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

Ye Mei; Caiyi Wei; Yew Mun Yip; Chun Ying Ho; John Z.H. Zhang; Dawei Zhang

doi:10.1007/s00214-012-1168-0

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

Ye Mei, Caiyi Wei, Yew Mun Yip, Chun Ying Ho, John Z.H. Zhang, Dawei Zhang

Chemistry

Research output: Contribution to journal › Letter › peer-review

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.

Original language	English (US)
Article number	1168
Pages (from-to)	1-7
Number of pages	7
Journal	Theoretical Chemistry Accounts
Volume	131
Issue number	3
DOIs	https://doi.org/10.1007/s00214-012-1168-0
State	Published - Mar 2012

Keywords

Charge update
MFCC
PPC
Trp-cage

ASJC Scopus subject areas

Physical and Theoretical Chemistry

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10.1007/s00214-012-1168-0

Cite this

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title = "Folding and thermodynamic studies of Trp-cage based on polarized force field",

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 Tm of ≈325 K was found to be in close agreement with experimental melting temperature, Tm 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.",

keywords = "Charge update, MFCC, PPC, Trp-cage",

author = "Ye Mei and Caiyi Wei and Yip, {Yew Mun} and Ho, {Chun Ying} and Zhang, {John Z.H.} and Dawei Zhang",

year = "2012",

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doi = "10.1007/s00214-012-1168-0",

language = "English (US)",

volume = "131",

pages = "1--7",

journal = "Theoretical Chemistry Accounts",

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publisher = "Springer New York",

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TY - JOUR

T1 - Folding and thermodynamic studies of Trp-cage based on polarized force field

AU - Mei, Ye

AU - Wei, Caiyi

AU - Yip, Yew Mun

AU - Ho, Chun Ying

AU - Zhang, John Z.H.

AU - Zhang, Dawei

PY - 2012/3

Y1 - 2012/3

N2 - 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 Tm of ≈325 K was found to be in close agreement with experimental melting temperature, Tm 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.

AB - 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 Tm of ≈325 K was found to be in close agreement with experimental melting temperature, Tm 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.

KW - Charge update

KW - MFCC

KW - PPC

KW - Trp-cage

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SP - 1

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JO - Theoretical Chemistry Accounts

JF - Theoretical Chemistry Accounts

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M1 - 1168

ER -

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

Abstract

Keywords

ASJC Scopus subject areas

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