25 results about "Protein folding" patented technology

The present invention relates to the technical field of enzyme engineering. Disclosed are an artificial intelligence-based enzyme engineering method and system, a device, and a medium. The method comprises: on the basis of structural information of an engineered enzyme to be modified, using an inverse protein folding model to obtain a plurality of structurally compatible protein sequences on the basis of a given scaffold structure; on the basis of the plurality of structurally compatible protein sequences, obtaining a mutant amino acid frequency and a wild-type amino acid frequency at each sequence position; and on the basis of the mutant amino acid frequency and the wild-type amino acid frequency at each sequence position and the structural information of said engineered enzyme, as well as a first creation strategy, a second creation strategy, and a third creation strategy, obtaining a single-mutation variant set and a combinatorial-mutation variant set of said engineered enzyme. The present invention enables efficient and low-cost generation of single-mutation and combinatorial-mutation variant sets of an engineered enzyme to be modified, thereby achieving precise and efficient gene editing and effectively expanding the applicability and safety of gene editing.

The invention relates to a protein solubility prediction method and system based on GCN and an improved attention network. The method comprises the following steps: constructing a protein sequence data set; the method comprises the following steps: acquiring a protein three-dimensional structure file through AlphaFold3, and constructing a node feature vector; extracting position embedding, bidirectional projection direction features, a cross-node atom pair distance and a rotation relation, and constructing an edge feature vector; extracting global physicochemical property feature vectors of the protein; and constructing protein graph structure data, inputting the data to the graph convolutional network module and the improved graph attention network module, and performing training to obtain a graph convolutional network and an improved attention network model to perform protein solubility prediction. By extracting node and edge features and protein global physicochemical property features, subsequent model training is facilitated; and the two-way projection and the rotation relation enable the model to accurately sense the spatial orientation between residues, so that the model has more quantitative understanding on the protein folding and gathering driving force, and the accuracy of protein solubility prediction is improved.

A peptide which is characterized by: (a) dissolving 2 g or more at 20 DEG C in 100 mL of a 50 mM Tris hydrochloric acid buffer solution (pH 7.5) containing 0.3 M sodium chloride; (b) reversibly performing phase change in the Tris hydrochloric acid buffer solution, wherein the transformation temperature is 40-70 DEG C when 2g of the solution is dissolved in 100mL of the Tris hydrochloric acid buffer solution; and (c) when 2 g of the Tris hydrochloric acid buffer solution is dissolved in 100 mL of the Tris hydrochloric acid buffer solution, droplets are formed under the temperature condition above the transition temperature.

The invention provides a gene expression cassette for improving CsCE expression quantity and application. The gene expression cassette provided by the invention comprises a regulatory element and a target gene, the regulatory element comprises at least one of a coding sequence of dtRNA, a coding sequence of a signal peptide and a coding sequence of a fusion tag, and the target gene comprises a coding sequence of CsCE enzyme. Wherein the dtRNA contributes to keeping the structural stability when the CsCE enzyme is transcribed into mRNA, the signal peptide can promote the secretion of the CsCE enzyme, and the fusion tag can assist the correct folding of the CsCE enzyme, so that the expression of the CsCE enzyme can be synergistically regulated under the three-tube alignment of a DNA transcriptional mRNA layer, a protein secretion layer and a protein folding layer, the expression quantity of the CsCE enzyme can be effectively up-regulated, and the expression quantity of the CsCE enzyme can be effectively up-regulated. Therefore, the volume enzyme activity of the CsCE enzyme is improved, and the CsCE enzyme with higher volume enzyme activity can catalyze lactose to be converted into lactulose in the preparation of lactulose, so that the preparation yield of lactulose is improved.

The invention belongs to the technical field of gene recombination, and particularly relates to a recombinant human III-type triple helix collagen, a recombinant yeast strain for expressing the recombinant human III-type triple helix collagen and a construction method of the recombinant human III-type triple helix collagen. The amino acid sequence of the recombinant human III-type triple-helix collagen is shown as SEQ ID NO. 1, and the recombinant human III-type triple-helix collagen has triple-helix conformation close to a natural biological structure of collagen and has good application value and potential. According to the recombinant yeast strain disclosed by the invention, human-derived III-type collagen and proline hydroxylase are co-expressed in yeast cells without YPS1 protease, and meanwhile, a gene beneficial to vesicle transport and protein folding is transferred, so that hydroxylation of the recombinant collagen can be realized, a natural triple helix conformation is formed, and the recombinant yeast strain can be used for preparing a recombinant collagen product. The degradation problem of the collagen in the expression process can be solved, and the extracellular secretion expression of the triple helix collagen is realized.

