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.
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 alpha-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.
Chen
Yantao
Y
Key Laboratory of Molecular Engineering of Polymers of Ministry of Education, Department of Macromolecular Science, Laboratory of Advanced Materials, Fudan University, Shanghai 200433, China.
Ding
Jiandong
J
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D006860:Hydrogen Bonding; D008958:Models, Molecular; D009010:Monte Carlo Method; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D013816:Thermodynamics
D011506:Proteins