Understanding the origin of the fidelity of DNA polymerases is a problem of enormous practical and fundamental importance. Despite great experimental progress we still do not have a detailed molecular picture of the factors that control the fidelity. Here we propose to use computer simulation approaches to gain a deeper insight that will complement the experimental advances in the field. The following projects are proposed: (i) The relative stabilities of right (R) and wrong (W) primer-template base pairs will be investigated both in the protein (polymerase) and in aqueous solution. These studies will help to determine the contribution of the binding step to the overall fidelity. (ii) X-ray structures of various polymerase/ DNA complexes will be used as a starting point for calculations of the mechanisms and activation energies of the chemical step for incorporating right (R) and wrong (W) nucleotides. (iii) The binding free energy of the transition state for R and W will be calculated. These calculations will be directly related to the corresponding overall fidelity. (iv) The reaction pathway and activation barriers in different conformational states of the pol b will be explored. This study will examine how the accommodation of W and R substrates in the nucleotide binding site are transmitted to the catalytic site. (v) The structures and energies of different TS-analogues (TSAs) will be used to refine the theoretical model of the TS. This study will also search for optimal TS-analogs and eventually for effective drugs. (vi) Computer simulation approaches will be used to study the consequences of key modifications in the substrate and the catalytic metal ions. (vii) The contributions of different protein residues to the overall fidelity will be analyzed in different polymerases. All the proposed studies will involve constant feedback from the experimental counterparts of the project. We hope that this collaboration will help us to develop a more general and coherent view about the nature of DNA polymerase fidelity.
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