The invention aims to provide a method and device for constructing a codon sequence optimization model, a medium and a program product, and the method comprises the steps: constructing graph structure information corresponding to sample protein sequence information based on the sample protein sequence information and corresponding protein three-dimensional structure information, the graph structure information comprises node information matched with each amino acid and side information matched with each amino acid pair; inputting the graph structure information into a codon sequence optimization model of an encoder-decoder architecture to obtain a predicted codon sequence; and based on the predicted codon sequence and the codon sequence corresponding to the sample protein sequence information, combining a corresponding loss function to carry out model optimization, and obtaining a trained codon sequence optimization model. Through the three-dimensional structure of the protein, the model is helped to select codons in a more targeted manner, so that the codon sequence predicted by the model is closer to the actual protein folding process, and the translation speed of amino acid is matched with the folding speed.

The application discloses a fermentation method for improving structural stability and yield of recombinant human serum albumin, and belongs to the technical field of biological fermentation. 600 ≥180, and the living cell rate is greater than or equal to 90%; (2) during a methanol induction period, L-cysteine and L-methionine are added in batches in pulse mode with a mass ratio (0.5-2.0):1, and the final concentration is 0.1%-0.3%. The application promotes correct formation of disulfide bonds by optimizing seed quality and protein folding microenvironment. By using the method, the expression amount of rHSA reaches 24.3 g / L, the monomer purity is greater than or equal to 92%, the free sulfhydryl content is less than or equal to 3%, and the monomer purity reduction rate is less than or equal to 4% after 14 days of accelerated storage at 37 DEG C. The application significantly improves product stability while maintaining high yield, and provides an innovative process for industrialized production of high-quality rHSA.

The application discloses a yeast strain with high yield of cannabinoid synthesis precursors, a construction method and application thereof, and belongs to the technical field of synthetic biology and microorganisms. The application takes Saccharomyces cerevisiae as a host, screens genes participating in protein folding proteins to obtain an engineering strain for improving the yield of OA / OLO, further down-regulates the expression of FAS1 and MvaE enzymes, and then inserts a gene expression cassette CsAAE1-TKS-OA cassette into the rDNA site of the Saccharomyces cerevisiae genome in multiple copies to obtain a genetic engineering strain with improved OA / OLO yield. The application further improves the yield of OA / OLO by optimizing the substrate in the fermentation system, i.e. using a mixed substrate of sodium caproate and ethyl caproate, and the yield of OA / OLO in a 10L fermenter is about 10 mM OA and 10 mM OLO, and the equivalent yield is 2.2 g / L and 1.8 g / L respectively.

This invention relates to a detection kit and preparation method for enhancing the detection efficacy of autoimmune encephalitis (CBA) antibodies. The kit comprises genetically engineered 293T cells stably integrating and co-expressing the eIF2α S52A mutant and HSP70, and transiently transfected with CBA-associated antigens. The preparation method includes constructing a co-expression vector, establishing a stable transfection cell line, stress preconditioning treatment, antigen transfection, and kit assembly. A method for assessing antibody affinity maturation using this kit is also provided. By synergistically modifying detection cells at three levels—translational regulation, protein folding, and anti-apoptosis—the invention significantly increases antigen expression, reduces apoptosis, and improves detection sensitivity and specificity. Furthermore, it integrates antibody affinity assessment into CBA detection for the first time, providing auxiliary information for clinical staging.

An apparatus, system, and method for studying protein folding in the native cellular environment is provided. The invention, termed pcIC-FPOP, combines pulse-chase experiments with in-cell protein footprinting coupled to mass spectrometry. This enables very high resolution information on the folding or mis-folding of proteins. The system (100) includes a multi-well plate (110), an incubator (120), a stage (130), a subsystem of reservoirs (172) and pumps (174), a laser source (140) and beam steering optics (150), and a computer system (160) programmed with a control module (162) to control the operation of the laser (140), optics (150), incubator (120), stage (130), or pumps (174), or some combination. This method permits studies that fill gaps in knowledge on protein folding and its role in disease.

The invention discloses construction and application of an engineering strain capable of normally growing at 35 DEG C and realizing high yield of xanthan gum. The method comprises the following steps: by taking xanthomonas campestris XC1 as an initial strain, carrying out ARTP mutagenesis treatment, and screening a mutant strain which can normally grow under the condition of 35 DEG C; the mutant strain is subjected to multiple rounds of superposition transformation, and multiple physiological restrictions under high temperature stress are systematically broken by sequentially strengthening a protein folding system (grpE-ATGA-dnaK), activating outer membrane stress regulation (rpoE), constructing an anti-oxidation barrier (katB) and strengthening a cell membrane structure (polCDE); the finally obtained engineering strain shows the performance far better than that of an initial strain under the condition of 35 DEG C; the biomass of the strain is increased by 207.7% compared with that of an initial strain XC1, and the yield of xanthan gum is increased by 75.5% and reaches 25.8 g / L, which is consistent with the yield of xanthan gum under the fermentation condition of 28 DEG C.

