is a protein structure prediction method based on the mutual attraction relationship between the low-entropy hydration layers of the side chains of amino acid residues. The present embodiment mainly predicts the secondary structure of the spatial structure of the amino acid sequence of the protein. First, it predicts which fragments in the amino acid residue sequence of the primary structure of the protein (polypeptide chain) are folded into secondary structures such as α-helix (referred to as helix in the present invention), β-fold (referred to as strand in the present invention), β-turn (referred to as turn in the present invention) and random coil (referred to as random coil in the present invention), then predicts the part between the helix and strand structure: turn or random coil, and finally predicts the tertiary structure of the protein.

[0099] In the prediction method of this embodiment, the common abbreviations of amino acid residues are used to represent each amino acid: alanine (A); valine (V); leucine (L); isoleucine (I); proline (P); phenylalanine (F); tryptophan (W); methionine (M); glycine (G); serine (S); threonine (T); cysteine ​​(C); tyrosine (Y); asparagine (N); glutamine (Q); aspartic acid (D); glutamic acid (E); histidine (H); lysine (K); arginine (R). Figure 1 . Figure 1 The molecular structures of 20 amino acid residues are shown, and the hydrophobic carbon atoms and sulfur atoms in the side chains of each amino acid residue are marked with wireframes.

[0100] The following is a detailed description of a protein folding dynamics mechanism disclosed by the present invention:

[0101] 1. The preliminary work for forecasting is as follows:

[0102] First, an entropy value is assigned to the side chains of amino acid residues in the primary structure of the protein. The entropy value is a relative measure of the entropy increase potential of the low-entropy hydration layer around the side chains of the amino acid residues. Specifically, the number of carbon-carbon bonds in the hydrophobic part of the side chains of the amino acid residues is used as a measurement indicator. The indicator is named "entropy value". The present invention defines the number of carbon-carbon bonds on the side chain of an amino acid residue as 1 entropy value. The "entropy value" refers to the relative measure of the entropy increase potential of the low-entropy hydration layer around the side chains of the amino acid residues. For example, the length of the hydrophobic part of the side chain of the amino acid E is 3, containing 3 carbon-carbon bonds. Therefore, the entropy value of the amino acid E residue is defined as 3, see Figure 6 .

[0103] The "entropy value" of each amino acid residue is marked below the amino acid residues on the polypeptide chain. Considering that amino acid residues I, V, L, and F are strongly hydrophobic residues, the present invention defines the entropy values ​​of I, V, L, and F to be 6; at the same time, considering the masking effect of hydrophilic atoms on hydrophobic atoms, the present invention modifies the "entropy value". Specifically, the entropy values ​​of the side chains of amino acid residues are defined as follows: S = 0.5, T = 0.5, D = 0.5, N = 0.5, G = 0, H = 3, R = 3, E = 3, K = 4, W = 5, I = 6, V = 6, L = 6, F = 6, P = 0, C = 4, Q = 3, A = 1, M = 4, Y = 5.

[0104] Then, the amino acid residues are classified as follows:

[0105] The residues with micro-entropy increase potential include: S, T, D, and N;

[0106] Hydrophilic residues include: H, R, K, E, Q, D, N, H, Y, W, S;

[0107] Common turn residues (referred to as turn residues) include: G, P;

[0108] Hydrophobic residues include: I, V, L, F, Y, W, A, M, C, H;

[0109] Residues with high entropy increase potential include: I, V, L, K, R, F, Y, W, A, M, C, E, Q, and H.

[0110] Among them, a microentropy residue means that the number of carbon atoms in the side chain of the residue is less than or equal to 2, and the side chain contains at least one oxygen atom or hydrogen atom.

[0111] Next, determine the preferred pairing between amino acid residue side chains:

[0112] Protein folding realizes the lateral fitting of multiple pairs of amino acid residue side chains in its polypeptide sequence. The present invention finds that many of these fitting states fully realize the entropy increase potential of the low-entropy hydration layer of each two amino acid residue side chains in multiple pairs of amino acid residue side chains. In other words, it is believed that the lateral fitting of certain pairs of amino acid residue side chains will cause the low-entropy hydration layer to disappear, and the low-entropy hydration layer of each of the two amino acid residue side chains will fully realize its entropy increase potential. Therefore, the present invention defines that the lateral fitting of multiple specific pairs of amino acid residue side chains will lead to a sufficient entropy increase in the low-entropy hydration layer of the two amino acid residue side chains, and these amino acid residue pair relationships are defined as the "preferred entropy increase pairing" of two amino acid residues, see Figure 7 .

[0113] The present invention believes that when the side chains of two amino acid residues are similar, the lateral fit of the side chains of the two amino acid residues will lead to a sufficient entropy increase in the low-entropy hydration layer outside the two side chains. The similarity between the side chains of amino acid residues is defined as follows: "When the difference in the "entropy value" of the side chains of two hydrophilic amino acid residues is smaller, the two hydrophilic residues are considered to be more similar. When the difference in the "entropy value" of the side chains of two hydrophobic amino acid residues is smaller, the two hydrophobic residues are considered to be more similar." For example, when the entropy values ​​of two amino acid residues are both less than or equal to 4, and their entropy value difference is less than or equal to 1, the side chains of the two amino acid residues are considered to be similar. When the entropy values ​​of two amino acid residues are both greater than or equal to 4, and their entropy value difference is less than or equal to 2, the side chains of the two amino acid residues are considered to be similar. For example, amino acid residue L is similar to amino acid residue W. For example, the side chain of an amino acid residue E is similar to the side chain of another amino acid residue Q. Because the entropy values ​​of the two amino acid residues are the same and both are hydrophilic residue side chains, the lateral adhesion of the side chains of the two amino acid residues will lead to sufficient mutual attraction and collapse between the low entropy water layers of the side chains of the two amino acid residues, and will not cause the hydrophilic end of one amino acid residue side chain to adhere to the hydrophobic part of the other amino acid residue side chain, see Figure 8 .

[0114] Based on the similarity between the side chains of amino acid residues, the present invention defines a list of preferred entropy-increasing pairings between the side chains of amino acid residues as follows:

[0115] FF, QQ, KK, EE, TT, RR, AA, SS, MM;

[0116] MA, QE, TS, RE, KR, EK, FY, WY, WE, RW, RY, KY, HV, DE, NE, DQ, NQ;

[0117] QR / K, I / V / L / FI / V / L / F, I / V / LY, I / V / LK, I / V / LR, I / V / LA, I / V / LW, I / V / L / F / YW, I / V / LM, CM / Y, MI / V / L; A / TD / N. “ / ” indicates the relationship of or.

[0118] For example, in the helix structure, the side chains of two amino acid residues that are separated by 2 and 3 amino acid residues in the sequence are in an approximately parallel fitting state. When the lateral fitting between the side chains of amino acid residues occurs between the side chains of amino acid residues in the "preferred entropy increasing pairing", it is believed that these amino acid residue side chains have achieved sufficient entropy increase in their low entropy hydration layer, that is, they have achieved "preferred entropy increasing pairing".

[0119] 2. Specific prediction of protein structure

[0120] Based on the sequence position of the amino acid residue side chains, the classification and entropy of the amino acid residues, and the preferred pairing between the amino acid residue side chains, the following process is used to predict the protein structure;

[0121] S100. Mark the entropy value under each amino acid in the amino acid sequence of the primary structure of the protein whose structure needs to be predicted to form a table.

