Computation of electron transfer properties for heme-containing oxidoreductases

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Atomistic computer simulations are proposed to advance aquantitative understanding of long-range electron transfer (ET) reactionsin electron transport proteins. This work is carried out to aid and complementexperimental work in this field. Existing computer simulation techniques areextended to compute key parameters that govern the rate of biologicalET reactions. These parameters are often unknown and usually ratherdifficult to measure. Using numerical methods we aim at providingquantitative estimates that can be used in electron tunneling simulations ofbiological electron carriers. Moreover, exploiting the microscopic information ofmolecular simulations, the contributions of single amino acid residues andthe surrounding solvent to the ET rate are analyzed and used to interpret effects ofprotein mutations that could guide the design of efficient biomimetics. In the short term the simulation methods are validated on simple and experimentally well characterized electron transport proteins (specific aim I). In the medium to long term redox and ET reactions in the more complex heme catalases are investigated (specific aim II). Research programme (specific aim I): Reliable experimental ET parameters areavailable for only very few biological ET reactions where donor and acceptor havea well defined structure. Among these systems are ruthenium modified cytochrome (cyt) proteins such as cyt c, myoglobin, cyt b5 and cyt b562. A wealth of structural, thermodynamic and kinetic data available for these proteins, which makes them possibly the best benchmark systems for assessment of the accuracy ofcomputer simulations. First objective is the computation of ET parametersfor ET from the heme group located inside the proteinto the ruthenium complex located at the surface of the protein. The simulationsof the proteins are carried out for models with increasing degree of complexity. Depending on the deviation with experimental data, new ideas for improvement of the simulation methodology are explored. The finite temperature motion of the different cytochromes are analyzed and used to investigate the influence of the different protein folds and heme groups on the ET parameters. Thereafter the focus of research will shift to the more complicated heme catalases described below.Research programme (specific aim II):Heme catalases prevent cells from oxidative damage by catalyzing the decomposition of hydrogen peroxide in oxygen and water. The catalytic activity is drasticallyreduced or even lost under certain conditions, if reaction intermediatecompound I undergoes one-electron reduction to compound II.Recent crystallographic and computational studies have given evidencethat the oxidized form of heme b containing catalase of H. pylori (HPC) formsthe catalytically less active compound II whereas the heme d containing catalase of P. vitale remains in theactive compound I form. Naturally, the question arises whether this difference is related to the different heme groups or to the different protein structure of the two catalases. Using the methods validated on simple cytochrome proteins (see above), we propose to calculate ET parameters for HPC and PVC and to determine the corresponding contributions of cofactor, protein and solvent.In the next step ionizable groups in the vicinity of the heme groups are identified and the ET parameters computed for ET from the ionizable group to the oxidized heme center. We hope that on the basis of these calculations one can explain the different tendencies of HPC and PVC to form the catalytically less active compound II.