Temperature evolution of Trp-cage folding pathways: An analysis by dividing the probability flux field into stream tubes

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Abstract

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.

Original languageEnglish
Pages (from-to)565-583
Number of pages19
JournalJournal of Biological Physics
Volume43
Issue number4
DOIs
Publication statusPublished - 1 Dec 2017

Keywords

  • Folding pathways
  • Hydrodynamic approach
  • Kinetics
  • Molecular dynamics
  • Protein folding
  • PROTEIN
  • FREE-ENERGY LANDSCAPE
  • HYDROPHOBIC COLLAPSE
  • MODEL
  • IMPLICIT SOLVENT
  • UNFOLDED STATE
  • BETA-SHEET MINIPROTEIN
  • KINETICS
  • FORCE-FIELD
  • MOLECULAR-DYNAMICS SIMULATIONS

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