[0122] S200. In another line below the amino acid sequence of the primary structure of the protein, the amino acids of these "high entropy increase potential residues" are repeatedly written below each high entropy amino acid residue, as a fragment composed of adjacent connected fragments of high entropy increase potential residues in the amino acid sequence of the primary structure of the protein, that is, the original "high entropy increase potential residue connected fragment". In addition, in another line, the amino acids are repeatedly written below the corresponding positions of the low entropy residues and corner residues in the amino acid sequence of the primary structure of the protein.

[0123] In the protein structure prediction method described in the present invention, it is first predicted which fragments of the amino acid sequence will fold into the typical strand structure and helix structure in the protein secondary structure: that is, it is first predicted which sequence fragment in the amino acid sequence of the protein primary structure will fold into the typical strand secondary structure or helix secondary structure, and then further predicted whether the fragment will fold into the strand structure or the helix structure.

[0124] The amino acid sequence of the predicted protein primary structure described in the present invention is folded into a strand secondary structure or a helix secondary structure, which is achieved based on an "unblocked high entropy increase potential residue connected segment". The definition of the "unblocked high entropy increase potential residue connected segment" of the present invention is: two adjacent high entropy increase potential residues in the protein primary structure amino acid sequence and a non-high entropy increase potential residue that does not block the connection of the high entropy increase potential residues, then this segment of the amino acid residue sequence is the "unblocked high entropy increase potential residue connected segment", and the length of the "unblocked high entropy increase potential residue connected segment" is greater than or equal to 3 amino acid residues.

[0125] The method for determining the "unblocked high entropy increase potential residue connected fragment" is as follows:

[0126] First, find the fragments consisting of consecutive high entropy increase potential residues in the sequence, which are named the original "high entropy increase potential residue connected fragments"; then determine the non-high entropy increase potential residues that do not block the high entropy increase potential residue connected fragments:

[0127] (1) When there is only one amino acid residue S or T between two residues with high entropy increase potential, it is considered that the S or T does not block the connected segment of residues with high entropy increase potential, that is, it is considered that the S or T amino acid residue does not block the connected segment of residues with high entropy increase potential, and participates in the formation of a continuous segment of residues with high entropy increase potential. The formation of a continuous segment of residues with high entropy increase potential means participating in the connected segment of residues with high entropy increase potential.

[0128] (2) When there is only one isolated N, D or G amino acid residue between two high entropy increase potential residues in an amino acid sequence, and there is a high entropy pairing between I, V, L, F, and Y with a 1-3 or 1-4 / 5 relationship across the D, N or G (at least one of the paired amino acid residues is I, V or L), it is considered that the D, N or G does not block the high entropy increase potential residue connected segment, that is, it is considered that the N, D or G constitutes a continuous high entropy increase potential residue segment.

[0129] If the D or N is predicted as a helix by subsequent methods, and if the side entropy value of the amino acid residue with a 1-4 / 5 relationship with the D or N in the helix structure is greater than or equal to 4, the D or N will be predicted as a turn structure.

[0130] (3) When any one of the amino acid residues of S, T, N, D, and G appears in the amino acid sequence of the polypeptide chain, and it is adjacent to any one of the amino acid residues of S, T, N, D, and G, the 1-4 / 5 sequence position relationship across the two adjacent amino acid residues is checked. When the two amino acid residues at the 1-4 / 5 position are both one of I, V, L, F, and Y, and at least one of the amino acid residues is I, V, or L, it is predicted that the two adjacent amino acid residues do not block the formation of a high entropy increase potential residue connected segment. If the high entropy increase potential residue connected segment where the two adjacent amino acid residues are located is not predicted as a helix by the following method, the two consecutive adjacent amino acid residues of S, T, N, D, and G are predicted to be a turn structure T as a prediction result.

[0131] (4) When a P amino acid residue appears in the amino acid sequence of a polypeptide chain, and the P amino acid residue is not in a 1-2 or 1-3 sequence position relationship with a D or N amino acid residue (e.g., PQD, PCCN), when there is a 1-4 / 5 sequence position relationship across the P amino acid residue, and the amino acid residues on 1-4 / 5 are I, V, L, or F, then the predicted P amino acid residue does not block the high entropy increase potential residue-connected fragment, but if the fragment containing P is ultimately not predicted to be a helix, then the P is predicted to be a turn structure.

[0132] (5) When a G or A amino acid residue appears in the amino acid sequence of a polypeptide chain, if an amino acid residue that forms a 1-4 / 5 sequence position relationship with the amino acid residue can be found on one side of the sequence where the G or A amino acid residue is located, and an amino acid residue that forms a 1-4 / 5 sequence position relationship with the G or A amino acid residue can also be found on the other side of the sequence where the G or A amino acid residue is located, and if there is a single D, N, G or P amino acid residue that is not adjacent to other low entropy residues or corner residues, or two adjacent S, T, N, D amino acid residues between the above-mentioned I, V, L residues, it is predicted that these single D, N, G or P amino acid residues or two adjacent S, T, N, D, G amino acid residues will not block the high entropy increase potential residues in the fragment from connecting the fragment.

[0133] For example: IVL 1-4 / 5G / A1-4 / 5IVLF (for example, VAAQGRARL), IVL 1-4 / 5A1-4 / 5A1-4 / 5IVLF, IVL 1-4 / 5A1-4 / 5A 1-4 / 5A (for example, IMQDAGVTANTRA).

[0134] S300. Find a fragment with a length of less than or equal to 5 amino acid residues and a number of 3 or more microentropy residues or corner residues in the amino acid sequence of the polypeptide chain, and predict that the fragment will fold into a corner structure. The two ends of the amino acid sequence of the polypeptide chain are not predicted. Find a fragment with a length of less than or equal to 5 amino acid residues and a number of 3 or more microentropy residues or corner residues in the amino acid sequence of the polypeptide chain. If the fragment contains at least one corner residue, that is, contains a G or P amino acid residue, it is predicted that these amino acid residues will fold into a corner structure.

[0135] Based on the above judgment, the predicted high entropy increase potential residue connected fragments are marked below the original amino acid sequence;

[0136] S400, predict whether the connected fragments of residues with high entropy increase potential in the amino acid sequence of a polypeptide chain are folded into a helix structure or a strand structure:

[0137] S401, assuming that the connected segments of residues with high entropy increase potential in the amino acid sequence of the polypeptide chain are helix or strand structures;

[0138] (A) Assuming that a certain high entropy increase potential residue connected segment folds into a helix structure, mark whether each amino acid residue side chain in the segment achieves a preferred pairing relationship when folded into a helix. If one of the amino acid residue side chains in the high entropy increase potential residue connected segment achieves a preferred pairing, mark it as * below the amino acid, otherwise do not mark it. The preferred pairing here refers to the preferred pairing achieved by the "1-4 / 5" sequence position relationship. In addition, if there is a preferred pairing of I / V / L and I / V / L achieved by a 1-2 sequence position relationship in the high entropy increase potential residue connected segment (for example, EAQRLL), or there is an I / V / L 1-4 / 5G / A 1-4 / 5I / V / L / F series position relationship in the high entropy increase potential residue connected segment, * is also marked below these IVFGA.

[0139] (B) Assuming that a connected segment of residues with high entropy increase potential is predicted to be a strand structure, mark whether the side chain of each amino acid residue has achieved a preferred pairing of I / V / L / F and I / V / L / F (for example, IDV) of a 1-3 sequence position relationship in the strand state. The two I / V / L / F amino acid residues that have achieved the preferred pairing of I / V / L / F and I / V / L / F of the 1-3 sequence position relationship are marked with & below.

