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

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