中国物理B ›› 2005, Vol. 14 ›› Issue (11): 2365-2369.doi: 10.1088/1009-1963/14/11/038

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Functional structures and folding dynamics of two peptides

盛乐标1, 李菁1, 马保亮1, 王炜2   

  1. (1)National Laboratory of Solid State Microstructure, Institute of Biophysics,and Department of Physics, Nanjing University 210093, China; (2)National Laboratory of Solid State Microstructure, Institute of Biophysics,and Department of Physics, Nanjing University 210093, China;Interdisciplinary Center of Theoretical Studies, Chinese Academy of Sciences, Beijing 100080, China
  • 收稿日期:2005-03-15 修回日期:2005-05-08 出版日期:2005-11-20 发布日期:2005-11-20
  • 基金资助:
    Project supported by the National Natural Science Foundation of China (Grant Nos 90103031, 10474041, 90403120 and 10021001),and the Nonlinear Project (973) of the NSM.

Functional structures and folding dynamics of two peptides

Sheng Yue-Biao (盛乐标)a, Li Jing (李菁)a, Ma Bao-Liang (马保亮)a, Wang Wei (王炜)ab   

  1. a National Laboratory of Solid State Microstructure, Institute of Biophysics,and Department of Physics, Nanjing University 210093, China; b Interdisciplinary Center of Theoretical Studies, Chinese Academy of Sciences, Beijing 100080, China
  • Received:2005-03-15 Revised:2005-05-08 Online:2005-11-20 Published:2005-11-20
  • Supported by:
    Project supported by the National Natural Science Foundation of China (Grant Nos 90103031, 10474041, 90403120 and 10021001),and the Nonlinear Project (973) of the NSM.

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摘要： The folding dynamics and structural characteristics of peptides RTKAWNRQLYPEW (P1) and RTKQLYPEW (P2) are investigated by using all-atomic simulation procedure CHARMM in this work. The results show that P1, a segment of an antigen, has a folding motif of α-helix, whereas P2, which is derived by deleting four residues AWNR from peptide P1, prevents the formation of helix and presents a β-strand. And peptide P1 experiences a more rugged energy landscape than peptide P2. From our results, it is inferred that the antibody CD8 cytolytic T lymphocyte prefers an antigen with a β-folding structure to that with an α-helical one.

关键词: peptide folding, molecular dynamics, protein secondary structure prediction

Abstract: The folding dynamics and structural characteristics of peptides RTKAWNRQLYPEW (P1) and RTKQLYPEW (P2) are investigated by using all-atomic simulation procedure CHARMM in this work. The results show that P1, a segment of an antigen, has a folding motif of $\alpha$-helix, whereas P2, which is derived by deleting four residues AWNR from peptide P1, prevents the formation of helix and presents a $\beta$-strand. And peptide P1 experiences a more rugged energy landscape than peptide P2. From our results, it is inferred that the antibody CD8 cytolytic T lymphocyte prefers an antigen with a $\beta$-folding structure to that with an α-helical one.

Key words: peptide folding, molecular dynamics, protein secondary structure prediction

中图分类号:  (Structure of biomolecules)

  • 87.15.B-
87.15.Cc (Folding: thermodynamics, statistical mechanics, models, and pathways) 87.15.H- (Dynamics of biomolecules) 87.14.E- (Proteins) 87.15.A- (Theory, modeling, and computer simulation)