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Volumn 54, Issue 3, 2012, Pages 245-256

The description of protein internal motions aids selection of ligand binding poses by the INPHARMA method

Author keywords

INPHARMA; Ligand binding; Order parameters; Protein dynamics

Indexed keywords

CYCLIC AMP DEPENDENT PROTEIN KINASE; GLOBULAR PROTEIN;

EID: 84868198365     PISSN: 09252738     EISSN: 15735001     Source Type: Journal    
DOI: 10.1007/s10858-012-9662-1     Document Type: Article
Times cited : (9)

References (49)
  • 2
    • 0842283895 scopus 로고    scopus 로고
    • Hydrophobic core fluidity of homologous protein domains: Relation of side-chain dynamics to core composition and packing
    • DOI 10.1021/bi035658e
    • Best RB, Rutherford TJ, Freund SM, Clarke J (2004) Hydrophobic core fluidity of homologous protein domains: Relation of sidechain dynamics to core composition and packing. Biochemistry 43(5):1145-1155 (Pubitemid 38176512)
    • (2004) Biochemistry , vol.43 , Issue.5 , pp. 1145-1155
    • Best, R.B.1    Rutherford, T.J.2    Freund, S.M.V.3    Clarke, J.4
  • 3
    • 0033541040 scopus 로고    scopus 로고
    • Transferred cross-correlated relaxation complements transferred NOE: Structure of an IL-4R-derived peptide bound to STAT-6
    • Blommers MJJ, Stark W, Jones CE, Head D, Owen CE, Jahnke W (1999) Transferred cross-correlated relaxation complements transferred NOE: Structure of an IL-4R-derived peptide bound to STAT-6. J Am Chem Soc 121:1949-1953
    • (1999) J Am Chem Soc , vol.121 , pp. 1949-1953
    • Blommers, M.J.J.1    Stark, W.2    Jones, C.E.3    Head, D.4    Owen, C.E.5    Jahnke, W.6
  • 4
    • 0001767250 scopus 로고
    • Influence of rapid intramolecular motion on NMR cross-relaxation rates. A molecular dynamics study of antamanide in solution
    • Brueschweiler R, Roux B, Blackledge M, Griesinger C, Karplus M, Ernst RR (1992) Influence of rapid intramolecular motion on NMR cross-relaxation rates. A molecular dynamics study of antamanide in solution. J Am Chem Soc 114(7):2289-2302
    • (1992) J Am Chem Soc , vol.114 , Issue.7 , pp. 2289-2302
    • Brueschweiler, R.1    Roux, B.2    Blackledge, M.3    Griesinger, C.4    Karplus, M.5    Ernst, R.R.6
  • 5
    • 20544455643 scopus 로고    scopus 로고
    • Ligand-target interactions: What can we learn from NMR?
    • DOI 10.1146/annurev.biophys.34.040204.144419
    • Carlomagno T (2005) Ligand-target interactions: What can we learn from NMR? Annu Rev Biophys Biomol Struct 34:245-266 (Pubitemid 40847725)
    • (2005) Annual Review of Biophysics and Biomolecular Structure , vol.34 , pp. 245-266
    • Carlomagno, T.1
  • 6
    • 0033541092 scopus 로고    scopus 로고
    • Transferred cross-correlated relaxation: Application to the determination of sugar pucker in an aminoacylated tRNA-mimetic weakly bound to EF-Tu
    • DOI 10.1021/ja9835887
    • Carlomagno T, Felli IC, Czech M, Fischer R, Sprinzl M, Griesinger C (1999) Transferred cross-correlated relaxation: Application to the determination of sugar pucker in an aminoacylated tRNAmimetic weakly bound to EF-Tu. J Am Chem Soc 121(9): 1945-1948. doi:10.1021/ja9835887 (Pubitemid 29132052)
    • (1999) Journal of the American Chemical Society , vol.121 , Issue.9 , pp. 1945-1948
    • Carlomagno, T.1    Felli, I.C.2    Czech, M.3    Fischer, R.4    Sprinzl, M.5    Griesinger, C.6
