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
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
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.
Received: 15 March 2005
Revised: 08 May 2005
Accepted manuscript online:
Fund: 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.
Cite this article:
Sheng Yue-Biao (盛乐标), Li Jing (李菁), Ma Bao-Liang (马保亮), Wang Wei (王炜) Functional structures and folding dynamics of two peptides 2005 Chinese Physics 14 2365
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