中国物理B ›› 2007, Vol. 16 ›› Issue (3): 868-875.doi: 10.1088/1009-1963/16/3/052

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The preferences of orientations between the pairs of amino acids

陈颖, 王骏, 王炜   

  1. National Laboratory of Solid State Microstructure,Department of Physics, and Institute of Biophysics, Nanjing University, Nanjing 210093, China
  • 收稿日期:2006-02-17 修回日期:2006-10-13 出版日期:2007-03-20 发布日期:2007-03-20
  • 基金资助:
    Project supported by the National Natural Science Foundation of China (Grant Nos10204013, 90103031, 10074030, 10474041, 90403120 and 10021001), and the Nonlinear Project (973) of the National Science Ministry, China.

The preferences of orientations between the pairs of amino acids

Chen Ying(陈颖), Wang Jun(王骏), and Wang Wei(王炜)†   

  1. National Laboratory of Solid State Microstructure,Department of Physics, and Institute of Biophysics, Nanjing University, Nanjing 210093, China
  • Received:2006-02-17 Revised:2006-10-13 Online:2007-03-20 Published:2007-03-20
  • Supported by:
    Project supported by the National Natural Science Foundation of China (Grant Nos10204013, 90103031, 10074030, 10474041, 90403120 and 10021001), and the Nonlinear Project (973) of the National Science Ministry, China.

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摘要： In this work, we make an investigation on the preferences of orientations between amino acids using the orientation defined based on the local geometry of the amino acids concerned. It is found that there are common preferences of orientations (70°, 30°}, 140°) and (110°, 340^{\circ}, 100°) for various pairs of amino acids. Different side chains may strengthen or weaken the common preferences, which is related to the effect of packing. Some amino acids having specific local flexibility may possess some preferences of orientations besides the common ones, such as (10°, 280°, 210°). Another analysis on the pairs of the amino acids with different secondary-structure preferences shows that the directional interaction may affect the distribution of orientation more effectively than the packing or local flexibility. All these results provide us some insight of the organization of amino acids in protein, and their relation with some related interactions.

关键词: native structure of protein, preferences of orientation, preferences of secondary structures

Abstract: In this work, we make an investigation on the preferences of orientations between amino acids using the orientation defined based on the local geometry of the amino acids concerned. It is found that there are common preferences of orientations (70°, 30°, 140°) and (110°, 340°, 100°) for various pairs of amino acids. Different side chains may strengthen or weaken the common preferences, which is related to the effect of packing. Some amino acids having specific local flexibility may possess some preferences of orientations besides the common ones, such as (10°, 280°, 210°). Another analysis on the pairs of the amino acids with different secondary-structure preferences shows that the directional interaction may affect the distribution of orientation more effectively than the packing or local flexibility. All these results provide us some insight of the organization of amino acids in protein, and their relation with some related interactions.

Key words: native structure of protein, preferences of orientation, preferences of secondary structures

中图分类号:  (Proteins)

  • 87.14.E-
87.15.B- (Structure of biomolecules) 87.15.K- (Molecular interactions; membrane-protein interactions) 87.15.N- (Properties of solutions of macromolecules)