Auto-FACE: An NMR based binding site mapping program for fast chemical exchange protein-ligand systems

PLoS ONE

Volumn 5, Issue 2, 2010, Pages

  Krishnamoorthy, Janarthanan ^a   Yu, Victor C K ^a   Mok, Yu Keung ^a  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

BH3I 1 PROTEIN; NITROGEN 15; PROTEIN; PROTEIN BCL XL; UNCLASSIFIED DRUG; 5 (4 BROMOBENZYLIDENE) ALPHA ISOPROPYL 4 OXO 2 THIOXO 3 THAZOLIDINEACETIC ACID; 5-(4-BROMOBENZYLIDENE)-ALPHA-ISOPROPYL-4-OXO-2-THIOXO-3-THAZOLIDINEACETIC ACID; LIGAND; PROTEIN BAX; PROTEIN BCL X; RECOMBINANT PROTEIN; THIAZOLE DERIVATIVE;

ARTICLE; AUTOANALYZER; AUTOMATION; BINDING AFFINITY; BINDING SITE; COMPUTER PROGRAM; CONCENTRATION (PARAMETERS); EQUILIBRIUM CONSTANT; FLUORESCENCE POLARIZATION; HETERONUCLEAR SINGLE QUANTUM COHERENCE; HYDROPHOBICITY; ISOTHERMAL TITRATION CALORIMETRY; LIGAND BINDING; MOLECULAR INTERACTION; NUCLEAR MAGNETIC RESONANCE; PEPTIDE MAPPING; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION; PROTEIN TRANSPORT; PROTON NUCLEAR MAGNETIC RESONANCE; TITRIMETRY; TRANSPORT KINETICS; ALGORITHM; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; GENETICS; HUMAN; KINETICS; METABOLISM; METHODOLOGY; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PROTEIN DOMAIN; THERMODYNAMICS;

ALGORITHMS; BCL-2-ASSOCIATED X PROTEIN; BCL-X PROTEIN; BINDING SITES; HUMANS; KINETICS; LIGANDS; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PROTEIN BINDING; PROTEIN INTERACTION DOMAINS AND MOTIFS; PROTEINS; RECOMBINANT PROTEINS; THERMODYNAMICS; THIAZOLES;

EID: 77949523858     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0008943     Document Type: Article

References (54)