[0140] In addition, when a pair of I / V / L and I / V / L with a sequence position relationship of 1-3 is marked with &, it is called marked with &-&, and these two I / V / L can find I / V / L / F / Y or A with a sequence position relationship of 1-4 / 5 in the connected fragment of residues with high entropy increase potential to form a preferred pair, then the &-& marked with these two I / V / L is considered invalid, that is, this &-& is no longer marked.

[0141] S402, the * and & marked below the amino acid residue sequence are subjected to the following comparative analysis:

[0142] When none of the amino acid residues in a high entropy increase potential residue connected segment are marked with &-&, and more than 80% of the amino acid residues are marked with *, the segment is predicted to be a helix;

[0143] When a high entropy increase potential residue patch connected segment is marked with &-& (excluding I / V / LSI / V / L marked with &-&, such as VSV), the segment is usually predicted to be a strand. The exception is that in the region marked with &-& (here "far away" is defined as two consecutive low entropy residues or corner residues, or at least 3 hydrophilic residues or one amino acid residue P) in a high entropy increase potential residue patch connected segment, a fragment of length greater than 5 can be found as a sub-fragment, in which more than 85% of the amino acid residues are marked with *, and there is a 1-4 / 5 sequence position relationship between I / V / L / F / Y and I / V / L / F / Y of other amino acid residues except the amino acid residue marked with &-&, then the sub-fragment is predicted to fold into a helix structure, and the rest of the high entropy increase potential residue patch is predicted to be a strand. When the number of “connected segments with high entropy increase potential residues” marked with * is less than 50% of the number of amino acid residues in the segment, the segment is predicted to be a strand.

[0144] In a fragment predicted to be a strand, if two microentropy residues D or N appear consecutively in the amino acid residue sequence, the two consecutive microentropy residues D or N are predicted to be a turn structure as a prediction result.

[0145] S403, searching for amino acid residues adjacent to the amino acid residue sequence fragment on both sides of the amino acid residue sequence fragment that has been predicted as a helix, and determining whether the side chains of the amino acid residues that have been searched have a preferred pairing relationship of 1-4 / 5 sequence positions with the amino acid residues in the predicted helix structure, and if there is a preferred pairing relationship, predicting that the preferred paired residues fold into a helix structure. Repeat this operation until the first adjacent amino acid residue that does not have a preferred pairing relationship of 1-4 / 5 sequence positions with the amino acid residue that has been initially predicted as a helix structure appears;

[0146] S404. Count the entropy increment of each amino acid residue in the folded helix and strand states. (Two start-up situations)

[0147] The calculation method for the entropy value of the folded strand is as follows: when a preferred pairing appears in the 1-3 sequence position relationship in the amino acid sequence of the polypeptide chain, the entropy value of the preferred paired amino acid residue is marked below the amino acid residue as the entropy value of the amino acid residue; when an amino acid residue has two preferred pairs in the 1-3 sequence position relationship, the entropy value of the amino acid residue is accumulated twice.

[0148] The calculation method of helix entropy increment is as follows: when a preferred pairing occurs in the 1-4 / 5 sequence position relationship in the sequence, the entropy value of the amino acid residue with the preferred pairing is marked below the amino acid residue as the entropy increment of the amino acid residue. When an amino acid residue achieves multiple preferred pairings in the 1-4 / 5 sequence position relationship, the entropy increment of the amino acid residue is accumulated twice. In the helix entropy increment statistics, when a certain I / V / L / M and a certain I / V / L / M are adjacent in the sequence, that is, a "1-2" sequence position relationship occurs, the two I / V / L / Ms are considered to have achieved an entropy increment and accumulated an entropy increment.

[0149] Compare the entropy increments of each amino acid residue side chain in the two schemes of folding into helix and strand. When the larger entropy increment calculated by the two schemes is 20% larger than the smaller one, the one with the larger overall entropy increment is the prediction result. When the difference in the overall entropy values ​​predicted as strand and helix does not exceed 20% of the smaller one, the fragment is predicted as strand and helix as two possible prediction results. When calculating the entropy of Strand, I / V / LGI / V / L is counted as the entropy-preferred pairing of two IVLs, where "-" represents an arbitrary residue.

[0150] S405. When a fragment with a length of 5 residues or more is in a strand state, and there is no situation where the hydrophilic atom (nitrogen atom and oxygen atom) of the side chain of an amino acid residue and the hydrophobic atom of the adjacent amino acid residue side chain are at the same height (the height of the residue side chain) (in this method, amino acid residues S and T are regarded as hydrophobic, that is, the oxygen atoms at the top of the side chains of S and T amino acid residues are regarded as hydrophobic atoms), then the fragment is finally predicted to be a strand. When the hydrophilic atom (nitrogen atom and oxygen atom) of the side chain of an amino acid residue and the hydrophobic atom of the adjacent amino acid residue side chain are at the same height, hydrophilic and hydrophobic repulsion will occur between the hydrophilic atom and the hydrophobic atom, and the strand state will be destroyed. The height of the residue side chain refers to the number of covalent bonds in the shortest path between the top atom of the amino acid residue side chain in the fragment and the carbon atom of its main chain, which is the height of the residue side chain.

[0151] When the predicted length of a strand is greater than or equal to 12 amino acid residues, a search is performed to determine whether there are three consecutive hydrophilic residues in the middle of the strand. If so, the three amino acid residues are predicted to form a turn structure, which becomes a prediction result.

[0152] S406. When a certain amino acid residue segment in the amino acid sequence of a polypeptide chain is predicted to be a helix, the IVLF groups of connected segments in the helix structure that are laterally attached to each other through a 1-4 / 5 sequence position relationship or a 1-2 sequence position relationship are marked, and the fragment sequence is searched to see whether there is an isolated I\V\LF amino acid residue that is not laterally attached to any I\V\LF residue side chain in the grouped IVLF amino acid residues. If there is, and the I\V\LF amino acid residue segment and the S\T\N\D amino acid residue segment are adjacent or adjacent with only one amino acid residue in between, then the segment where the I\V\L\F and S\T\N\D are located is predicted to no longer be a helix.

[0153] When the length of the predicted helix structure is less than or equal to 6 amino acid residues, predicting the fragment as a random coil is also a possible prediction result.

[0154] S500. Two consecutive amino acid residues in a connected segment of high entropy increase potential residues that are not predicted as helix are predicted as a turn structure, marked as T; the two consecutive amino acid residues are any one or two of S, T, N, D, and G, such as SS, or ST.

[0155] A segment of 4 or more consecutive hydrophilic amino acid residues in the primary structure of a protein is named a "continuous hydrophilic residue segment", such as EEQQK. When there is a segment longer than 7 amino acid residues in a high entropy increase potential residue connected segment that is not predicted as a helix, and the proportion of residues in the low entropy increase potential residue and / or corner residue and / or amino acid residue A and / or continuous hydrophilic residue segment is greater than or equal to 50%, the segment is predicted to fold into a random coil structure as a prediction result.

[0156] S600, searching for a fragment consisting of 5 or more consecutive hydrophilic residues in the amino acid sequence of the polypeptide chain, and if the fragment has been predicted as a connected fragment of residues with high entropy increase potential, predicting the fragment consisting of 5 or more consecutive hydrophilic residues as a random coil as a prediction result.

[0157] Based on the above judgment, the fragments predicted to have turn structures are marked below the original amino acid sequences.

