Occupying a flat subpocket in a tRNA-modifying enzyme with ordered or disordered side chains: Favorable or unfavorable for binding?

[1]  Luzi J. Barandun,et al.  Beyond affinity: enthalpy-entropy factorization unravels complexity of a flat structure-activity relationship for inhibition of a tRNA-modifying enzyme. , 2014, Journal of medicinal chemistry.

[2]  Gerhard Klebe,et al.  Chasing protons: how isothermal titration calorimetry, mutagenesis, and pKa calculations trace the locus of charge in ligand binding to a tRNA-binding enzyme. , 2014, Journal of medicinal chemistry.

[3]  Gerhard Klebe,et al.  Methyl, Ethyl, Propyl, Butyl: Futile But Not for Water, as the Correlation of Structure and Thermodynamic Signature Shows in a Congeneric Series of Thermolysin Inhibitors , 2014, ChemMedChem.

[4]  Luzi J. Barandun,et al.  High-affinity inhibitors of Zymomonas mobilis tRNA-guanine transglycosylase through convergent optimization. , 2013, Acta crystallographica. Section D, Biological crystallography.

[5]  Gerhard Klebe,et al.  Dissecting the hydrophobic effect on the molecular level: the role of water, enthalpy, and entropy in ligand binding to thermolysin. , 2013, Angewandte Chemie.

[6]  Luzi J. Barandun,et al.  From lin-benzoguanines to lin-benzohypoxanthines as ligands for Zymomonas mobilis tRNA-guanine transglycosylase: replacement of protein-ligand hydrogen bonding by importing water clusters. , 2012, Chemistry.

[7]  Yongyue Wei,et al.  Comparison of the prevalence and changing resistance to nalidixic acid and ciprofloxacin of Shigella between Europe-America and Asia-Africa from 1998 to 2009. , 2012, International journal of antimicrobial agents.

[8]  Nathaniel Echols,et al.  Accessing protein conformational ensembles using room-temperature X-ray crystallography , 2011, Proceedings of the National Academy of Sciences.

[9]  Gerhard Klebe,et al.  Fconv: Format Conversion, Manipulation and Feature Computation of Molecular Data , 2011, Bioinform..

[10]  Randy J. Read,et al.  Overview of the CCP4 suite and current developments , 2011, Acta crystallographica. Section D, Biological crystallography.

[11]  G. Klebe,et al.  Congeneric but still distinct: how closely related trypsin ligands exhibit different thermodynamic and structural properties. , 2011, Journal of molecular biology.

[12]  Elspeth F. Garman,et al.  Radiation damage in macromolecular crystallography: what is it and why should we care? , 2010, Acta crystallographica. Section D, Biological crystallography.

[13]  G. Robertson,et al.  Synthesis and characterization of a novel iNOS/Akt inhibitor Se,Se'-1,4-phenylenebis(1,2-ethanediyl)bisisoselenourea (PBISe)--against colon cancer. , 2010, Bioorganic & medicinal chemistry letters.

[14]  Randy J. Read,et al.  Acta Crystallographica Section D Biological , 2003 .

[15]  Gerhard Klebe,et al.  How to Replace the Residual Solvation Shell of Polar Active Site Residues to Achieve Nanomolar Inhibition of tRNA‐Guanine Transglycosylase , 2009, ChemMedChem.

[16]  G. Klebe,et al.  High-affinity inhibitors of tRNA-guanine transglycosylase replacing the function of a structural water cluster. , 2009, Chemistry.

[17]  Gerhard Klebe,et al.  Crystal Structure Analysis and in Silico pKa Calculations Suggest Strong pKa Shifts of Ligands as Driving Force for High‐Affinity Binding to TGT , 2009, Chembiochem : a European journal of chemical biology.

[18]  G. Klebe,et al.  Hochaffine Inhibitoren der tRNA‐Guanin‐Transglycosylase, eines Schlüsselenzyms in der Pathogenese der Shigellen‐Ruhr: ladungsverstärkte Wasserstoffbrücken , 2007 .

[19]  G. Klebe,et al.  Potent inhibitors of tRNA-guanine transglycosylase, an enzyme linked to the pathogenicity of the Shigella bacterium: charge-assisted hydrogen bonding. , 2007, Angewandte Chemie.

