Molecular dynamics simulations of a protein model in uniform and elongational flows.
We present a molecular dynamics study of the conformational deformation of a minimalist beta-barrel protein model in two different types of hydrodynamic flows: uniform and elongational. We investigate the characteristics of protein stretching, paying special attention to the unfolding intermediate states and their relationship to the protein folding/unfolding problem. In the uniform flow simulations, one end of the modeled protein was tethered to a fixed point in space and the forced unfolding process was observed. The unfolding takes place via a few stages involving one or two intermediate states, depending on which end is tethered. The calculated force-extension curves show plateau regimes and hysteresis as the protein is stretched and refolded, in qualitative agreement with the experimental measurements. The physical behavior observed in our numerical simulations of the forced unfolding in an elongational flow is very different from that in uniform flow. The protein unfolds abruptly from the globular state to a fully stretched state without going through any observable intermediate states. From these observation, we stress that protein unfolding pathways under the influence of an external force are highly dependent on the mechanism of the exerted force.
Lemak
Alexandre S
AS
Department of Physics, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1.
Lepock
James R
JR
Chen
Jeff Z Y
JZ
D003198:Computer Simulation; D008956:Models, Chemical; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
D011506:Proteins