Provided is a protein folding agent containing a compound (A) represented by general formula (A). In general formula (A), R1 to R6 are each independently a C1-24 aliphatic hydrocarbon group. Y1and Y2each independently represent a C1-6 aliphatic hydrocarbon group. Moreover, n is an integer of 1 or greater, and Xn- is an n-valent anion. Also provided is a protein folding composition containing the compound (A) and a protein aggregation inhibitor. Furthermore, also provided is a protein folding method including a step (a) for incubating a protein in the presence of the protein folding agent.

The invention provides a gene expression cassette for improving CsCE expression quantity and application. The gene expression cassette provided by the invention comprises a regulatory element and a target gene, the regulatory element comprises a coding sequence of a fusion tag, and the target gene comprises a coding sequence of CsCE enzyme. The fusion tag can promote the expression quantity of the CsCE enzyme on the level of regulating and controlling protein folding, and the expression quantity of the CsCE enzyme is improved through the synergistic effect of the fusion tag and the CsCE enzyme, so that the volume enzyme activity of the CsCE enzyme is improved, the CsCE enzyme with higher volume enzyme activity can catalyze lactose to be converted into lactulose in the preparation of lactulose, and the lactulose can be used for preparing lactulose. Further, the preparation yield of the lactulose is improved.

The invention discloses a preparation method of an HIV (Human Immunodeficiency Virus) envelope protein gp160. The preparation method comprises an effective interception and selection mode of amino acid sequences of envelope proteins gp160-I and gp160-II of HIV-I and HIV-II, an optimized nucleotide sequence, an expression plasmid construction method and a purification and preservation method. The gp160-I protein and the gp160-II protein are expressed through mammalian cells, the protein expression efficiency and the protein folding modification accuracy are greatly improved by adding the artificial signal peptide and the JSD promoter, and the gp160-I protein and the gp160-II protein have high biological activity and thermal stability and have the advantages that fermentation is easy to amplify, separation and purification are easy, and the coating use amount is low.

The invention discloses application of brazilin in preparation of a medicine for inducing endoplasmic reticulum stress of bladder cancer cells. Experiments provided by the invention prove that brazilin can inhibit the progress of bladder cancer in vitro and in vivo, and reduce the Khib level of protein enriched in a protein folding pathway, so that endoplasmic reticulum stress is triggered, a PERK-eIF2alpha-ATF4-CHOP axis is activated, and CHOP-mediated cell apoptosis is driven. According to the application disclosed by the invention, the anti-tumor effect of the brazilin is researched by associating with Khib proteome remodeling and endoplasmic reticulum stress-induced apoptosis for the first time, and the research shows that the brazilin can be used for preparing medicines for treating bladder cancer or assisting in postoperative treatment.

A protein folding agent which contains at least one compound selected from the group consisting of (A) to (B): (A) a cyclic polyamine that contains one or more thiol groups or disulfide bonds and is capable of bonding to transition metal ions; (B) a compound in which two or more cyclic polyamines (A) are bonded to each other via disulfide bonds between the thiol groups; (C) a complex of the cyclic polyamine of (A) or the compound of (B) with a transition metal ion; (D) a salt of the cyclic polyamine of (A) or the compound of (B); and (E) a solvate of the cyclic polyamine of (A) or the compound of (B).

It is an object of the present invention to provide a method for determining a folding trajectory of a given protein comprising: - generating a starting conformation; - defining a metric for assessing the distance between conformations; - generating an array of protein conformations constituting a trajectory. It is another object of the present invention to provide a method for identifying target conformations suitable for testing as targets of a drug discovery program.

A peptide has the following characteristics (a) to (c): (a) dissolving the peptide at an amount of 2 g or more at 20°C in 100 mL of a 50 mM Tris-HCl buffer (pH: 7.5) containing 0.3 M sodium chloride; (b) undergoing a reversible phase transition in the Tris-HCl buffer, in which a transition temperature when 2 g of the peptide is dissolved in 100 mL of the Tris-HCl buffer is 40°C to 70°C; and (c) forming droplets under a temperature condition at or above the transition temperature when 2 g of the peptide is dissolved in 100 mL of the Tris-HCl buffer.

