Diffusive dynamics on multidimensional rough free energy surfaces.
The dynamics of processes relevant to chemistry and biophysics on rough free energy landscapes is investigated using a recently developed algorithm to solve the Smoluchowski equation. Two different processes are considered: ligand rebinding in MbCO and protein folding. For the rebinding dynamics of carbon monoxide (CO) to native myoglobin (Mb) from locations around the active site, the two-dimensional free energy surface (FES) is constructed using extensive molecular dynamics simulations. The surface describes the minima in the A state (bound MbCO), CO in the distal pocket and in the Xe4 pocket, and the transitions between these states and allows to study the diffusion of CO in detail. For the folding dynamics of protein G, a previously determined two-dimensional FES was available. To follow the diffusive dynamics on these rough free energy surfaces, the Smoluchowski equation is solved using the recently developed hierarchical discrete approximation method. From the relaxation of the initial nonequilibrium distribution, experimentally accessible quantities such as the rebinding time for CO or the folding time for protein G can be calculated. It is found that the free energy barrier for CO in the Xe4 pocket and in the distal pocket (B state) closer to the heme iron is approximately 6 kcal/mol which is considerably larger than the inner barrier which separates the bound state and the B state. For the folding of protein G, a barrier of approximately 10 kcal/mol between the unfolded and the folded state is consistent with folding times of the order of milliseconds.
Banushkina
Polina
P
Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland.
Meuwly
Markus
M
D002245:Carbon Dioxide / Q000737:chemistry*; D003198:Computer Simulation; D004735:Energy Transfer; D007700:Kinetics; D008956:Models, Chemical; D008958:Models, Molecular; D009211:Myoglobin / Q000737:chemistry*; D009419:Nerve Tissue Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D013499:Surface Properties
C029152:G-substrate; D009211:Myoglobin; D009419:Nerve Tissue Proteins; D002245:Carbon Dioxide