Loop motion and base release in purine-specific nucleoside hydrolase: A molecular dynamics study

Ogawa, 2001, Purification, characterization, and gene cloning of purine nucleosidase from Ochrobactrum anthropi, Appl. Environ. Microbiol., 67, 1783, 10.1128/AEM.67.4.1783-1787.2001 Cui, 2001, A nonspecific nucleoside hydrolase from Leishmania donovani: implications for purine salvage by the parasite, Gene, 280, 153, 10.1016/S0378-1119(01)00768-5 Kurtz, 2002, The URH1 uridine ribohydrolase of Saccharomyces cerevisiae, Curr. Genet., 41, 132, 10.1007/s00294-002-0296-9 Petersen, 2001, The RihA, RihB, and RihC ribonucleoside hydrolases of Escherichia coli. Substrate specificity, gene expression, and regulation, J. Biol. Chem., 276, 884, 10.1074/jbc.M008300200 Ribeiro, 2003, The salivary purine nucleosidase of the mosquito, Aedes aegypti, Insect Biochem. Mol. Biol., 33, 13, 10.1016/S0965-1748(02)00078-4 Versees, 2003, Cloning, preliminary characterization and crystallization of nucleoside hydrolases from Caenorhabditis elegans and Campylobacter jejuni, Acta Crystallogr. D: Biol. Crystallogr., 59, 1087, 10.1107/S0907444903007078 Pelle, 1998, Molecular cloning and expression of a purine-specific N-ribohydrolase from Trypanosoma brucei brucei. Sequence, expression, and molecular analysis, J. Biol. Chem., 273, 2118, 10.1074/jbc.273.4.2118 Versees, 2003, Catalysis by nucleoside hydrolases, Curr. Opin. Struct. Biol., 13, 731, 10.1016/j.sbi.2003.10.002 el Kouni, 2003, Potential chemotherapeutic targets in the purine metabolism of parasites, Pharmacol. Ther., 99, 283, 10.1016/S0163-7258(03)00071-8 Downie, 2008, Purine salvage pathways in the intraerythrocytic malaria parasite Plasmodium falciparum, Eukaryot. Cell, 7, 1231, 10.1128/EC.00159-08 Miles, 1999, Iminoribitol transition state analogue inhibitors of protozoan nucleoside hydrolases, Biochemistry, 38, 13147, 10.1021/bi990829u Ranquin, 2005, Therapeutic nanoreactors: combining chemistry and biology in a novel triblock copolymer drug delivery system, Nano Lett., 5, 2220, 10.1021/nl051523d Evans, 2008, Azetidine based transition state analogue inhibitors of N-ribosyl hydrolases and phosphorylases, J. Med. Chem., 51, 948, 10.1021/jm701265n Berg, 2009, Synthesis of bicyclic N-arylmethyl-substituted iminoribitol derivatives as selective nucleoside hydrolase inhibitors, ChemMedChem, 4, 249, 10.1002/cmdc.200800231 Goeminne, 2008, N-Arylmethyl substituted iminoribitol derivatives as inhibitors of a purine specific nucleoside hydrolase, Bioorg. Med. Chem., 16, 6752, 10.1016/j.bmc.2008.05.056 Vandemeulebroucke, 2010, Structure and mechanism of the 6-oxopurine nucleosidase from Trypanosoma brucei brucei, Biochemistry, 49, 8999, 10.1021/bi100697d Parkin, 1996, Purine-specific nucleoside N-ribohydrolase from Trypanosoma brucei brucei. Purification, specificity, and kinetic mechanism, J. Biol. Chem., 271, 21713, 10.1074/jbc.271.36.21713 Versees, 2001, Structure and function of a novel purine specific nucleoside hydrolase from Trypanosoma vivax, J. Mol. Biol., 307, 1363, 10.1006/jmbi.2001.4548 Versees, 2002, Enzyme-substrate interactions in the purine-specific nucleoside hydrolase from Trypanosoma vivax, J. Biol. Chem., 277, 15938, 10.1074/jbc.M111735200 Versees, 2004, Leaving group activation by aromatic stacking: an alternative to general acid catalysis, J. Mol. Biol., 338, 1, 10.1016/j.jmb.2004.02.049 Versees, 2006, Transition-state complex of the purine-specific nucleoside hydrolase of T. vivax: enzyme conformational changes and implications for catalysis, J. Mol. Biol., 359, 331, 10.1016/j.jmb.2006.03.026 Vandemeulebroucke, 2008, A flexible loop as a functional element in the catalytic mechanism of nucleoside hydrolase from Trypanosoma vivax, J. Biol. Chem., 283, 22272, 10.1074/jbc.M803705200 Versees, 2009, Crystal structures of T. vivax nucleoside hydrolase in complex with new potent and specific inhibitors, Biochim. Biophys. Acta, 1794, 953, 10.1016/j.bbapap.2009.02.011 Vandemeulebroucke, 2006, Multiple transients in the pre-steady-state of nucleoside hydrolase reveal complex substrate binding, product base release, and two apparent rates of chemistry, Biochemistry, 45, 9307, 10.1021/bi060666r Vandemeulebroucke, 2003, Pre-steady-state analysis of the nucleoside hydrolase of Trypanosoma vivax. Evidence for half-of-the-sites reactivity and rate-limiting product release, Biochemistry, 42, 12902, 10.1021/bi0347914 Berti, 2006, Toward a detailed understanding of base excision repair enzymes: transition state and mechanistic analyses of N-glycoside hydrolysis and N-glycoside transfer, Chem. Rev., 106, 506, 10.1021/cr040461t Barlow, 2007, Examination of the mechanism and energetic contribution of leaving group activation in the purine-specific nucleoside hydrolase from Trypanosoma vivax, Biochim. Biophys. Acta, 1774, 1451, 10.1016/j.bbapap.2007.08.027 Wu, 2012, QM/MM molecular dynamics study of purine-specific nucleoside hydrolase, J. Phys. Chem. B, 116, 1984, 10.1021/jp211403j Durrant, 2011, Molecular dynamics simulations and drug discovery, BMC Biol., 9, 71, 10.1186/1741-7007-9-71 Duan, 2003, A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations, J. Comput. Chem., 24, 1999, 10.1002/jcc.10349 Wang, 2004, Development and testing of a general amber force field, J. Comput. Chem., 25, 1157, 10.1002/jcc.20035 Bayly, 1993, A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model, J. Phys. Chem., 97, 10269, 10.1021/j100142a004 Frisch, 2009 Jorgensen, 1983, Comparison of simple potential functions for simulating liquid water, J. Chem. Phys., 79, 926, 10.1063/1.445869 Case, 2005, The Amber biomolecular simulation programs, J. Comput. Chem., 26, 1668, 10.1002/jcc.20290 Berendsen, 1984, Molecular dynamics with coupling to an external bath, J. Chem. Phys., 81, 3684, 10.1063/1.448118 Ryckaert, 1977, Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes, J. Comput. Phys., 23, 327, 10.1016/0021-9991(77)90098-5 Torrie, 1977, Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling, J. Comput. Phys., 23, 187, 10.1016/0021-9991(77)90121-8 Vijayaraj, 2012, Molecular dynamics and umbrella sampling study of stabilizing factors in cyclic peptide-based nanotubes, J. Phys. Chem. B, 116, 9922, 10.1021/jp303418a A. Grossfield, WHAM: an implementation of the weighted histogram analysis method, http://membrane.urmc.rochester.edu/content/wham/, version XXXX. Kale, 1999, NAMD2: Great scalability for parallel molecular dynamics, J. Comput. Phys., 151, 283, 10.1006/jcph.1999.6201