[0158] In addition, the hydrophilic residues with entropy values ​​greater than or equal to 3 in the current turn structure and random coil structure as a prediction result are marked, and the preferred pairing relationship between these hydrophilic residues is marked, and the lateral fitting state of the amino acid residue side chains in the preferred pairing relationship is used as a prediction result; when the turn structure as a prediction result cannot be determined to be the turn structure, the micro-entropy residues in the predicted turn structure are marked, and the preferred pairing relationship between these micro-entropy residues is marked, and the lateral fitting state of the amino acid residue side chains in the preferred pairing relationship is used as a prediction result.

[0159] At the same time, the hydrophobic residues I / V / L / F / M in the turn structure and the random coil structure are marked, and the side chains of the hydrophobic residues will fit with the side chains of the adjacent I / V / L / F / Y / W / K amino acid residues as a prediction result; the I / V / L / F amino acid residues in the two secondary structures linked by the turn structure and the random coil structure are marked, and the I / V / L / F in the two secondary structures will fit as a prediction result.

[0160] After the above judgment, if the protein primary structure is not predicted to be a helix or turn sequence and there is a fragment with a number of 5 or more amino acid residues, when the fragment is in the universal initial thermodynamic metastable state of the unfolded protein, if there is no hydrophilic atom of the hydrophilic amino acid residue side chain minus the height of the adjacent hydrophobic residue side chain in the fragment, the fragment is predicted to be a strand. The universal initial thermodynamic metastable state of the unfolded protein can be determined according to Yang Lin et al.'s "Universal Initial Thermodynamic Metastable State of Unfolded Proteins". Specific implementation method 2:

[0162] The present embodiment is a protein structure prediction method based on the mutual attraction relationship between low-entropy hydration layers of amino acid residue side chains. The present embodiment predicts the spatial tertiary structure of the protein on the basis of the prediction of the spatial structure of the amino acid sequence of the protein in the specific embodiment one, that is, the secondary structure is first predicted using the specific embodiment one, and then the tertiary structure is further predicted based on the secondary structure.

[0163] First, the similarity of the side chains of amino acid residues is defined: the smaller the difference in the "entropy values" of the side chains of two hydrophilic residues, the more similar the two hydrophilic residues are; the smaller the difference in the "entropy values" of the side chains of two hydrophobic residues, the more similar the two hydrophobic residues are.

[0164] The amino acid residues that achieve the preferred pairing between I / V / L / F in the predicted secondary structure are marked, and the hydrophobic surface of the hydrophobic side chain cluster that achieves lateral fit between the side chains of the I / V / L / F amino acid residues is marked and named "cluster hydrophobic surface", such as Fig. 9 As shown, it is predicted that the surface adhesion between the hydrophobic surface of one I / V / L / F cluster and the hydrophobic surface of another adjacent I / V / L / F cluster is a protein structure;

[0165] When there is no preferred pairing relationship between I / V / L / F in a strand or helix secondary structure, the secondary structure is searched for a preferred pairing relationship between I / V / LY. If so, the hydrophobic surface of the hydrophobic side chain clusters that are laterally attached between the side chains of the I / V / LY amino acid residues are also marked as "cluster hydrophobic surface"; it is predicted that a I / V / L / Y cluster hydrophobic surface and another adjacent cluster hydrophobic surface will be attached to form a protein structure.

[0166] When a helix structure has two cluster hydrophobic surfaces and the two cluster hydrophobic surfaces are not connected in the axial direction of the helix, it is predicted as a possible prediction result that one of the cluster hydrophobic surfaces with a smaller number of I / V / L / F / Y will not fit together with another I / V / LF / cluster hydrophobic surface in an adjacent strand or helix secondary structure.

[0167] For the current prediction of a strand, it is necessary to mark the strong hydrophobic residues (I / V / L / F / W / Y) of the preferred paired connected segments in the 1-3 position relationship in the strand, and at the same time mark these hydrophobic segments connected by the 1-3 position relationship, compare the lengths of adjacent strands in the sequence, and predict that strands with similar lengths will fold into a sheet structure. Then, based on the distribution of the side chains of the strong hydrophobic residues of the two strands, the most strongly hydrophobic residues (I / V / L / F / W / Y) on one strand in the corresponding position relationship between the two strands are laterally aligned in a way that can achieve preferred pairing with the side chains of the amino acid residues on the other strand. The state of the two strands being aligned is the predicted sheet folding structure (in fact, βsheet is composed of βstrands), such as Fig.10 shown.

[0168] In the process of predicting the protein structure where the cluster hydrophobic surface undergoes surface adhesion, we can actually start with the prediction based on a secondary structure predicted to be a turn structure. For the two predicted secondary structures connected to the turn structure, the hydrophobic surface of the hydrophobic side chain cluster is marked and named "cluster hydrophobic surface". The "cluster hydrophobic surface" is used to determine the local tertiary structure of the successfully predicted secondary structure based on the relative position of the two secondary structures connected to the turn structure. At the same time, we must also consider the adhesion state of the two secondary structures and the adhesion state of the "cluster hydrophobic surfaces" of other secondary structures to ensure that the "cluster hydrophobic surfaces" are fully adhered to each other. The corresponding configuration of the fully adhered state is the prediction result, such as Fig.11 shown.

[0169] Example 1

[0170] For the convenience of explanation, in the examples, the amino acid residues folded into a helix structure are marked as H, the amino acid residues folded into a strand structure are marked as E, the turn structure is marked as T, and the amorphous structure (random coil) is marked as C. It should be noted that the present invention includes but is not limited to these labeling methods, and in other embodiments, other labeling forms may also be used.

[0171] The method of gradually predicting the tertiary structure of proteins is achieved by predicting four secondary structures:

[0172] 1. The four secondary structures are as follows:

[0173] ① Helix (see Fig.12 );

[0174] ②Layer structure (beta strand) (see Fig.13 );

[0175] ③ Turn structure (see Fig.14 );

[0176] ④Amorphous structure (random coil) (see Fig.15 ).

[0177] 2. Preprocessing steps:

[0178] The amino acid residue fragments predicted to be helix are marked as H, the amino acid residue fragments predicted to be strand are marked as E, and the amino acid residue fragments predicted to be turn structures are marked as T.

[0179] This example uses the protein with sequence number 1054 in the PDB database to predict its structure:

[0180] 1. Mark the entropy value under each amino acid in the protein amino acid sequence whose structure needs to be predicted to form a table, where a represents an entropy value of 0.5. As follows:

[0181]

[0182] 2. In a new line below the protein amino acid sequence, repeat these "high entropy increase potential residues" below each high entropy increase potential residue. This marks the fragments composed of adjacent connected fragments of high entropy increase potential residues in the sequence, which is the original "high entropy increase potential residue connected fragment". In addition, in a new line below the protein amino acid sequence, repeat these micro-entropy residues and corner residues below the corresponding positions of the micro-entropy residues and corner residues in the amino acid residue sequence, as follows:

[0183]

[0184] 3. Find the fragments composed of consecutive high entropy increase potential residues in the sequence, which are named the original "high entropy increase potential residue connected fragment". In addition, when there is only one amino acid residue S or T between two high entropy increase potential residues, it is considered that the S or T does not block the high entropy increase potential residue connected fragment, and the high entropy increase potential residue connected fragment still exists; that is, it is considered that the S or T amino acid residue participates in the formation of a continuous high entropy increase potential residue fragment.

[0185] After removing these S and T residues, the remaining low-entropy residues and corner residues that may block the connection segment of high entropy increase potential residues are marked in the fourth row of the table below.