A method for identifying target protein folding intermediates, suitable to be tested as targets for drug discovery procedures. The method is carried out by means of electronic computing. The method provides a step of modelling a sequence in time of events defining a folding pathway of a protein, which includes modelling and / or calculating structural and / or energy and / or physical-chemical properties of one or more protein folding intermediate states along the folding pathway. Then, the method includes identifying at least one candidate protein folding intermediate, along the modelled folding pathway, based on identification properties, and selecting one or more target protein folding intermediates, among the at least one candidate protein folding intermediate, based on selection properties. The selection properties are related to the druggability of the protein folding intermediate. A related method for in silico drug discovery based on folding intermediate targeting is also provided.

The invention relates to a preparation method of an APP gene humanized mutation vector and a non-human animal model. The APP gene humanized mutation vector comprises an APP gene knockout vector and an APP gene homologous recombination vector, and the APP gene knockout vector comprises at least one of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3 and SEQ ID NO: 4; the APP gene homologous recombinant vector comprises a part of nucleotide sequence for coding non-human animal APP protein, and the non-human animal APP protein contains human APP protein pathogenic mutation sites which are specifically as shown in SEQ ID NO: 5. Humanized mutation is carried out on the non-human animal APP, the original nature of the in-vivo environment of the non-human animal is maintained to the maximum extent, expression and folding of the gene are facilitated, the situation that protein folding is abnormal and conflicts with existing protein of the non-human animal are caused due to direct insertion of the human APP gene is prevented, and the method is closer to the real pathological process; and a more real and reliable disease model in pathology can be obtained.

This invention discloses a recombinant human type III collagen, its preparation method, and its applications. The amino acid sequence of the recombinant human type III collagen is shown in SEQ ID NO.1. This invention optimizes the codons for the CHO cell expression system (as shown in SEQ ID NO.2), successfully achieving efficient expression of the recombinant human type III collagen. Furthermore, since CHO cells, as mammalian cells, possess the ability to fold and modify proteins, this facilitates the formation of positive glycosylation modification of the product. Experimental verification shows that the recombinant human type III collagen prepared by this invention exhibits activity in promoting the adhesion, proliferation, and migration of human fibroblasts.

The invention provides a two-dimensional infrared spectrum protein physicochemical property prediction method and system based on a Transform model, and the method comprises the steps: firstly constructing a source domain data set which comprises massive static protein conformations and simulative 2D IR spectrums, and training the Transform model to learn a universal spectrum characteristic and physicochemical property mapping rule; and then, by taking the dynamic spectrum data of a small amount of protein folding trajectory as a target domain, carrying out fine adjustment on the Transform model to obtain a target model, so that the target model understands the dynamic evolution law of the physicochemical properties of the protein along with time in the folding process. According to the method, an end-to-end learning process from original two-dimensional infrared spectrum data to protein physicochemical property prediction is established, data modeling and feature association can be automatically completed without manual intervention or feature extraction, and the modeling efficiency and repeatability are greatly improved.

Provided is a method for predicting a protein structure on the basis of the interactive attraction relationships between low-entropy hydration layers of residue side chains. The method solves the problem of poor prediction performance in existing methods for predicting a protein folding structure. The method realizes the prediction of a protein structure using a water entropic force, wherein 'prediction' refers to the prediction of the secondary structure and tertiary structure of a protein on the basis of the primary structure of the protein; 'water entropic force' refers to the interactive attraction force between low-entropy hydration layers of amino acid residue side chains; 'interactive attraction force' refers to a force in which the entropy increase of low-entropy water molecules in the low-entropy hydration layers drives lateral association between the amino acid residue side chains; and 'lateral association' refers to a state where two residue side chains are nearly parallel to each other. The method is used for predicting the structure of a protein.

The application relates to an E. coli recombinant strain for producing nanobody, a construction method and application thereof. The application compares three engineering bacteria E. coli BL21(DE3)pET28a-5-D8, E. coli BL21(DE3)pET28a-P T5 -5-D8 and E. coli ArcticExpress(DE3)pRARE2pET28a-P T5 -5-D8, finds that E. coli BL21(DE3)pET28a-5-D8 and E. coli BL21(DE3)pET28a-PT5-5-D8 are mainly expressed in a non-soluble manner, and E. coli ArcticExpress(DE3)pRARE2pET28a-PT5-5-D8 adopts a weak promoter to control nanobody 5-D8 and changes an expression host, and the specific process is as follows: the pET28a plasmid has BglII / XbaI enzyme cutting sites, a weak promoter (T5) is inserted, the transcription rate is down-regulated through promoter replacement, protein folding is promoted, and the soluble expression proportion is improved. In the E. coli ArcticExpress(DE3)pRARE2, the expression amount of the nanobody is significantly higher than that of E. coli(DE3), and the soluble protein proportion is further improved, so that the balance optimization of the expression amount and the solubility is realized.