  • 7
    • 0036283096 scopus 로고    scopus 로고
    • Molecular dynamics and NMR spin relaxation in proteins
    • Case DA (2002) Molecular dynamics and NMR spin relaxation in proteins. Acc Chem Res 35(6):325-331
    • (2002) Acc Chem Res , vol.35 , Issue.6 , pp. 325-331
    • Case, D.A.1
  • 10
    • 0032474435 scopus 로고    scopus 로고
    • The effect of boundary selection on the stability and folding of the third fibronectin type III domain from human tenascin
    • DOI 10.1021/bi9801659
    • Hamill S, Meekhof A, Clarke J (1998). The effect of boundary selection on the stability and folding of the third fibronectin type III domain from human tenascin. Biochemistry 37(22):8071-8079 (Pubitemid 28307068)
    • (1998) Biochemistry , vol.37 , Issue.22 , pp. 8071-8079
    • Hamill, S.J.1    Meekhof, A.E.2    Clarke, J.3
  • 11
    • 70049114950 scopus 로고    scopus 로고
    • Detection of functional modes in protein dynamics
    • Hub JS, de Groot BL (2009) Detection of functional modes in protein dynamics. PLoS Comput Biol 5(8):e1000480
    • (2009) PLoS Comput Biol , vol.5 , Issue.8
    • Hub, J.S.1    De Groot, B.L.2
  • 13
    • 0036290185 scopus 로고    scopus 로고
    • Complete relaxation and conformational exchange matrix (CORCEMA) analysis of intermolecular saturation transfer effects in reversibly forming ligand-receptor complexes
    • Jayalakshmi V, Krishna NR (2002) Complete relaxation and conformational exchange matrix (CORCEMA) analysis of intermolecular saturation transfer effects in reversibly forming ligand-receptor complexes. J Magn Reson 155(1):106-118
    • (2002) J Magn Reson , vol.155 , Issue.1 , pp. 106-118
    • Jayalakshmi, V.1    Krishna, N.R.2
  • 14
    • 0000386638 scopus 로고
    • Proton magnetic-relaxation and spin diffusion in proteins
    • doi10 1016/0022-343-366 doi23647690115
    • Kalk A, Berendsen HJC (1976) Proton magnetic-relaxation and spin diffusion in proteins. J Magn Reson 24(3):343-366. doi:10. 1016/0022-2364(76) 90115-3
    • (1976) J Magn Reson , vol.24 , Issue.3 , pp. 343-366
    • Kalk, A.1    Berendsen, H.J.C.2
  • 17
    • 0001053688 scopus 로고
    • A theoretical-study of distances determination from NMR-two-dimensional nuclear overhauser effect spectra
    • doi101016/0022-404-426 do23648490257
    • Keepers JW, James TL (1984) A theoretical-study of distances determination from NMR-two-dimensional nuclear overhauser effect spectra. J Magn Reson 57(3):404-426. doi:10.1016/0022-2364(84)90257-9
    • (1984) J Magn Reson , vol.57 , Issue.3 , pp. 404-426
    • Keepers, J.W.1    James, T.L.2
  • 19
    • 0026490256 scopus 로고
    • Structure of a fibronectin type III domain from tenascin phased by MAD analysis of the selenomethionyl protein
    • Leahy DJ, Hendrickson WA, Aukhil I, Erickson HP (1992) Structure of a fibronectin type III domain from tenascin phased by MAD analysis of the selenomethionyl protein. Science 258(5084): 987-991
    • (1992) Science , vol.258 , Issue.5084 , pp. 987-991
    • Leahy, D.J.1    Hendrickson, W.A.2    Aukhil, I.3    Erickson, H.P.4
  • 22
    • 0033257882 scopus 로고    scopus 로고
    • Theoretical analysis of the inter-ligand overhauser effect: A new approach for mapping structural relationships of macromolecular ligands
