title: Molecular Dynamics Simulation Studies of dTTP Binding and Catalysis Mediated by YhdE Dimerization.
abstract: YhdE is a Maf-like (multicopy associated filamentation) protein that primarily acts as dTTPase to hydrolyze dTTP into dTMP and two phosphate molecules in cell metabolism pathway. Two crystal structures of YhdE have been previously determined, representing the open and closed active site conformations, respectively. Based on the structures, we have carried out molecular dynamics simulations and free energy calculations to investigate dTTP binding to and hydrolysis by YhdE. Our results suggest that YhdE closed state is structurally more compact than its open state at room temperature. YhdE open state is a favorable conformation for dTTP binding and closed state is a structurally favorable conformation for catalytic reaction. This observation is supported by the structure of YhdE homolog in complex with a nucleotide analog. Free energy calculations reveal that YhdE dimerization occurs preferentially in dTTP binding and is favorable for successive cooperative reaction. The key residues R11, R12 and K80, are found to contribute to the substrate stabilization. Further, YhdE dimerization and binding of dTTP induce the cooperative effect through a direct allosteric communication network in YhdE from the dTTP binding sites in the catalytic center to the intermolecular β-strand in YhdE dimer.
authors.affiliation: College of Chemistry, Beijing Normal University, Beijing, China.
authors.forename: Nan
authors.initials: N
authors.lastname: Wang
authors.affiliation: College of Chemistry, Beijing Normal University, Beijing, China.
authors.forename: Jiahong
authors.initials: J
authors.lastname: Jiang
authors.affiliation: College of Chemistry, Beijing Normal University, Beijing, China.
authors.forename: Xichen
authors.initials: X
authors.lastname: Li
authors.affiliation: College of Chemistry, Beijing Normal University, Beijing, China.
authors.forename: Hongwei
authors.initials: H
authors.lastname: Tan
authors.affiliation: College of Chemistry, Beijing Normal University, Beijing, China.
authors.forename: Jimin
authors.initials: J
authors.lastname: Zheng
authors.affiliation: College of Chemistry, Beijing Normal University, Beijing, China.
authors.forename: Guangju
authors.initials: G
authors.lastname: Chen
authors.affiliation: Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada.
authors.forename: Zongchao
authors.initials: Z
authors.lastname: Jia
mesh_terms: D000494:Allosteric Regulation; D001665:Binding Sites; D002384:Catalysis; D018360:Crystallography, X-Ray; D004926:Escherichia coli / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000378:metabolism*; D005163:Factor Analysis, Statistical; D006860:Hydrogen Bonding; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D055503:Protein Multimerization; D017433:Protein Structure, Secondary; D011755:Pyrophosphatases / Q000737:chemistry / Q000378:metabolism*; D013816:Thermodynamics; D013942:Thymine Nucleotides / Q000737:chemistry / Q000378:metabolism*
chemical_list: D029968:Escherichia coli Proteins; D013942:Thymine Nucleotides; D011755:Pyrophosphatases; C000607522:YhdE protein, E coli; C024157:thymidine 5'-triphosphate