Reaction center protein simulation

Molecular Modeling and Simulation of a Reaction Center Protein... 

Studies of ferredoxin [152] and a photosynthetic reaction center [151] have analyzed further the protein s dielectric response to electron transfer, and the protein s role in reducing the reorganization free energy so as to accelerate electron transfer [152], Different force fields were compared, including a polarizable and a non-polarizable force field [151]. One very recent study considered the effect of point mutations on the redox potential of the protein azurin [56]. Structural relaxation along the simulated reaction pathway was analyzed in detail. Similar to the Cyt c study above, several slow relaxation channels were found, which limited the ability to obtain very precise free energy estimates. Only semiquantitative values were... 

It is important to note, however, that synthetic bioinorganic model compoimds, which can compete with the reactivity of their natural cormterparts, are still extremely rare. This is probably due to the fact that despite huge efforts devoted to this topic, a real breakthrough in simulating the crucial role of the protein matrix which surroimds the native reaction centers has not yet been accomplished. 

Lin, J., Beratan, D.N. Simulation of electron transfer between cytochrome c2 and the bacterial photosynthetic reaction center Brownian dynamics analysis of the native proteins and double mutants. J. Phys. Chem. B 2005,109, 7529-34. 

Multi-Mode Coupling of Protein Motion to Electron Transfer in the Photosynthetic Reaction Center Spin— Boson Theory Based on a Classical Molecular Dynamics Simulation ... 

M. Nonella and K. Schulten. Molecular dynamics simulation of electron transfer in proteins — theory and application to Qa Qb transfer in the photosynthetic reaction center. J. Phys. Chem., 95 2059-2067, 1990. 

Mullet JE and Arntzen CJ (1980) Simulation of grana stacking in a model membrane - Mediation by a purified light-harvesting pigment protein complex from chloroplasts. Biochim Biophys Acta 589, 100-117 Nakatani HY (1983) Correlation of the low temperature 695 nm fluorescence emission with the reaction center of PS II (CP47). In Inoue Y, ed., Proc Inti Symp on Photosynthetic Water-oxidation and PS II Photochemistry, NY, Acad Press, in press... 

In special cases (as in colloidal solutions) some particles can be considered as essential and other particles as irrelevant , but in most cases the essential space will itself consist of collective degrees of freedom. A reaction coordinate for a chemical reaction is an example where not a particle, but some function of the distance between atoms is considered. In a simulation of the permeability of a lipid bilayer membrane for water [132] the reaction coordinate was taken as the distance, in the direction perpendicular to the bilayer, between the center of mass of a water molecule and the center of mass of the rest of the system. In proteins (see below) a few collective degrees of freedom involving all atoms of the molecule, describe almost all the... 

Docking simulations carried out with the aldol adducts bound into the active center of RAMA and RhuA suggested that in all cases the bulky N-protecting group cannot get into the catalytic site of the protein. That would explain the small effect of the N-protecting groups with different sizes and shapes on the stereochemical outcome of the reactions, since those groups would remain far from the reactive atoms. 

---