Physics & Astronomy
Computational Chemical Physics
P. Wang, R. B. Best, J. Blumberger, "Multiscale simulation
reveals multiple pathways for H2 and O2 transport in a
[NiFe]-hydrogenase", J. Am. Chem. Soc., ASAP article (2011). (Click for the full text article.)
Hydrogenases are enzymes that catalyze the reversible conversion of hydrogen molecules to protons and electrons. The mechanism by which the gas molecules reach the active site is important for understanding the function of the enzyme, and may play a role in the selectivity for hydrogen over inhibitor molecules. Here we develop a general multiscale molecular simulation approach for the calculation of diffusion rates and determination of pathways by which substrate or inhibitor gases can reach the protein active site.
Combining kinetic data from both equilibrium simulations and enhanced sampling, we construct a master equation describing the movement of gas molecules within the enzyme. We find that the time-dependent gas population of the active site can be fit to the same phenomenological rate law used to interpret experiments, with corresponding diffusion rates in very good agreement with experimental data. However, in contrast to the conventional picture, in which the gases follow a well-defined hydrophobic tunnel, we find that there is a diverse network of accessible pathways by which the gas molecules can reach the active site. The previously identified tunnel accounts for only about 60% of the total flux.
Our results suggest that the dramatic decrease in the diffusion rate for mutations involving the residue Val74 could be in part due to the narrowing of the passage Val74-Arg476, immediately adjacent to the binding site, explaining why mutations of Leu122 had only a negligible effect in experiment. Our method is not specific to the [NiFe]-hydrogenase, and should be generally applicable to the transport of small molecules in proteins.
V.Tipmanee, H. Oberhofer, M. Park, K. S. Kim, J. Blumberger, "Prediction of reorganization free energies for biological electron transfer: a comparative study of Ru-modified cytochromes and a 4-helix bundle protein", J. Am. Chem. Soc. 132, 17032 (2010). (Click for the full text article.)
The acceleration of electron transfer (ET) rates in redox proteins relative to aqueous solutes can be attributed to the protein's ability to reduce the nuclear response or reorganization upon ET, while maintaining sufficiently high electronic coupling.
Quantitative predictions of reorganization free energy remain a challenge, both experimentally and computationally. Using density functional calculations and molecular dynamics simulation with an electronically polarizable force field, we report reorganization free energies for intraprotein ET in four heme containing ET proteins that differ in their protein fold, hydrophilicity and solvent accessibility of the electron accepting group. The reorganization free energies for ET from the heme cofactors of cytochrome c and b5 to solvent exposed Ru-complexes docked to histidine residues at the surface of these proteins, fall within a narrow range of 1.2-1.3 eV. Reorganization free energy is significantly lowered in a designed 4-helix bundle protein where both redox active cofactors are protected from the solvent.
For all ET reactions investigated the major components of reorganization are the solvent and the protein, with the solvent contributing close to or more than 50% of the total. In three out of four proteins the protein reorganization free energy can be viewed as a collective effect including many residues, each of which contributing a small fraction.
These results have important implications for the design of artificial electron transport proteins. They suggest that reorganization free energy may in general not be effectively controlled by single point mutations, but to a large extent by the degree of solvent exposure of the ionizable cofactors.