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Method of statistically analyzing protein peptide bond cis and trans structures

A technology of protein structure and statistical analysis, applied in structure prediction and cis and trans configurational isomerism research, in the field of protein structure analysis, it can solve the problems of lack of precision and limited trans and cis configuration analysis methods

Active Publication Date: 2017-03-15
BEIJING INSTITUTE OF TECHNOLOGYGY
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

However, we have limited methods for analyzing the trans and cis configurations of protein peptide bonds, and know little about their formation, geometric properties, and functions. More and more effective analytical methods and methods are needed
At present, the study of cis and trans configurations usually adopts traditional structural chemistry methods, mainly focusing on the bond length, bond angle and torsion angle formed by the atoms of the peptide group, and the structural analysis is not accurate to the atomic scale

Method used

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  • Method of statistically analyzing protein peptide bond cis and trans structures
  • Method of statistically analyzing protein peptide bond cis and trans structures
  • Method of statistically analyzing protein peptide bond cis and trans structures

Examples

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Embodiment 1

[0060] This example elaborates in detail the "a method for statistically analyzing the cis- and trans-structures of protein peptide bonds" of the present invention. During the specific implementation, it aims at high-precision statistical analysis of the central carbon atoms in the cis- and trans-structures of protein peptide bonds. The flow of geometric features.

[0061] figure 1 A flowchart of a method for statistical analysis of the cis and trans structures of protein peptide bonds. As can be seen from the figure, the method includes the following steps: step (1): obtain the protein experimental structure, and establish a protein structure database; step (2): establish a carbon, nitrogen and oxygen coordinate frame; step (3): determine the atoms to be investigated Coordinates in the CNO coordinate frame; step (4): calculate the latitude and longitude angle of the atom to be investigated in the unit sphere; step (5): convert all cis and trans in the protein experimental st...

Embodiment 2

[0079] In this example, according to the steps of "A method for statistically analyzing the cis and trans structures of protein peptide bonds" of the present invention and the process described in Example 1, the statistical analysis of the side chain C β i+1 Properties of the distribution of atoms in the cis and trans structures of protein peptide bonds and their consequences.

[0080] High-precision statistical analysis side chain C β i+1 The distribution characteristics of atoms in the cis and trans structures of protein peptide bonds, steps A and B are the same as in Example 1 (one) and (two); steps C, D, E are the same as in Example 1 (three), The difference between (4) and (5) is that this embodiment calculates the side chain C β i+1 Coordinates, latitude and longitude of atoms and drawing side chains C β i+1 The atoms are distributed on the unit sphere, and the secondary structure α-helix, α-left-handed-helix, and β-strand are added to the step (5) to determine, an...

Embodiment 3

[0083] In this embodiment, according to the steps of the present invention and the process described in Embodiment 1, the statistical analysis main chain C is specifically described. i+1 The distribution characteristics of atoms in the cis and trans structures of protein peptide bonds, the results are as follows Figure 5 .

[0084] Figure 5 is the backbone C of all cis and trans structures in the protein experimental structure of the high-resolution protein structure database i+1 Distribution diagram of atoms on the unit sphere; in the diagram, the symbol u i 、w i , v i Mark the CNO coordinate frame axis, trans, cis, cis-nonproline point out the main chain C of trans structure, cis structure, and cis structure without proline i+1 Atomic distribution, α-helix, α L -helix, β-strand represents the main chain C corresponding to the helix, left-handed helix, and sheet i+1 Atom distribution position; Figure 5 shows that the main chain C in the trans structure trans i+1 A...

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Abstract

The invention relates to a method of statistically analyzing protein peptide bond cis and trans structures, and belongs to the fields of protein structure analysis, structure prediction and cis and trans configuration isomerism research. The method is mainly characterized in that protein peptide planar carbon, nitrogen and oxygen atoms are used for setting up a coordinate frame, the longitude and latitude angles, in the unit sphere, of the atoms to be inspected are calculated, and all the atoms to be inspected are projected to the unit sphere to obtain a three-dimensional statistic distribution diagram of the atoms to be inspected. The visual protein structure analysis method can effectively express difference in peptide bond cis and trans structures and disclose the distribution characteristics of the atoms in the peptide bond cis and trans structures. The method is more novel than the existing method based on the structural chemistry, is capable of analyzing the structural characteristics of any side chain atoms and visually expressing geometric structure characteristics of certain atom or certain kinds of atoms in protein and is of important significance in protein structure predicting, structure optimizing, structure constraining and cis and trans configuration isomerism analyzing.

Description

technical field [0001] The invention relates to a method for analyzing the three-dimensional spatial structure characteristics of protein molecules, in particular to a method for statistically analyzing the cis and trans structures of protein peptide bonds, belonging to protein structure analysis, structure prediction and cis and trans configuration isomerism Research areas. Background technique [0002] In proteins, peptide bonds are the basic way amino acids are linked. Due to the resonant interaction between the amide nitrogen and the carboxyl oxygen, the peptide bond has a partial double bond nature and cannot rotate freely, and the six atoms involved in the peptide bond (C α 1 、C α 2 , C, H, O, N) tend to be coplanar. Therefore, the peptide group of the protein has only two planar configurations, cis and trans. In the cis configuration, C α i -N i -C i+1 -C α i+1 The dihedral angle formed by the atoms is about 0 degrees; in the trans configuration, C α i -...

Claims

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Application Information

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IPC IPC(8): G06F19/18
CPCG16B20/00
Inventor 何建锋
Owner BEIJING INSTITUTE OF TECHNOLOGYGY
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