Folding and thermodynamic studies of Trp-cage based on polarized force field

Theoretical Chemistry Accounts - 2012
Ye Mei1, Caiyi Wei2, Yew Mun Yip2, Chun Ying Ho2, John Z. H. Zhang1,3, Dawei Zhang2
1State Key Laboratory of Precision Spectroscopy and Department of Physics, Institute of Theoretical and Computational Science, East China Normal University, Shanghai, China
2Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
3Department of Chemistry, New York University, New York, USA

Tóm tắt

Two replica exchange molecular dynamics (REMD) simulations were carried out to study the thermodynamics of a 20-residue Trp-cage folding based on a newly developed polarized protein-specific charge (PPC). Starting from a fully extended conformation, Trp-cage native conformation was successfully sampled using REMD based on a 3-step PPC update. Next, the obtained Trp-cage folded conformation was then used to calculate the PPC in which another REMD was performed to explore the thermodynamic stability of Trp-cage. The theoretical melting temperature T m of ≈325 K was found to be in close agreement with experimental melting temperature, T m of 315 K. This indicates that the PPC was correctly predicting the temperature dependence. The current study provides a direct proof of how electrostatic polarization affects protein folding.

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