Roles of non‐native hydrogen‐bonding interaction in helix‐coil transition of a single polypeptide as revealed by comparison between Gō‐like and non‐Gō models |
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Authors: | Yantao Chen Jiandong Ding |
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Affiliation: | 1. Key Laboratory of Molecular Engineering of Polymers of Ministry of Education, Department of Macromolecular Science, Laboratory of Advanced Materials, Fudan University, Shanghai 200433, China;2. Shenzhen Key Laboratory of Functional Polymer, College of Chemistry and Chemical Engineering, Shenzhen University, Shenzhen 518060, China |
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Abstract: | To explore the role of non‐native interactions in the helix‐coil transition, a detailed comparison between a Gō‐like model and a non‐Gō model has been performed via lattice Monte Carlo simulations. Only native hydrogen bonding interactions occur in the Gō‐like model, and the non‐native ones with sequence interval more than 4 is also included into the non‐Gō model. Some significant differences between the results from those two models have been found. The non‐native hydrogen bonds were found most populated at temperature around the helix‐coil transition. The rearrangement of non‐native hydrogen bonds into native ones in the formation of α‐helix leads to the increase of susceptibility of chain conformation, and even two peaks of susceptibility of radius of gyration versus temperature exist in the case of non‐Gō model for a non‐short peptide, while just a single peak exists in the case of Gō model for a single polypeptide chain with various chain lengths. The non‐native hydrogen bonds have complicated the temperature‐dependence of Zimm‐Bragg nucleation constant. The increase of relative probability of non‐native hydrogen bonding for long polypeptide chains leads to non‐monotonous chain length effect on the transition temperature. Proteins 2010. © 2010 Wiley‐Liss, Inc. |
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Keywords: | helix‐coil transition Gō model non‐native interaction protein folding lattice Monte Carlo simulation |
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