1. Van Dongen M, Weigelt J, Uppenberg J, Schultz J, Wikstrom M (2002) Structure-based screening and design in drug discovery. Drug Discov Today 7: 471-478.
2. Carlomagno T (2005) Ligand-target interactions: what can we learn from NMR? Annu Rev Biophys Biomol Struct 34: 245-266.
3. Takeuchi K, Wagner G (2006) NMR studies of protein interactions. Curr Opin Struct Biol 16: 109-117.
4. Roberts G (2000) Applications of NMR in drug discovery. Drug Discov Today 5: 230-240.
5. Bain AD (2003) Chemical exchange in NMR. Prog Nucl Magn Reson Spectrosc 43: 63-103.
6. Palmer A III (2004) NMR characterization of the dynamics of biomacromolecules. Chem Rev 104: 3623-3640.
7. Jayalakshmi V, Krishna NR (2002) Complete relaxation and conformational exchange matrix analysis (CORCEMA) of intermolecular saturation transfer effects in reversibly forming ligand-receptor complexes. J Magn Reson 155: 106-118.
8. Jayalakshmi V, Rama Krishna N (2004) CORCEMA refinement of the bound ligand conformation within the protein binding pocket in reversibly forming weak complexes using STD-NMR intensities. J Magn Reson 168: 36-45.
9. Moseley H, Lee W, Arrowsmith C, Krishna N (1997) Quantitative determination of conformational, dynamic, and kinetic parameters of a ligand-protein/DNA complex from a complete relaxation and conformational exchange matrix analysis of intermolecular transferred NOESY. Biochemistry-US 36: 5293-5299.
10. Keeler J (2005) Understanding NMR spectroscopy Wiley West Sussex. 459 p.
11. Cavanagh J (1996) Protein NMR spectroscopy: principles and practice Academic Press. 885 p.
12. Bain AD, Duns GJ (1996) A unified approach to dynamic NMR based on a physical interpretation of the transition probability. Can J Chem 74: 819-824.
13. Gutowsky H, Holm C (1956) Rate processes and nuclear magnetic resonance spectra. II. Hindered internal rotation of amides. J Chem Phys 25: 1228-1234.
14. Binsch G (1969) Unified theory of exchange effects on nuclear magnetic resonance line shapes. J Am Chem Soc 91: 1304-1309.
15. McConnell HM (1958) Reaction rates by nuclear magnetic resonance. J Chem Phys 28: 430-431.
16. Johnson CS (1965) Chemical rate processes and magnetic resonance. Adv Magn Reson 1: 33-102.
17. Bain AD (1998) Blurring the distinction between slow and intermediate chemical exchange. Biochem Cell Biol 76: 171-176.
18. Davies D, Eaton R, Baranovsky S, Veselkov A (2000) NMR investigation of the complexation of daunomycin with deoxytetranucleotides of different base sequence in aqueous solution. J Biomol Struct Dyn 17: 887.
19. Davies D, Veselkov A (1996) Structural and thermodynamical analysis of molecular complexation by 1H NMR spectroscopy. Intercalation of ethidium bromide with the isomeric deoxytetranucleoside triphosphates 5-d (GpCpGpC) and 5-d (CpGpCpG) in aqueous solution. J Chem Soc Faraday T 92: 3545-3557.
20. Veselkov A, Evstigneev M, Rozvadovskaya A, Hernandez Santiago A, Zubchenok O, et al. (2004) 1H NMR structural and thermodynamical analysis of the hetero-association of daunomycin and novatrone in aqueous solution. J Mol Struct 701: 31-37.
21. Deb K, Pratap A, Agarwal S, Meyarivan T (2002) A fast and elitist multiobjective genetic algorithm: NSGA-II. IEEE T Evolut Comput 6: 182-197.
22. Vaux D, Strasser A (1996) The molecular biology of apoptosis. Proc Natl Acad Sci U S A 93: 2239-2244.
23. Adams J, Cory S (2007) Bcl-2 regulated apoptosis: mechanism and therapeutic potential. Curr opin Immunol 19: 488.
24. Berghella AM, Pellegrini P, Contasta I, Beato TD, Adorno D (1998) Bcl-2 and drugs used in the treatment of cancer: new strategies of biotherapy which should not be underestimated. Cancer Biother Radio 13: 225-236.
25. Huang Z (2000) Bcl-2 family proteins as targets for anticancer drug design. Oncogene 19: 6627-6631.
26. XL that are not the classic BH3 binding cleft. J Mol Biol 364: 536-549.
27. Lugovskoy AA, Degterev AI, Fahmy AF, Zhou P, Gross JD, et al. (2002) A novel approach for characterizing protein ligand complexes: molecular basis for specificity of small-molecule Bcl-2 inhibitors. J Am Chem Soc 124: 1234-1240.
28. Tjelvar SG, Olsson, Mark A, Williams, William R, et al. (2008) The thermodynamics of protein-ligand interaction and solvation: insights for ligand design. J Mol Biol 384: 1002-1017.
29. Harding S, Chowdhry B (2001) Protein-ligand interactions: hydrodynamics and calorimetry. , USA: Oxford University Press. 360 p.
30. Mandel A, Akke M, Palmer A III (1995) Backbone dynamics of Escherichia coli ribonuclease HI: correlations with structure and function in an active enzyme. J Mol Biol 246: 144-163.
31. Kovrigin E, Loria J (2006) Characterization of the transition state of functional enzyme dynamics. J Am Chem Soc 128: 7724-7725.
32. Beach H, Cole R, Gill M, Loria J (2005) Conservation of mus-ms enzyme motions in the apo- and substrate-mimicked state. J Am Chem Soc 127: 9167-9176.
33. Kovrigin E, Kempf J, Grey M, Loria J (2006) Faithful estimation of dynamics parameters from CPMG relaxation dispersion measurements. J Magn Reson 180: 93-104.
34. Osapay K, Case DA (1991) A new analysis of proton chemical shifts in proteins. J Am Chem Soc 113: 9436-9444.
35. Neal S, Nip AM, Zhang H, Wishart DS (2003) Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts. J Biomol NMR 26: 215-240.
36. Sharma Y, Kwon OY, Brooks B, Tjandra N (2002) An ab initio study of amide proton shift tensor dependence on local protein structure. J Am Chem Soc 124: 327-335.
37. Le H, Oldfield E (1996) Ab initio studies of amide - N chemical shifts in dipeptides: applications to protein NMR spectroscopy. J Phys Chem 100: 16423-16428.
38. Gorecki A, Kkepys B, Bonarek P, Wasylewski Z (2009) Kinetic studies of cAMPinduced propagation of the allosteric signal in the cAMP receptor protein from Escherichia coli with the use of site-directed mutagenesis. Int J Biol Macromol 44: 262-270.
39. McCoy MA, Wyss DF (2002) Spatial localization of ligand binding sites from electron current density surfaces calculated from NMR chemical shift perturbations. J Am Chem Soc 124: 11758-11763.
40. McCoy M, Wyss D (2002) Structures of protein-protein complexes are docked using only NMR restraints from residual dipolar coupling and chemical shift perturbations. J Am Chem Soc 124: 2104-2105.
41. XL protein in complex with BH3 peptides of pro-apoptotic Bak, Bad, and Bim proteins: comparative molecular dynamics simulations. Proteins 73: 492-514.
42. Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, et al. (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6: 277-293.
43. NMRpipe 9. http://spin.niddk.nih.gov/NMRPipe.
44. Goddard TD, Kneller DG. SPARKY 3.1.1. http://www.cgl.ucsf.edu/home/ sparky/distrib-3.106.
45. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, et al. (1998) Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem 19: 1639-1662.
46. PDB. http://www.rcsb.org/pdb.
47. Dallakyan S, Omelchenko A, Sanner M, Karnati S. MGLTools 1. 5. 2. http://mgltools.scripps.edu.
48. Merritt E. gnuplot 4. 2. 4. http://www.gnuplot.info/download.html.
49. King EL, Altman (1956) A schematic method of deriving the rate laws for enzyme-catalyzed reactions. J Phys Chem 60: 1375-1378.
50. Bowden AEC (1977) An automatic method for deriving steady-state rate equations. J Biochem 165: 55-59.
51. Huang CY (1979) Derivation and initial velocity and isotope exchange rate equations. Method Enzymol 63: 54-84.
52. Segel HL (1975) Enzyme kinetics. New York: John Wiley and Sons press. 992 p.
53. Bain AD (2002) MEXICO 3.1 : The McMaster program for exchange lineshape calculations. http://www.chemistry.mcmaster.ca/bain/exchange.html.
54. Ferrin T. Chimera 1. 3. 2577. http://www.cgl.ucsf.edu/chimera/download. html.