[0186]

[0187] 4. When there is only one isolated N, D or G amino acid residue between two high entropy increase potential residues in the amino acid sequence, and there is a high entropy pairing between I / V / L / F / Y with a 1-3 or 1-4 / 5 sequence position relationship across the D, N or G (at least one of the paired amino acid residues is I / V / L), it is considered that the D, N or G does not block the high entropy increase potential residue connected segment, and the high entropy increase potential residue connected segment still exists; that is, it is considered that the N, D or G constitutes a continuous high entropy increase potential residue segment. The remaining micro-entropy residues and corner residues that may block the high entropy increase potential residue connected segment are marked in the last row (add one row below the above table, which is the last row in this step).

[0188] When two adjacent S / T / N / D / G residues appear in an amino acid sequence, if there is a 1-4 / 5 sequence position relationship between the I / V / L / F amino acid residues across these two amino acid residues, it is predicted that the two adjacent S / T / N / D / G residues do not block the formation of a high entropy increase potential residue connected segment. If the high entropy increase potential residue connected segment where the two adjacent S / T / N / D / G residues are located is not predicted as a helix by the following method, the two consecutive S / T / N / D / G residues are predicted as a turn structure T as a prediction result.

[0189] When a P amino acid residue appears in the amino acid sequence, and the P is not in a 1-2 or 1-3 sequence position relationship with D / N (e.g., PQD, PCCN), when there is a 1-4 / 5 sequence position relationship between I / V / L / F amino acid residues across the P, the predicted P amino acid residue does not block the high entropy increase potential residue-connected fragment, but if the fragment containing P is ultimately not predicted to be a helix, the P is predicted to be a turn structure.

[0190] The remaining low entropy residues and corner residues that may block the high entropy potential residue connectivity segment are marked in the last row:

[0191]

[0192] 5. When the amino acid residue position relationship of IVL 1-4 / 5 G / A1-4 / 5 IVLF (for example, VAAQGRARL), IVL1-4 / 5 A1-4 / 5 A1-4 / 5 IVLF (for example, IMQDAGVTANTRV), and IVL 1-4 / 5 A1-4 / 5 A 1-4 / 5 A (for example, IMQDAGVTANTRA) appears in the amino acid sequence, if there is a single D, N, G, P or two adjacent S / T / N / D amino acid residues in the fragment, it is predicted that these single D, N, G or P two adjacent S / T / N / D / G amino acid residues will not block the fragment from being connected by the residues with high entropy increase potential in the fragment.

[0193] When a fragment of the amino acid residue position relationship of IVL 1-4 / 5 G / A 1-4 / 5 IVLF (for example, VAAQGRARL), IVL 1-4 / 5A1-4 / 5 A 1-4 / 5 IVLF (for example, ), IVL 1-4 / 5 A 1-4 / 5 A 1-4 / 5 A appears in the amino acid sequence, if there is a single D, N, G or P amino acid residue or two adjacent S / T / N / D amino acid residues that are not adjacent to other low entropy residues or corner residues in the fragment, it is predicted that these single D, N, G or P amino acid residues or two adjacent S / T / N / D / G amino acid residues do not block the high entropy increase potential residues in the fragment from connecting the fragment:

[0194]

[0195] 6. According to S300: Find a fragment in the sequence with a length of less than or equal to 5 amino acid residues and a number of microentropy residues or turn residues greater than or equal to 3, and predict that the fragment is folded into a turn structure. If there are two adjacent microentropy residues or turn residues in the fragment and they are not adjacent to another microentropy residue or turn residue, then accurately predict that the two adjacent microentropy residues or turn residues are folded into a turn structure. For the specific prediction method of the turn structure, see Articles 30, 31, and 32. Find a fragment in the sequence with a length of less than or equal to 5 amino acid residues and a number of microentropy residues or turn residues greater than or equal to 3. If the fragment contains at least one turn residue, that is, contains a G or P amino acid residue, then these amino acid residues are predicted to fold into the turn structure T.

[0196] Based on this, the predicted turn structure of the protein is marked in the third row:

[0197]

[0198] 7. In summary, the fragments with corner structures that are initially predicted are marked in the third row of the table below:

[0199]

[0200] 8. The corresponding predicted microentropy residue connected segments are as follows

[0201]

[0202] 9. The method for predicting whether a connected segment of residues with high entropy increase potential in an amino acid residue sequence is folded into a helix structure or a strand structure is as follows: First, assume that a connected segment of residues with high entropy increase potential is folded into a helix structure, and mark whether each amino acid residue side chain in the segment has achieved a preferred pairing relationship when folded into a helix. If an amino acid residue side chain has achieved a preferred pairing, it is marked as * below the amino acid, otherwise it is not marked. The preferred pairing here refers to the preferred pairing achieved through the "1-4 / 5" sequence position relationship. In addition, if there is a preferred pairing of IVL and IVL achieved by a 1-2 sequence position relationship in the sequence (for example, EAQRLL), if there is an IVL 1-4 / 5 G / A1-4 / 5IVLF series position relationship in the sequence, * is also marked below these IVFGA.

[0203]

[0204] 10. Assuming that a connected segment of residues with high entropy increase potential is predicted to be a strand structure, mark whether the side chain of each amino acid residue has achieved a preferred pairing (such as IDV) of IVLF and IVLF in a 1-3 position relationship when folded into a strand state, and the two IVLF amino acid residues that have achieved the preferred pairing of IVLF and IVLF in the 1-3 position relationship are marked with & below. In addition, when a pair of IVL and IVL in a 1-3 position relationship are marked with & (called marked with &-&), and both IVLs can find IVLFY or A in a 1-4 / 5 relationship sequence position relationship in the connected segment of residues with high entropy increase potential to form a preferred pairing, then the &-& marked on the two IVLs is considered invalid, that is, the &-& is no longer marked.

[0205]

[0206] 11. Compare the * and & in the first two tables, and perform the following comparative analysis on the * and & marked below the amino acid residue sequence: When none of the amino acid residues in a high entropy increase potential residue connected segment are marked with &-&, and more than 80% of the residues are marked with *, the segment is predicted to be a "helix".

[0207]

[0208] 12. When a high entropy increase potential residue segment connected segment is marked with &-& (excluding I / V / LSI / V / L marked with &-&, such as the sequence VSV), the segment is usually predicted to be a strand. The exception is that in the region marked with &-& (here "far away" is defined as two consecutive low entropy residues or corner residues, or at least 3 hydrophilic residues) in a high entropy increase potential residue connected segment, a sub-segment of an amino acid sequence with a length greater than 5 can be found, in which more than 85% of the amino acid residues are marked with *, and there is a 1-4 / 5 sequence position relationship between IVLFY and IVLFY that is unrelated to the amino acid residues marked with &-&, then the sub-segment is predicted to fold into a helix structure, and the rest of the high entropy increase potential residue connected segment is predicted to be a strand. When the number of "high entropy increase potential residue connected segments" marked with * is less than 50% of the number of amino acid residues in the segment, the segment is predicted to be a strand.

[0209]

[0210] 13. When a high entropy increase potential residue segment connected segment is marked with &-& (excluding I / V / LSI / V / L marked with &-&, such as VSV), the segment is usually predicted to be a strand. The exception is that in the region marked with &-& (here "far away" is defined as two consecutive low entropy residues or corner residues, or at least 3 hydrophilic residues) of a high entropy increase potential residue connected segment, a sub-segment of an amino acid sequence greater than 5 can be found, in which more than 85% of the amino acid residues are marked with *, and there is a 1-4 / 5 sequence position relationship between IVLFY and IVLFY that is unrelated to the amino acid residues marked with &-&, then the sub-segment is predicted to fold into a helix structure, and the rest of the high entropy increase potential residue connected segment is predicted to be a strand. When the number of "high entropy increase potential residue connected segments" marked with * is less than 50% of the number of amino acid residues in the segment, the segment is predicted to be a strand.

