Hydrodynamic description of protein folding.
A hydrodynamic description of protein folding is proposed and illustrated with a lattice protein model, which has a free energy surface (FES) typical of proteins with two-state folding kinetics. The flows from the unfolded to the native state are concentrated in a limited region of the FES. The rest is occupied by a flow "vortex", which does not lead to the native state. In contrast with intermediates that are associated with local minima, the vortex is not visible on the FES. The hydrodynamic interpretation thus provides new insights into the mechanism of protein folding and can be a useful complement to standard analyses.
Chekmarev
Sergei F
SF
Institute of Thermophysics, SB RAS, 630090 Novosibirsk, Russia. chekmarev@itp.nsc.ru
Palyanov
Andrey Yu
AY
Karplus
Martin
M
D008956:Models, Chemical; D008958:Models, Molecular; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
D011506:Proteins