TY - JOUR

T1 - Temperature evolution of Trp-cage folding pathways

T2 - An analysis by dividing the probability flux field into stream tubes

AU - Andryushchenko, Vladimir A.

AU - Chekmarev, Sergei F.

PY - 2017/12/1

Y1 - 2017/12/1

N2 - Owing to its small size and very fast folding rate, the Trp-cage miniprotein has become a benchmark system to study protein folding. Two folding pathways were found to be characteristic of this protein: pathway I, in which the hydrophobic collapse precedes the formation of α-helix, and pathway II, in which the events occur in the reverse order. At the same time, the relative contribution of these pathways at different temperatures as well as the nature of transition from one pathway to the other remain unclear. To gain insight into this issue, we employ a recently proposed hydrodynamic description of protein folding, in which the process of folding is considered as a motion of a “folding fluid” (Chekmarev et al., Phys. Rev. Lett. 100(1), 018107 2008). Using molecular dynamics simulations, we determine the field of probability fluxes of transitions in a space of collective variables and divide it into stream tubes. Each tube contains a definite fraction of the total folding flow and can be associated with a certain pathway. Specifically, three temperatures were considered, T = 285K, T = 315K, and T = 325K. We have found that as the temperature increases, the contribution of pathway I, which is approximately 90% of the total folding flow at T = 285K, decreases to approximately 10% at T = 325K, i.e., pathway II becomes dominant. At T = 315K, both pathways contribute approximately equally. All these temperatures are found below the calculated melting point, which suggests that the Trp-cage folding mechanism is determined by kinetic factors rather than thermodynamics.

AB - Owing to its small size and very fast folding rate, the Trp-cage miniprotein has become a benchmark system to study protein folding. Two folding pathways were found to be characteristic of this protein: pathway I, in which the hydrophobic collapse precedes the formation of α-helix, and pathway II, in which the events occur in the reverse order. At the same time, the relative contribution of these pathways at different temperatures as well as the nature of transition from one pathway to the other remain unclear. To gain insight into this issue, we employ a recently proposed hydrodynamic description of protein folding, in which the process of folding is considered as a motion of a “folding fluid” (Chekmarev et al., Phys. Rev. Lett. 100(1), 018107 2008). Using molecular dynamics simulations, we determine the field of probability fluxes of transitions in a space of collective variables and divide it into stream tubes. Each tube contains a definite fraction of the total folding flow and can be associated with a certain pathway. Specifically, three temperatures were considered, T = 285K, T = 315K, and T = 325K. We have found that as the temperature increases, the contribution of pathway I, which is approximately 90% of the total folding flow at T = 285K, decreases to approximately 10% at T = 325K, i.e., pathway II becomes dominant. At T = 315K, both pathways contribute approximately equally. All these temperatures are found below the calculated melting point, which suggests that the Trp-cage folding mechanism is determined by kinetic factors rather than thermodynamics.

KW - Folding pathways

KW - Hydrodynamic approach

KW - Kinetics

KW - Molecular dynamics

KW - Protein folding

KW - PROTEIN

KW - FREE-ENERGY LANDSCAPE

KW - HYDROPHOBIC COLLAPSE

KW - MODEL

KW - IMPLICIT SOLVENT

KW - UNFOLDED STATE

KW - BETA-SHEET MINIPROTEIN

KW - KINETICS

KW - FORCE-FIELD

KW - MOLECULAR-DYNAMICS SIMULATIONS

UR - http://www.scopus.com/inward/record.url?scp=85030663278&partnerID=8YFLogxK

U2 - 10.1007/s10867-017-9470-7

DO - 10.1007/s10867-017-9470-7

M3 - Article

C2 - 28983809

AN - SCOPUS:85030663278

VL - 43

SP - 565

EP - 583

JO - Journal of Biological Physics

JF - Journal of Biological Physics

SN - 0092-0606

IS - 4

ER -