TY - JOUR

T1 - Hydrodynamic description of protein folding

T2 - the decrease of the probability fluxes as an indicator of transition states in two-state folders

AU - Palyanov, Andrey Yu

AU - Chekmarev, Sergei F.

N1 - Publisher Copyright: © 2016 Informa UK Limited, trading as Taylor & Francis Group.

PY - 2017/10/26

Y1 - 2017/10/26

N2 - Using hydrodynamic description of protein folding, the process of the first-passage folding of ubiquitin has been studied. Since a large number of folding trajectories were required to obtain converged folding flows, a coarse-grained representation of the protein in the form of a C-bead Gō-model was employed, and discrete molecular dynamics was used to perform simulations. It has been found that the free energy surface has a maximum width in the transition state region, so that the densities of folding flows (probability fluxes) decrease to minimum when the system passes through the transition state. There are indications that the increasing number of different protein conformations in the transition state region compared with those in the neighboring regions of semi-compact and native-like states is responsible for the present phenomena. It has also been shown that if the free energy is projected onto a single reaction coordinate, the low populations of the transition states can be compensated by the increasing number of states, which can lead to a considerable decrease or even disappearance of the free energy barrier in the transition state.

AB - Using hydrodynamic description of protein folding, the process of the first-passage folding of ubiquitin has been studied. Since a large number of folding trajectories were required to obtain converged folding flows, a coarse-grained representation of the protein in the form of a C-bead Gō-model was employed, and discrete molecular dynamics was used to perform simulations. It has been found that the free energy surface has a maximum width in the transition state region, so that the densities of folding flows (probability fluxes) decrease to minimum when the system passes through the transition state. There are indications that the increasing number of different protein conformations in the transition state region compared with those in the neighboring regions of semi-compact and native-like states is responsible for the present phenomena. It has also been shown that if the free energy is projected onto a single reaction coordinate, the low populations of the transition states can be compensated by the increasing number of states, which can lead to a considerable decrease or even disappearance of the free energy barrier in the transition state.

KW - molecular dynamics

KW - probability fluxes

KW - protein folding

KW - transition state

KW - UBIQUITIN

KW - RESOLUTION

KW - MODEL

KW - STRANGE KINETICS

KW - TEMPERATURE

KW - SPECTROSCOPY

KW - BETA-SHEET MINIPROTEIN

KW - MOLECULAR-DYNAMICS SIMULATIONS

KW - HYDROGEN-EXCHANGE

KW - PSI-ANALYSES

KW - Models, Molecular

KW - Hydrodynamics

KW - Molecular Dynamics Simulation

KW - Protein Folding

KW - Algorithms

KW - Proteins/chemistry

KW - Protein Conformation

KW - Kinetics

KW - Ubiquitin/chemistry

UR - http://www.scopus.com/inward/record.url?scp=84994344964&partnerID=8YFLogxK

U2 - 10.1080/07391102.2016.1248490

DO - 10.1080/07391102.2016.1248490

M3 - Article

C2 - 27819623

AN - SCOPUS:84994344964

VL - 35

SP - 3152

EP - 3160

JO - Journal of Biomolecular Structure and Dynamics

JF - Journal of Biomolecular Structure and Dynamics

SN - 0739-1102

IS - 14

ER -