Theoretical characterization of the shikimate 5-dehydrogenase reaction from Mycobacterium tuberculosis by hybrid QC/MM simulations and quantum chemical descriptors

[1]  Gerd Bruno Rocha,et al.  Semiempirical methods do Fukui functions: Unlocking a modeling framework for biosystems , 2020, J. Comput. Chem..

[2]  Gerd Bruno Rocha,et al.  Elucidating Enzymatic Catalysis Using Fast Quantum Chemical Descriptors , 2020, J. Chem. Inf. Model..

[3]  D. Goodwin,et al.  A multifaceted approach to identify non-specific enzyme inhibition: Application to Mycobacterium tuberculosis shikimate kinase. , 2017, Bioorganic & medicinal chemistry letters.

[4]  Jianzhuang Yao,et al.  Understanding the Catalytic Mechanism and the Nature of the Transition State of an Attractive Drug-Target Enzyme (Shikimate Kinase) by Quantum Mechanical/Molecular Mechanical (QM/MM) Studies. , 2017, Chemistry.

[5]  Osmar Norberto de Souza,et al.  EPSP synthase flexibility is determinant to its function: computational molecular dynamics and metadynamics studies , 2017, Journal of Molecular Modeling.

[6]  Amit Nargotra,et al.  Benzothiazole Derivative as a Novel Mycobacterium tuberculosis Shikimate Kinase Inhibitor: Identification and Elucidation of Its Allosteric Mode of Inhibition , 2016, J. Chem. Inf. Model..

[7]  P. Yogeeswari,et al.  Structure-based virtual screening as a tool for the identification of novel inhibitors against Mycobacterium tuberculosis 3-dehydroquinate dehydratase. , 2015, Journal of molecular graphics & modelling.

[8]  Martin J. Field,et al.  GTKDynamo: A PyMOL plug‐in for QC/MM hybrid potential simulations , 2013, J. Comput. Chem..

[9]  M. Field,et al.  A hybrid elastic band string algorithm for studies of enzymatic reactions. , 2012, Physical Chemistry, Chemical Physics - PCCP.

[10]  Marcus D. Hanwell,et al.  Avogadro: an advanced semantic chemical editor, visualization, and analysis platform , 2012, Journal of Cheminformatics.

[11]  Wim F Vranken,et al.  ACPYPE - AnteChamber PYthon Parser interfacE , 2012, BMC Research Notes.

[12]  D. Christendat,et al.  Structural and mechanistic analysis of a novel class of shikimate dehydrogenases: evidence for a conserved catalytic mechanism in the shikimate dehydrogenase family. , 2011, Biochemistry.

[13]  Jan H. Jensen,et al.  PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa Predictions. , 2011, Journal of chemical theory and computation.

[14]  James J. P. Stewart,et al.  Application of the PM6 method to modeling proteins , 2009, Journal of molecular modeling.

[15]  M. W. van der Kamp,et al.  Computational enzymology: insight into biological catalysts from modelling. , 2008, Natural product reports.

[16]  Martin J Field,et al.  The pDynamo Program for Molecular Simulations using Hybrid Quantum Chemical and Molecular Mechanical Potentials. , 2008, Journal of chemical theory and computation.

[17]  K Fukushima,et al.  An insight into the general relationship between the three dimensional structures of enzymes and their electronic wave functions: Implication for the prediction of functional sites of enzymes , 2008, Proteins.

[18]  Yue Li,et al.  Structural and biochemical analyses of shikimate dehydrogenase AroE from Aquifex aeolicus: implications for the catalytic mechanism. , 2007, Biochemistry.

[19]  Martin J. Field,et al.  A Practical Introduction to the Simulation of Molecular Systems: Subject index , 2007 .

[20]  D. York,et al.  Specific Reaction Parametrization of the AM1/d Hamiltonian for Phosphoryl Transfer Reactions:  H, O, and P Atoms. , 2007, Journal of chemical theory and computation.

[21]  O. N. de Souza,et al.  Kinetic and chemical mechanisms of shikimate dehydrogenase from Mycobacterium tuberculosis. , 2007, Archives of biochemistry and biophysics.

[22]  M. Parrinello,et al.  Canonical sampling through velocity rescaling. , 2007, The Journal of chemical physics.

[23]  Alfredo Mayall Simas,et al.  RM1: A reparameterization of AM1 for H, C, N, O, P, S, F, Cl, Br, and I , 2006, J. Comput. Chem..

[24]  Gerrit Groenhof,et al.  GROMACS: Fast, flexible, and free , 2005, J. Comput. Chem..

[25]  Darrin M York,et al.  Insights into the regioselectivity and RNA-binding affinity of HIV-1 nucleocapsid protein from linear-scaling quantum methods. , 2003, Journal of molecular biology.

[26]  F. von Delft,et al.  The Crystal Structure of Shikimate Dehydrogenase (AroE) Reveals a Unique NADPH Binding Mode , 2003, Journal of bacteriology.

[27]  P. Geerlings,et al.  Conceptual density functional theory. , 2003, Chemical reviews.

[28]  Tanya Parish,et al.  The common aromatic amino acid biosynthesis pathway is essential in Mycobacterium tuberculosis. , 2002, Microbiology.

[29]  R. Wolfenden,et al.  The depth of chemical time and the power of enzymes as catalysts. , 2001, Accounts of chemical research.

[30]  W. Kabsch,et al.  Interaction of the herbicide glyphosate with its target enzyme 5-enolpyruvylshikimate 3-phosphate synthase in atomic detail. , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[31]  U. Ryde,et al.  Redesign of the coenzyme specificity in L-lactate dehydrogenase from bacillus stearothermophilus using site-directed mutagenesis and media engineering. , 1999, Protein engineering.

[32]  K. Herrmann,et al.  THE SHIKIMATE PATHWAY. , 1999, Annual review of plant physiology and plant molecular biology.

[33]  Berk Hess,et al.  LINCS: A linear constraint solver for molecular simulations , 1997, J. Comput. Chem..

[34]  A. Becke.  Density-functional thermochemistry. III. The role of exact exchange , 1993 .

[35]  J. Stewart.  Optimization of parameters for semiempirical methods. III Extension of PM3 to Be, Mg, Zn, Ga, Ge, As, Se, Cd, In, Sn, Sb, Te, Hg, Tl, Pb, and Bi , 1991 .

[36]  R. Pearson.  Recent advances in the concept of hard and soft acids and bases , 1987 .

[37]  Eamonn F. Healy,et al.  Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model , 1985 .

[38]  H. Berendsen,et al.  Molecular dynamics with coupling to an external bath , 1984 .

[39]  Robert G. Parr,et al.  Density functional approach to the frontier-electron theory of chemical reactivity , 1984 .

[40]  N. Amrhein,et al.  The herbicide glyphosate is a potent inhibitor of 5-enolpyruvyl-shikimic acid-3-phosphate synthase. , 1980, Biochemical and biophysical research communications.

[41]  R. Parr,et al.  Electronegativity: The density functional viewpoint , 1978 .

[42]  Frank Neese,et al.  The ORCA program system , 2012 .