[0211]

[0212] 14. If the connected fragment of the residues with high entropy increase potential where the two adjacent S / T / N / D / G are located is not predicted as a helix by the following method, then the two consecutive S / T / N / D / G are predicted as a turn structure T as a prediction result.

[0213]

[0214] 15. Search the amino acid residues adjacent to the amino acid residue sequence fragment predicted to be helix on both sides of the fragment to determine whether the side chain of the amino acid residue has a 1-4 / 5 preferred pairing relationship with the amino acid residue in the predicted helix structure. If there is a preferred pairing relationship, it is predicted that the amino acid residue with the preferred pairing folds into a helix structure. Repeat this operation until the first adjacent amino acid residue appears that does not have a 1-4 / 5 preferred pairing relationship with the amino acid residue in the predicted helix structure.

[0215]

[0216] 16. The prediction results are listed in the third row of the table below. The results of the software's analysis of the true structure of the protein are predicted in the fourth row. It can be seen that the prediction is accurate.

[0217]

[0218] 17. When the turn structure cannot be predicted yet, mark the microentropy residues in the predicted turn structure, and then mark the preferred pairing relationship between these microentropy residues. The lateral fitting state of the side chains of these amino acid residues with preferred pairing relationship is a prediction result.

[0219]

[0220] 18. Mark the amino acid residues that achieve optimal matching between IVLF in the predicted secondary structure:

[0221]

[0222] The hydrophobic surface of the hydrophobic side chain cluster that achieves lateral adhesion between the side chains of IVLF amino acid residues is marked and named as "cluster hydrophobic surface". It is predicted that the state in which a hydrophobic surface of an IVLF cluster and the hydrophobic surface of another adjacent IVLF cluster in the amino acid residue sequence are adhered is a protein structure. When there is no preferred pairing relationship between IVLFs in a secondary structure, it is searched whether there is a preferred pairing relationship between IVLYs in the secondary structure, and the hydrophobic surface of the hydrophobic side chain cluster that is laterally adhered between the side chains of IVLY amino acid residues is marked as "cluster hydrophobic surface", and it is predicted that the state in which a hydrophobic surface of an IVLY cluster and the hydrophobic surface of another adjacent cluster in the amino acid residue sequence are adhered is a protein structure. When a helix structure is represented by two cluster hydrophobic surfaces, and the two cluster hydrophobic surfaces do not have a connected segment in the axial direction of the helix, it is predicted that one of the clusters with a smaller number of IVLFYs will not be adhered to the hydrophobic surface of another adjacent IVLF cluster as a possible prediction result, such as Fig.16 shown.

[0223] The above calculation examples of the present invention are only used to explain the calculation model and calculation process of the present invention in detail, and are not intended to limit the implementation methods of the present invention. For ordinary technicians in the relevant field, other different forms of changes or modifications can be made based on the above description. It is impossible to list all the implementation methods here. All obvious changes or modifications derived from the technical solution of the present invention are still within the scope of protection of the present invention.

Claims

1. A protein structure prediction method based on the mutual attraction between low entropy hydration layers of residue side chains, characterized by: The prediction method is to use water entropy force to realize protein structure prediction; the prediction is to predict the secondary structure of protein based on the primary structure of protein; the water entropy force refers to the interaction attraction between the low entropy hydration layers of the side chains of amino residues; the interaction attraction refers to the entropy increase of low entropy water molecules in the low entropy hydration layer driving the lateral adhesion between the side chains of amino acid residues; the lateral adhesion refers to the side chains of two residues being in a nearly parallel state.

2. The prediction method according to claim 1, characterized in that: The process of using water entropy force to predict protein structure includes:

1. Forecasting preparation: Firstly, an entropy value is assigned to the side chains of amino acid residues in the primary structure of the protein, wherein the entropy value is a relative measure of the entropy increase potential of the low entropy hydration layer outside the side chains of the amino acid residues; Then, the amino acid residue side chains in the primary structure of the protein after entropy assignment are divided into five residue forms: Residues with micro-entropy increase potential: serine S, threonine T, aspartic acid D, asparagine N; Hydrophilic residues: histidine H, arginine R, lysine K, glutamic acid E, glutamine Q, aspartic acid D, asparagine N, tyrosine Y, tryptophan W, serine S; Turn residues: glycine G, proline P; Hydrophobic residues: isoleucine I, valine V, leucine L, phenylalanine F, tyrosine Y, tryptophan W, alanine A, methionine M, cysteine ​​C, histidine H; Residues with high entropy increase potential: isoleucine I, valine V, leucine L, lysine K, arginine R, phenylalanine F, tyrosine Y, tryptophan W, alanine A, methionine M, cysteine ​​C, glutamate E, glutamine Q, histidine H; Finally, determine the preferred pairing between amino acid residue side chains The preferred pairing between the side chains of amino acid residues is that the side chains of multiple pairs of amino acid residues are laterally fitted together, resulting in sufficient entropy increase of the low entropy hydration layers of the side chains of multiple pairs of amino acid residues. The pair relationship between the multiple pairs of amino acid residues is the preferred pairing between the side chains of amino acid residues. The preferred pairing between the side chains of amino acid residues includes the preferred pairing between the side chains of amino acid residues in a 1-4 / 5 sequence position relationship, the preferred pairing between the side chains of amino acid residues in a 1-3 sequence position relationship, and the preferred pairing between the side chains of amino acid residues in a 1-2 sequence position relationship; The 1-4 / 5 sequence position relationship refers to the relationship between the sequence positions of one residue side chain and another residue side chain in the amino acid residue sequence in the primary structure of the protein, which are separated by 2 or 3 amino acid residues; The 1-3 sequence position relationship refers to the relationship between the sequence positions of one residue side chain and another residue side chain in the amino acid residue sequence in the primary structure of the protein, with an interval of one amino acid residue; The 1-2 sequence position relationship refers to the sequence position relationship between a residue side chain and another adjacent residue side chain in the amino acid residue sequence in the primary structure of the protein; 2. Protein secondary structure prediction: Based on the sequence position of the residue side chains in step 1, the classification and entropy value of the amino acid residues, and the preferred pairing between the residue side chains, the following process is used to predict the secondary structure of the protein: S100, starting a new line below the amino acid sequence marked with entropy values, repeatedly listing the amino acid residues in the amino acid sequence that are high entropy increase potential residues as a high entropy increase potential residue connected segment; then, starting a new line, repeatedly listing the amino acid residues in the amino acid sequence that are low entropy residues and corner residues; S200. List the unblocked connected segments of residues with high entropy increase potential, and assume the listed unblocked connected segments of residues with high entropy increase potential to be α-helices or β-folds in the secondary structure of the protein: S201. Assuming that the connected segment of residues with high entropy increase potential forms an α-helix, if a residue side chain in the connected segment of residues with high entropy increase potential achieves preferred pairing between amino acid residue side chains, the amino acid residue in the connected segment of residues with high entropy increase potential is marked as * below; S202, assuming that the high entropy increase potential residue connected segment forms a β-fold, if the high entropy increase potential residue connected segment is a preferred pairing between the side chains of the amino acid residues in the 1-3 sequence position relationship, then the amino acid residues in the high entropy increase potential residue connected segment are marked as &; S203, analyze the marked * and &: S2031. If none of the connected segments of residues with high entropy increase potential in the primary structure of the protein are marked as &-&, and more than 80% of the amino acid residues in the connected segment of residues with high entropy increase potential are marked as *, then it is predicted that the connected segment of residues with high entropy increase potential forms an α-helix; S2032. If the connected segment of residues with high entropy increase potential in the primary structure of the protein is marked with &-&, it is predicted that the connected segment of residues with high entropy increase potential forms a β-fold; if the number of * marked in the connected segment of residues with high entropy increase potential in the primary structure of the protein is less than 50% of the number of amino acid residues in the connected segment of residues with high entropy increase potential, it is predicted that the connected segment of residues with high entropy increase potential forms a β-fold; S300, searching the amino acid side chains on both sides of the connected segment of high entropy increase potential residues that have been predicted by S200 to form an α-helix, if the amino acid residues in the amino acid side chains on both sides have a preferred pairing between the amino acid residue side chains in a 1-4 / 5 sequence position relationship with the amino acid residues in the connected segment of high entropy increase potential residues, then it is predicted that the amino acid residue side chains in a 1-4 / 5 sequence position relationship preferably pair to form an α-helix; S400, determine whether the S200 hypothesis predicts the formation of α-helix or β-fold in the protein secondary structure: The entropy increments of the amino acid residues in the primary structure of the protein predicted to be α-helix and β-fold are respectively counted, and the entropy increments of the α-helix predicted to be β-fold are compared; when the value of the relatively larger entropy increment of the two is greater than the value of the other entropy increment by more than 20%, the prediction result of the relatively larger entropy value of the two is determined as the final prediction result; when the value of the relatively larger entropy increment of the two is less than 20% of the other entropy increment, the prediction of the formation of α-helix or β-fold in the secondary structure of the protein by S200 hypothesis is determined as a potential result; Among them, the entropy value-added statistical method of β-folding: the side chains of amino acid residues with a 1-3 sequence position relationship in the primary structure of the protein are preferably paired, and the entropy value of the amino acid residues in the preferred pairing is used as the entropy value; Statistical method for entropy increment of α-helix: the preferred pairing between the side chains of amino acid residues with a 1-4 / 5 sequence position relationship in the primary structure of the protein is used, and the entropy value of the amino acid residues in the preferred pairing is used as the entropy increment; S500, if there are two consecutive amino acid residues with low entropy increase potential in the connected segment of high entropy increase potential residues that are not predicted to be α-helices in the primary structure of the protein, the two amino acid residues are predicted to form a turn and are marked as T; A segment of 4 or more consecutive hydrophilic amino acid residues in the primary structure of a protein is named a "continuous hydrophilic residue segment"; if there is a segment with more than 7 amino acid residues in the high entropy increase potential residue connected segment that is not predicted to be an α-helix in the primary structure of a protein, and the number of residues with low entropy increase potential and / or corner residues and / or amino acid residue A and / or residues in the continuous hydrophilic residue segment accounts for more than or equal to 50% of the number of the segment with more than 7 amino acid residues, then the segment with more than 7 amino acid residues is predicted to form a random curl and is used as a potential prediction result; S600. A fragment consisting of 5 or more consecutive hydrophilic amino acid residues in the primary structure of a protein, if the fragment has been predicted to be a connected fragment of residues with high entropy increase potential, then the fragment consisting of 5 or more consecutive hydrophilic amino acid residues is predicted to form a random curl, and used as a potential prediction result, thereby completing the protein structure prediction method based on the mutual attraction relationship between the low entropy hydration layers of the residue side chains.