[20]  G. Klebe,et al.  Crystal structures of tRNA-guanine transglycosylase (TGT) in complex with novel and potent inhibitors unravel pronounced induced-fit adaptations and suggest dimer formation upon substrate binding. , 2007, Journal of molecular biology.

[21]  M. Levine,et al.  Clinical trials of Shigella vaccines: two steps forward and one step back on a long, hard road , 2007, Nature Reviews Microbiology.

[22]  Airlie J. McCoy,et al.  Solving structures of protein complexes by molecular replacement with Phaser , 2006, Acta crystallographica. Section D, Biological crystallography.

[23]  R. Thorne,et al.  Hyperquenching for protein cryocrystallography. , 2006, Journal of applied crystallography.

[24]  V. Hornak,et al.  Comparison of multiple Amber force fields and development of improved protein backbone parameters , 2006, Proteins.

[25]  G. Klebe,et al.  Expect the unexpected or caveat for drug designers: multiple structure determinations using aldose reductase crystals treated under varying soaking and co-crystallisation conditions. , 2006, Journal of molecular biology.

[26]  Holger Gohlke,et al.  The Amber biomolecular simulation programs , 2005, J. Comput. Chem..

[27]  G. Klebe,et al.  Mechanism and Substrate Specificity of tRNA–Guanine Transglycosylases (TGTs): tRNA‐Modifying Enzymes from the Three Different Kingdoms of Life Share a Common Catalytic Mechanism , 2005, Chembiochem : a European journal of chemical biology.

[28]  Kevin Cowtan,et al.  research papers Acta Crystallographica Section D Biological , 2005 .

[29]  Junmei Wang,et al.  Development and testing of a general amber force field , 2004, J. Comput. Chem..

[30]  J. Tellinghuisen,et al.  The role of backlash in the "first injection anomaly" in isothermal titration calorimetry. , 2004, Analytical biochemistry.

[31]  W. Xie,et al.  Chemical trapping and crystal structure of a catalytic tRNA guanine transglycosylase covalent intermediate , 2003, Nature Structural Biology.

[32]  Christopher I. Bayly,et al.  Fast, efficient generation of high‐quality atomic charges. AM1‐BCC model: II. Parameterization and validation , 2002, J. Comput. Chem..

[33]  T. Hahn International tables for crystallography , 2002 .

[34]  Y. Pang Successful molecular dynamics simulation of two zinc complexes bridged by a hydroxide in phosphotriesterase using the cationic dummy atom method , 2001, Proteins.

[35]  G Klebe,et al.  A new target for shigellosis: rational design and crystallographic studies of inhibitors of tRNA-guanine transglycosylase. , 2000, Journal of molecular biology.

[36]  Araz Jakalian,et al.  Fast, efficient generation of high‐quality atomic charges. AM1‐BCC model: I. Method , 2000 .

[37]  G. V. Paolini,et al.  Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes , 1997, J. Comput. Aided Mol. Des..

[38]  P Willett,et al.  Development and validation of a genetic algorithm for flexible docking. , 1997, Journal of molecular biology.

[39]  Z. Otwinowski,et al.  [20] Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[40]  D. Suck,et al.  Purification, crystallization, and preliminary X‐ray diffraction studies of tRNA‐guanine transglycosylase from Zymomonas mobilis , 1996, Proteins.

[41]  K. Reuter,et al.  Sequence analysis and overexpression of the Zymomonas mobilis tgt gene encoding tRNA-guanine transglycosylase: purification and biochemical characterization of the enzyme , 1995, Journal of bacteriology.

[42]  M. Watarai,et al.  vacC, a virulence-associated chromosomal locus of Shigella flexneri, is homologous to tgt, a gene encoding tRNA-guanine transglycosylase (Tgt) of Escherichia coli K-12 , 1994, Journal of bacteriology.

[43]  T. Darden,et al.  Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .

[44]  J. Thornton,et al.  PROCHECK: a program to check the stereochemical quality of protein structures , 1993 .

[45]  M. L. Connolly Analytical molecular surface calculation , 1983 .

[46]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[47]  G. Ciccotti,et al.  Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .

[48]  M. Dixon The determination of enzyme inhibitor constants. , 1953, The Biochemical journal.