Structural and functional studies on DNA synthesis and repair proteins

Abstract

The work reported in this thesis includes structural and functional studies on thymidylate kinase and RecFOR pathway proteins from Thermus thermophilus HB8. In the first part, a study was performed on the thymidylate kinase from the thymidine tri-phosphate biosynthesis pathway. Thymidylate kinase is an important enzyme in DNA synthesis. It catalyzes the conversion of thymidine monophosphate (TMP) to thymidine diphosphate (TDP), with ATP as the preferred phosphoryl donor, in the presence of Mg2+. In this study, the dynamics of the active site and the communication paths between the substrates, ATP and TMP, are reported for thymidylate kinase from Thermus thermophilus. Conformational changes upon ligand binding and the path for communication between the substrates and the protein are important in understanding the catalytic mechanism of the enzyme. High-resolution X-ray crystal structures of thymidylate kinase in apo and ligand-bound states were solved. Structural analyses provide an insight into the mode of substrate binding at the active site. The residues involved in communication between the substrates were identified through network analysis using molecular dynamics simulations. The analyses of mutants suggest that the proper positioning of TMP is important for catalysis and provide an insight into the phosphoryl-transfer mechanism. The substrate binding, catalysis or the product release could be the rate-limiting step in the enzyme catalysis. Most of the studies on thymidylate kinase have either focused on understanding the mode of substrate binding or the mechanism of catalysis, but the product release event remains largely unexplored. This work reports four high-resolution crystal structures of thymidylate kinase from T. thermophilus in apo and product bound states. Random accelerated molecular dynamics (RAMD) simulations were performed to study the product release from the product bound high-resolution crystal structures of thymidylate kinase from T. thermophilus and human. The water molecules present around the Mg2+ ion contribute to the sequential release of the products. The presence of ADP-Mg2+ complex has a minor effect on the release of TDP. Thus, the release of the products from the active site could be random in order. The second part deals with the homologous recombination pathway, the RecFOR pathway. RecF, RecO and RecR proteins mediate the binding of RecA protein on the single strand binding (SSB) protein coated 3’ overhang of DNA. However, their interaction with each other and the DNA molecule is not clear. RecF exists as a monomer in solution but exhibits ATP dependent dimerization and DNA dependent ATP hydrolysis. The interaction assembly of RecF with RecR and DNA is not clear. RecR exists as a dimer in solution, although the crystallographic assembly suggests a tetramer. Thus, the dimeric assembly and the tetrameric assembly of RecF and RecR were stabilized by cysteine mutations at the interface residues and their interactions have been studied