3. The prediction method according to claim 2, characterized in that: The determination of the preferred pairing between amino acid residue side chains, the preferred pairing between amino acid residue side chains includes: FF, QQ, KK, EE, TT, RR, AA, SS, MM; MA, QE, TS, RE, KR, EK, FY, WY, WE, RW, RY, KY, HV, DE, NE, DQ, NQ; QR / K, I / V / L / FI / V / L / F, I / V / L / F / YI / V / L / F / Y, I / V / LY, I / V / LK, I / V / LR, I / V / LA, I / V / LW, I / V / L / F / YW, I / V / LM, CM / Y, MI / V / L, A / TD / N.

4. The prediction method according to claim 2, characterized in that: The preferred pairing between the side chains of amino acid residues in step S201 refers to the preferred pairing between the side chains of amino acid residues with a 1-4 / 5 sequence position relationship; if there is a preferred pairing between the side chains of amino acid residues with a 1-2 sequence position relationship in the connected segment of residues with high entropy increase potential, or there is a sequence position relationship of IVL 1-4 / 5G / A1-4 / 5IVLF in the connected segment of residues with high entropy increase potential, it is marked as * below the amino acid.

5. The prediction method according to claim 2, characterized in that: The preferred pairing between the side chains of the amino acid residues in the 1-3 sequence position relationship described in S202 is I / V / L / FI / V / L / F; if taking the amino acids in I / V / L / FI / V / L / F as the starting point, there is a preferred pairing between the side chains of the amino acid residues in the 1-4 / 5 sequence position relationship in the adjacent high entropy increase potential residue connected fragment, then the amino acids in the preferred pairing between the side chains of the amino acid residues in the 1-3 sequence position relationship are not marked as &.

6. The prediction method according to claim 2, characterized in that: If a connected segment of residues with high entropy increase potential in the primary structure of a protein is marked with &-&, and more than 85% of the amino acid residues in the amino acid side chain region in the primary structure of the protein far away from the connected segment of residues with high entropy increase potential marked with &-& are marked with *, and there is a preferred pairing between the side chains of amino acid residues that has a 1-4 / 5 sequence position relationship of I / V / L / F / YI / V / L / F / Y with the irrelevant residues marked with &-&, then it is predicted that the connected segment of residues with high entropy increase potential marked with &-& forms an α-helix; wherein, the distance refers to a continuous interval of two low entropy residues or corner residues, or an interval of at least 3 hydrophilic residues, or an interval of one amino acid residue P; the irrelevant residues refer to other amino acid residues in the primary structure of the protein except those marked with &-&; the amino acid side chain region refers to a region composed of amino acid side chains with a number of amino acid residues greater than 5.

7. The prediction method according to claim 2 or 6, characterized in that: The connected segment of residues with high entropy increase potential described in S2032 is predicted to form a β-fold, and the connected segment of residues with high entropy increase potential contains two consecutive low entropy residues aspartic acid D or asparagine N, then the two consecutive low entropy residues aspartic acid D or asparagine N are predicted to form a turn as a prediction result.

8. The prediction method according to claim 2, characterized in that: In the entropy increment statistics of the β-fold described in S400, if the same amino acid residue in the primary structure of the protein realizes the preferred pairing between the side chains of two amino acid residues with a 1-3 sequence position relationship, the entropy increment of the amino acid residue is accumulated twice; In the entropy increment statistics of α-helix, if the same amino acid residue in the primary structure of the protein realizes multiple preferred pairings between the side chains of amino acid residues with a 1-4 / 5 sequence position relationship, the entropy increment of the amino acid residue is accumulated twice.

9. The prediction method according to claim 2 or 8, characterized in that: In the entropy increment statistics of the α-helix described in S400, if there is a preferred pairing between the side chains of amino acid residues with a 1-2 sequence position relationship in the primary structure of the protein, and the preferred pairing is I / V / L / MI / V / L / M, then the two pairs of I / V / L / M are recorded as one entropy increment.

10. The prediction method according to claim 2, characterized in that: The amino acid residues in the two consecutive amino acid residues in S600 are one or two of S, T, N, D, and G.

11. The prediction method according to claim 2, characterized in that: The relative measurement value of the entropy increase potential of the low entropy hydration layer outside the side chains of amino acid residues in the primary structure of the protein is a measurement indicator that takes the length of the hydrophobic part on the side chains of amino acid residues in the primary structure of the protein as the relative measurement value.

