Vibrational energy flow in the villin headpiece subdomain: Master equation simulations

被引：46

作者：

Leitner, David M. ^{[1
,2
,3
]}

Buchenberg, Sebastian ^{[4
]}

Brettel, Paul ^{[4
]}

Stock, Gerhard ^{[3
,4
]}

机构：

[1] Univ Nevada, Dept Chem, Reno, NV 89557 USA

[2] Univ Nevada, Chem Phys Program, Reno, NV 89557 USA

[3] Univ Freiburg, Freiburg Inst Adv Studies FRIAS, D-79106 Freiburg, Germany

[4] Univ Freiburg, Inst Phys, Biomol Dynam, D-79106 Freiburg, Germany

来源：

JOURNAL OF CHEMICAL PHYSICS | 2015年 / 142卷 / 07期

基金：

美国国家科学基金会;

关键词：

MOLECULAR-DYNAMICS SIMULATIONS; THERMAL-CONDUCTIVITY; TEMPERATURE-DEPENDENCE; IR SPECTROSCOPY; PROTEIN; RELAXATION; HEME; TRANSPORT; RESOLUTION; MECHANISM;

D O I：

10.1063/1.4907881

中图分类号：

O64 [物理化学（理论化学）、化学物理学];

学科分类号：

070304 ; 081704 ;

摘要：

We examine vibrational energy flow in dehydrated and hydrated villin headpiece subdomain HP36 by master equation simulations. Transition rates used in the simulations are obtained from communication maps calculated for HP36. In addition to energy flow along the main chain, we identify pathways for energy transport in HP36 via hydrogen bonding between residues quite far in sequence space. The results of the master equation simulations compare well with all-atom non-equilibrium simulations to about 1 ps following initial excitation of the protein, and quite well at long times, though for some residues we observe deviations between the master equation and all-atom simulations at intermediate times from about 1-10 ps. Those deviations are less noticeable for hydrated than dehydrated HP36 due to energy flow into the water. (C) 2015 AIP Publishing LLC.

引用

页数：9

共 50 条

[41] Bridging the Gap between Folding Simulations and Experiments: The Case of the Villin Headpiece
Saladino, G.
Marenchino, M.
Gervasio, F. L.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2011, 7 (09) : 2675 - 2680
[42] Analysis of core packing in a cooperatively folded minature protein: The ultrafast folding villin headpiece helical subdomain
Xiao, Shifeng
Bi, Yuan
Shan, Bing
Raleigh, Daniel P.
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2009, 238
[43] All-atom fast protein folding simulations: The villin headpiece
Shen, MY
Freed, KF
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2002, 49 (04) : 439 - 445
[44] Master equation simulations of the vibrational overtone activation of methylcyclopropene
J Chem Phys, 15 (5852):
[45] Master equation simulations of the vibrational overtone activation of methylcyclopropene
Ouporov, I
Grinevich, O
Snavely, DL
JOURNAL OF CHEMICAL PHYSICS, 1996, 104 (15): : 5852 - 5859
[46] Folding stability modulation of the villin headpiece helical subdomain by 4-fluorophenylalanine and 4-methylphenylalanine
Hsu, Wei-Lin
Shih, Ting-Chia
Horng, Jia-Cherng
BIOPOLYMERS, 2015, 103 (11) : 627 - 637
[47] Using an amino acid fluorescence resonance energy transfer pair to probe protein unfolding: Application to the villin headpiece subdomain and the LysM domain
Glasscock, Julie M.
Zhu, Yongjin
Chowdhury, Pramit
Tang, Jia
Gai, Feng
BIOCHEMISTRY, 2008, 47 (42) : 11070 - 11076
[48] Folding of the villin headpiece subdomain from random structures. analysis of the charge distribution as a function of pH
Ripoll, DR
Vila, JA
Scheraga, HA
JOURNAL OF MOLECULAR BIOLOGY, 2004, 339 (04) : 915 - 925
[49] Analysis of Core Packing in a Cooperatively Folded Miniature Protein: The Ultrafast Folding Villin Headpiece Helical Subdomain
Xiao, Shifeng
Bi, Yuan
Shan, Bing
Ralelgh, Daniel P.
BIOCHEMISTRY, 2009, 48 (21) : 4607 - 4616
[50] Probing the folding transition state structure of the villin headpiece subdomain via side chain and backbone mutagenesis
Bunagan, Michelle R.
Gao, Jianmin
Kelly, Jeffery W.
Gai, Feng
Journal of the American Chemical Society, 2009, 131 (21): : 7470 - 7476

← 1 2 3 4 5 →