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Folding and thermodynamic studies of Trp-cage based on polarized force field |
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| Authors: | Ye?Mei,Caiyi?Wei,Yew?Mun?Yip,Chun?Ying?Ho,John?Z.?H.?Zhang,Dawei?Zhang author-information" > author-information__contact u-icon-before" > mailto:zhangdw@ntu.edu.sg" title=" zhangdw@ntu.edu.sg" itemprop=" email" data-track=" click" data-track-action=" Email author" data-track-label=" " >Email author |
| Affiliation: | (1) State Key Laboratory of Precision Spectroscopy and Department of Physics, Institute of Theoretical and Computational Science, East China Normal University, Shanghai, China;(2) Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore;(3) Department of Chemistry, New York University, New York, NY 10003, USA; |
| Abstract: | 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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