Chasing protons: how isothermal titration calorimetry, mutagenesis, and pKa calculations trace the locus of charge in ligand binding to a tRNA-binding enzyme.
暂无分享,去创建一个
Gerhard Klebe | François Diederich | Paul Czodrowski | Luzi J. Barandun | G. Klebe | F. Diederich | A. Heine | Paul Czodrowski | Andreas Heine | Manuel Neeb | Luzi Jakob Barandun | Christoph Hohn | C. Hohn | M. Neeb | P. Czodrowski
[1] Bernard Testa,et al. Lipophilicity in Molecular Modeling , 1996, Pharmaceutical Research.
[2] 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.
[3] K. P. Murphy,et al. Evaluation of linked protonation effects in protein binding reactions using isothermal titration calorimetry. , 1996, Biophysical journal.
[4] G Klebe,et al. Impact of ligand and protein desolvation on ligand binding to the S1 pocket of thrombin. , 2012, Journal of molecular biology.
[5] U. K. Laemmli,et al. Cleavage of Structural Proteins during the Assembly of the Head of Bacteriophage T4 , 1970, Nature.
[6] Randy J. Read,et al. Acta Crystallographica Section D Biological , 2003 .
[7] Philippe Dumas,et al. kinITC: a new method for obtaining joint thermodynamic and kinetic data by isothermal titration calorimetry. , 2012, Journal of the American Chemical Society.
[8] Gerhard Klebe,et al. Tracing changes in protonation: a prerequisite to factorize thermodynamic data of inhibitor binding to aldose reductase. , 2007, Journal of molecular biology.
[9] Z. Otwinowski,et al. Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.
[10] H. Heerklotz,et al. Uptake and release protocol for assessing membrane binding and permeation by way of isothermal titration calorimetry , 2007, Nature Protocols.
[11] A. Velázquez‐Campoy,et al. Isothermal titration calorimetry to determine association constants for high-affinity ligands , 2006, Nature Protocols.
[12] H. Hall,et al. Correlation of the Base Strengths of Amines1 , 1957 .
[13] 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.
[14] D. Suck,et al. Purification, crystallization, and preliminary X‐ray diffraction studies of tRNA‐guanine transglycosylase from Zymomonas mobilis , 1996, Proteins.
[15] G. Klebe,et al. High-affinity inhibitors of tRNA-guanine transglycosylase replacing the function of a structural water cluster. , 2009, Chemistry.
[16] Gerhard Klebe,et al. Development, validation, and application of adapted PEOE charges to estimate pKa values of functional groups in protein–ligand complexes , 2006, Proteins.
[17] Gerhard Klebe,et al. Protonation changes upon ligand binding to trypsin and thrombin: structural interpretation based on pK(a) calculations and ITC experiments. , 2007, Journal of molecular biology.
[18] C. Sasakawa,et al. The modified nucleoside 2-methylthio-N6-isopentenyladenosine in tRNA of Shigella flexneri is required for expression of virulence genes , 1997, Journal of bacteriology.
[19] T. J. Murray,et al. New triply hydrogen bonded complexes with highly variable stabilities , 1992 .
[20] Jay Painter,et al. Electronic Reprint Biological Crystallography Optimal Description of a Protein Structure in Terms of Multiple Groups Undergoing Tls Motion Biological Crystallography Optimal Description of a Protein Structure in Terms of Multiple Groups Undergoing Tls Motion , 2005 .
[21] M. L. Connolly. Analytical molecular surface calculation , 1983 .
[22] Gerhard Klebe,et al. Flexible Adaptations in the Structure of the tRNA‐Modifying Enzyme tRNA–Guanine Transglycosylase and Their Implications for Substrate Selectivity, Reaction Mechanism and Structure‐Based Drug Design , 2003, Chembiochem : a European journal of chemical biology.
[23] J. Tellinghuisen,et al. The role of backlash in the "first injection anomaly" in isothermal titration calorimetry. , 2004, Analytical biochemistry.
[24] 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.
[25] A. Bogan,et al. Anatomy of hot spots in protein interfaces. , 1998, Journal of molecular biology.
[26] Gerhard Klebe,et al. Ligand binding stepwise disrupts water network in thrombin: enthalpic and entropic changes reveal classical hydrophobic effect. , 2012, Journal of medicinal chemistry.
[27] 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.
[28] G. Klebe,et al. Glutamate versus glutamine exchange swaps substrate selectivity in tRNA-guanine transglycosylase: insight into the regulation of substrate selectivity by kinetic and crystallographic studies. , 2007, Journal of molecular biology.
[29] Airlie J. McCoy,et al. Solving structures of protein complexes by molecular replacement with Phaser , 2006, Acta crystallographica. Section D, Biological crystallography.
[30] L. Schanker. Passage of drugs across body membranes. , 1962, Pharmacological reviews.
[31] Z. Zhang,et al. Low-affinity binding determined by titration calorimetry using a high-affinity coupling ligand: a thermodynamic study of ligand binding to protein tyrosine phosphatase 1B. , 1998, Analytical biochemistry.
[32] J. Richardson,et al. Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. , 1999, Journal of molecular biology.
[33] D. Suck,et al. Crystal structure of tRNA‐guanine transglycosylase: RNA modification by base exchange. , 1996, The EMBO journal.
[34] R. Raffa,et al. Protonation effect on drug affinity. , 2004, European Journal of Pharmacology.
[35] Donald Bashford,et al. An Object-Oriented Programming Suite for Electrostatic Effects in Biological Molecules , 1997, ISCOPE.
[36] D. Suck,et al. Mutagenesis and crystallographic studies of Zymomonas mobilis tRNA-guanine transglycosylase reveal aspartate 102 as the active site nucleophile. , 1996, Biochemistry.
[37] G Klebe,et al. Factorising ligand affinity: a combined thermodynamic and crystallographic study of trypsin and thrombin inhibition. , 2001, Journal of molecular biology.
[38] Gerhard Klebe,et al. Adding calorimetric data to decision making in lead discovery: a hot tip , 2010, Nature Reviews Drug Discovery.
[39] R. Conradi,et al. The Influence of Peptide Structure on Transport Across Caco-2 Cells , 1991, Pharmaceutical Research.
[40] William L. Jorgensen,et al. Importance of secondary interactions in triply hydrogen bonded complexes: guanine-cytosine vs uracil-2,6-diaminopyridine , 1990 .
[41] N el Tayar,et al. Partitioning of solutes in different solvent systems: the contribution of hydrogen-bonding capacity and polarity. , 1991, Journal of pharmaceutical sciences.
[42] E. Gasteiger,et al. Excitability of a penicillin-induced cortical epileptic focus , 1980, Experimental Neurology.
[43] J. Thornton,et al. PROCHECK: a program to check the stereochemical quality of protein structures , 1993 .
[44] G. Klebe,et al. Think twice: understanding the high potency of bis(phenyl)methane inhibitors of thrombin. , 2009, Journal of molecular biology.
[45] Kevin Cowtan,et al. research papers Acta Crystallographica Section D Biological , 2005 .
[46] H. Fukada,et al. Enthalpy and heat capacity changes for the proton dissociation of various buffer components in 0.1 M potassium chloride , 1998, Proteins.
[47] 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.
[48] 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.