Please wait a minute...
Chinese Physics, 2007, Vol. 16(3): 868-875    DOI: 10.1088/1009-1963/16/3/052
CROSS DISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY Prev   Next  

The preferences of orientations between the pairs of amino acids

Chen Ying(陈颖), Wang Jun(王骏), and Wang Wei(王炜)
National Laboratory of Solid State Microstructure,Department of Physics, and Institute of Biophysics, Nanjing University, Nanjing 210093, China
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.
Keywords:  native structure of protein      preferences of orientation      preferences of secondary structures  
Received:  17 February 2006      Revised:  13 October 2006      Accepted manuscript online: 
PACS:  87.14.E- (Proteins)  
  87.15.B- (Structure of biomolecules)  
  87.15.K- (Molecular interactions; membrane-protein interactions)  
  87.15.N- (Properties of solutions of macromolecules)  
Fund: 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.

Cite this article: 

Chen Ying(陈颖), Wang Jun(王骏), and Wang Wei(王炜) The preferences of orientations between the pairs of amino acids 2007 Chinese Physics 16 868

[1] Single-molecular methodologies for the physical biology of protein machines
Shuang Wang(王爽), Ying Lu(陆颖), and Ming Li(李明). Chin. Phys. B, 2022, 31(12): 128702.
[2] Evaluation on performance of MM/PBSA in nucleic acid-protein systems
Yuan-Qiang Chen(陈远强), Yan-Jing Sheng(盛艳静), Hong-Ming Ding(丁泓铭), and Yu-Qiang Ma(马余强). Chin. Phys. B, 2022, 31(4): 048701.
[3] Diffusion of nucleotide excision repair protein XPA along DNA by coarse-grained molecular simulations
Weiwei Zhang(张伟伟) and Jian Zhang(张建). Chin. Phys. B, 2021, 30(10): 108703.
[4] Tunable inhibition of β-amyloid peptides by fast green molecules
Tiantian Yang(杨甜甜), Tianxiang Yu(俞天翔), Wenhui Zhao(赵文辉), and Dongdong Lin(林冬冬). Chin. Phys. B, 2021, 30(8): 088701.
[5] Modeling hydrogen exchange of proteins by a multiscale method
Wentao Zhu(祝文涛), Wenfei Li(李文飞), and Wei Wang(王炜). Chin. Phys. B, 2021, 30(7): 078701.
[6] Equilibrium folding and unfolding dynamics to reveal detailed free energy landscape of src SH3 protein by magnetic tweezers
Huanhuan Su(苏环环), Hao Sun(孙皓), Haiyan Hong(洪海燕), Zilong Guo(郭子龙), Ping Yu(余平), and Hu Chen(陈虎). Chin. Phys. B, 2021, 30(7): 078201.
[7] Multi-scale molecular dynamics simulations and applications on mechanosensitive proteins of integrins
Shouqin Lü(吕守芹), Qihan Ding(丁奇寒), Mingkun Zhang(张明焜), and Mian Long(龙勉). Chin. Phys. B, 2021, 30(3): 038701.
[8] Statistical potentials for 3D structure evaluation: From proteins to RNAs
Ya-Lan Tan(谭雅岚), Chen-Jie Feng(封晨洁), Xunxun Wang(王勋勋), Wenbing Zhang(张文炳), and Zhi-Jie Tan(谭志杰). Chin. Phys. B, 2021, 30(2): 028705.
[9] Structural and dynamical mechanisms of a naturally occurring variant of the human prion protein in preventing prion conversion
Yiming Tang(唐一鸣), Yifei Yao(姚逸飞), and Guanghong Wei(韦广红)†. Chin. Phys. B, 2020, 29(10): 108710.
[10] Application of topological soliton in modeling protein folding: Recent progress and perspective
Xu-Biao Peng(彭绪彪)†, Jiao-Jiao Liu(刘娇娇), Jin Dai(戴劲), Antti J Niemi‡, and Jian-Feng He(何建锋)§. Chin. Phys. B, 2020, 29(10): 108705.
[11] Different potential of mean force of two-state protein GB1 and downhill protein gpW revealed by molecular dynamics simulation
Xiaofeng Zhang(张晓峰), Zilong Guo(郭子龙), Ping Yu(余平), Qiushi Li(李秋实), Xin Zhou(周昕), Hu Chen(陈虎). Chin. Phys. B, 2020, 29(7): 078701.
[12] Lipoprotein in cholesterol transport: Highlights and recent insights into its structural basis and functional mechanism
Shu-Yu Chen(陈淑玉), Na Li(李娜), Tao-Li Jin(金桃丽), Lu Gou(缑璐), Dong-Xiao Hao(郝东晓), Zhi-Qi Tian(田芷淇), Sheng-Li Zhang(张胜利), Lei Zhang(张磊). Chin. Phys. B, 2018, 27(2): 028702.
[13] Optimizing the atom types of proteins through iterative knowledge-based potentials
Xin-Xiang Wang(汪心享), Sheng-You Huang(黄胜友). Chin. Phys. B, 2018, 27(2): 020503.
[14] A network of conformational transitions in an unfolding process of HP-35 revealed by high-temperature MD simulation and a Markov state model
Dandan Shao(邵丹丹), Kaifu Gao(高恺夫). Chin. Phys. B, 2018, 27(1): 018701.
[15] Computational study of non-catalytic T-loop pocket on CDK proteins for drug development
Huiwen Wang(王慧雯), Kaili Wang(王凯丽), Zeyu Guan(管泽雨), Yiren Jian(简弋人), Ya Jia(贾亚), Fatah Kashanchi, Chen Zeng(曾辰), Yunjie Zhao(赵蕴杰). Chin. Phys. B, 2017, 26(12): 128702.
No Suggested Reading articles found!