12. The prediction method according to claim 2 or 11, characterized in that: The relative measure of the entropy increase potential of the low entropy hydration layer on the periphery of the amino acid residue side in the primary structure of the protein specifically takes the length of a carbon-carbon bond on the amino acid residue chain in the primary structure of the protein as 1 entropy value.

13. The prediction method according to claim 2, characterized in that: The entropy values ​​of the 20 amino acids are as follows: Serine S=0.5, threonine T=0.5, aspartic acid D=0.5, asparagine N=0.5, glycine G=0, histidine H=3, arginine R=3, glutamic acid E=3, lysine K=4, tryptophan W=5, isoleucine I=6, valine V=6, leucine L=6, phenylalanine F=6, proline P=0, cysteine ​​C=4, glutamine Q=3, alanine A=1, methionine M=4, tyrosine Y=5.

14. The prediction method according to claim 2, characterized in that: The sufficient entropy increase described in step one means that when the side chains of two amino acid residues in the primary structure of the protein are similar, the two residue side chains are laterally fitted together, so that the low entropy hydration layer of the two side chains undergoes sufficient entropy increase; the similarity of the amino acid residue side chains means that the smaller the difference in entropy values ​​of the two hydrophilic amino acid residues is, the more similar the two hydrophilic residues are; and the smaller the difference in entropy values ​​of the two hydrophobic amino acid residues is, the more similar the two hydrophobic residues are.

15. The prediction method according to claim 2, characterized in that: In the process of determining the unblocked high entropy increase potential residue connected segments, first find the segments consisting of consecutive high entropy increase potential residues in the sequence, name the original "high entropy increase potential residue connected segments", then determine the non-high entropy increase potential residues that do not block the high entropy increase potential residue connected segments, and then determine the unblocked high entropy increase potential residue connected segments, specifically including: (1) When there is only one amino acid residue S or T between two high entropy increase potential residues, the S or T residue participates in forming an unblocked high entropy increase potential residue connected segment; (2) When there is only one isolated N, D or G residue between two high entropy increase potential residues in the amino acid sequence, and there is a high entropy pairing between I, V, L, F, and Y with a 1-3 or 1-4 / 5 relationship across the D, N or G, then the D, N or G is considered to participate in the formation of an unblocked high entropy increase potential residue connected segment; (3) When any one of the amino acid residues S, T, N, D, and G appears in the amino acid sequence of the polypeptide chain, and it is adjacent to any one of the amino acid residues S, T, N, D, and G, check the 1-4 / 5 sequence position relationship across the two adjacent amino acid residues. When the two amino acid residues at the 1-4 / 5 position are both I, V, L, F, and Y residues, and at least one of the amino acid residues is I, V, or L, it is predicted that the two adjacent amino acid residues participate in forming an unblocked high entropy increase potential residue connected segment; (4) When a P residue appears in the amino acid sequence of a polypeptide chain, and the P residue is not in a 1-2 or 1-3 sequence position relationship with a D or N residue, and there is a 1-4 / 5 sequence position relationship across the P residue, and the amino acid residues on 1-4 / 5 are I, V, L, or F, then the predicted P residue participates in the formation of an unblocked high entropy increase potential residue connected segment; (5) When a G or A residue appears in the amino acid sequence of a polypeptide chain, if an amino acid residue that forms a 1-4 / 5 sequence position relationship with the residue can be found on one side of the sequence where the G or A residue is located, and an amino acid residue that forms a 1-4 / 5 sequence position relationship with the G or A residue can also be found on the other side of the sequence where the G or A residue is located, and if there is a single D, N, G or P residue that is not adjacent to other microentropy residues or corner residues between the I, V, L residues, or there are two adjacent S, T, N, D residues, then it is predicted that these single D, N, G or P residues or two adjacent S, T, N, D, G residues participate in the formation of an unblocked high entropy increase potential residue connected segment.

16. The prediction method according to claim 15, characterized in that: The length of the unblocked high entropy increase potential residue connected segment is greater than or equal to 3 amino acid residues.

17. The prediction method according to claim 15, characterized in that: If there is a fragment of 5 or more amino acid residues in the sequence whose primary structure is not predicted to be an α-helix or β-turn, when the fragment is in the general initial thermodynamic metastable state of unfolded protein, if there is no hydrophilic atom of the side chain of a hydrophilic amino acid residue in the fragment whose value minus the height of the adjacent hydrophobic residue side chain is less than or equal to 1, then the fragment is predicted to be a β-fold; wherein the height of the residue side chain refers to the number of covalent bonds in the shortest path between the top atom of the amino acid residue side chain and the main chain carbon atom in the fragment as the height of the residue side chain.

18. A protein structure prediction method based on the mutual attraction between low entropy hydration layers of residue side chains, characterized by: The prediction method is to use water entropy force to predict protein structure; the prediction is based on the secondary structure of the protein predicted by the protein structure prediction method based on the mutual attraction relationship between the low entropy hydration layers of the residue side chains according to any one of claims 6 to 17 to predict the tertiary structure of the protein, comprising the following steps: Definition of the similarity of amino acid residue side chains: the smaller the difference in the "entropy value" of the side chains of two hydrophilic residues, the more similar the two hydrophilic residues are; the smaller the difference in the "entropy value" of the side chains of two hydrophobic residues, the more similar the two hydrophobic residues are; The amino acid residues that have achieved the preferred pairing between I / V / L / F in the predicted secondary structure are marked, and the hydrophobic surface of the hydrophobic side chain cluster that achieves the lateral fit between the side chains of the I / V / L / F amino acid residues is marked and named "cluster hydrophobic surface". The protein structure is predicted to be the one where the hydrophobic surface of an I / V / L / F cluster and the hydrophobic surface of another adjacent I / V / L / F cluster are fitted on the surface; When there is no preferred pairing relationship between I / V / L / F in a β-sheet or α-helix secondary structure, the secondary structure is searched for a preferred pairing relationship between I / V / LY. If so, the hydrophobic surface of the hydrophobic side chain clusters that are laterally attached between the side chains of the I / V / LY amino acid residues is also marked as a "cluster hydrophobic surface"; the surface attachment of an I / V / L / Y cluster hydrophobic surface and another adjacent cluster hydrophobic surface is predicted to be a protein structure; When an α-helical structure has two clustered hydrophobic surfaces and the two clustered hydrophobic surfaces are not connected in the axial direction of the α-helix, it is predicted that one of the clustered hydrophobic surfaces with a smaller number of I / V / L / F / Y will not fit with the other I / V / LF / clustered hydrophobic surface in an adjacent β-sheet or α-helical secondary structure as a possible prediction result.

19. The protein structure prediction method based on the mutual attraction relationship between low entropy hydration layers of residue side chains according to claim 18, characterized in that: It also includes the following steps: For the current prediction of β-fold, it is necessary to mark the strong hydrophobic residues of the 1-3 position relationship preferred pairing connected fragments in the β-fold, i.e., I / V / L / F / W / Y, and mark these hydrophobic fragments connected by the 1-3 position relationship at the same time, compare the lengths of adjacent β-folds in the sequence, and predict that α-helices of similar lengths will fold into a sheet structure, and then based on the distribution of the side chains of the strong hydrophobic residues of the two β-folds, the corresponding positions of the two are based on the most strong hydrophobic residues on one β-fold to achieve preferred pairing with the side chains of the amino acid residues on the other α-helix. The state of the two β-folds being attached is the predicted sheet folding structure.

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