    • London RE (1999) Theoretical analysis of the inter-ligand overhauser effect: A new approach for mapping structural relationships of macromolecular ligands. J Magn Reson 141(2):301-311 (Pubitemid 129608329)
    • (1999) Journal of Magnetic Resonance , vol.141 , Issue.2 , pp. 301-311
    • London, R.E.1
  • 23
    • 0041784950 scopus 로고    scopus 로고
    • All-atom empirical potential for molecular modeling and dynamics studies of proteins
    • MacKerell AD et al (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102:3586-3616
    • (1998) J Phys Chem B , vol.102 , pp. 3586-3616
    • MacKerell, A.D.1
  • 24
    • 52949121796 scopus 로고    scopus 로고
    • Structural biology by NMR: Structure, dynamics, and interactions
    • Markwick PR, Malliavin T, Nilges M (2008) Structural biology by NMR: Structure, dynamics, and interactions. PLoS Comput Biol 4(9):e1000168
    • (2008) PLoS Comput Biol , vol.4 , Issue.9
    • Markwick, P.R.1    Malliavin, T.2    Nilges, M.3
  • 25
    • 0034823890 scopus 로고    scopus 로고
    • Group epitope mapping by saturation transfer difference NMR to identify segments of a ligand in direct contact with a protein receptor
    • DOI 10.1021/ja0100120
    • Mayer M, Meyer B (2001) Group epitope mapping by saturation transfer difference NMR to identify segments of a ligand in direct contact with a protein receptor. J Am Chem Soc 123(25): 6108-6117 (Pubitemid 32888480)
    • (2001) Journal of the American Chemical Society , vol.123 , Issue.25 , pp. 6108-6117
    • Mayer, M.1    Meyer, B.2
  • 26
    • 0037009985 scopus 로고    scopus 로고
    • Spatial localization of ligand binding sites from electron current density surfaces calculated from NMR chemical shift perturbations
    • 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(39):11758-11763
    • (2002) J Am Chem Soc , vol.124 , Issue.39 , pp. 11758-11763
    • McCoy, M.A.1    Wyss, D.F.2
  • 27
    • 3042763969 scopus 로고    scopus 로고
    • Prediction of methyl-side chain dynamics in proteins
    • DOI 10.1023/B:JNMR.0000032612.70767.35
    • Ming D, Brueschweiler R (2004) Prediction of methyl-side chain dynamics in proteins. J Biomol NMR 29(3):363-368 (Pubitemid 38864834)
    • (2004) Journal of Biomolecular NMR , vol.29 , Issue.3 , pp. 363-368
    • Ming, D.1    Bruschweiler, R.2
  • 28
    • 33645834303 scopus 로고    scopus 로고
    • New tools provide new insights in NMR studies of protein dynamics
    • Mittermaier A, Kay LE (2006) New tools provide new insights in NMR studies of protein dynamics. Science 312(5771):224-228
    • (2006) Science , vol.312 , Issue.5771 , pp. 224-228
    • Mittermaier, A.1    Kay, L.E.2
  • 29
    • 0041866668 scopus 로고    scopus 로고
    • 2H NMR side-chain order parameters and sequence conservation in globular proteins
    • DOI 10.1021/ja034856q
    • Mittermaier A, Davidson AR, Kay LE (2003) Correlation between 2H NMR side-chain order parameters and sequence conservation in globular proteins. J Am Chem Soc 125(30):9004-9005 (Pubitemid 36903807)
    • (2003) Journal of the American Chemical Society , vol.125 , Issue.30 , pp. 9004-9005
    • Mittermaier, A.1    Davidson, A.R.2    Kay, L.E.3
  • 31
    • 0025894164 scopus 로고
    • Relaxation matrix refinement of the solution structure of squash trypsin inhibitor
    • Nilges M, Habazettl J, Brunger AT, Holak TA (1991) Relaxation matrix refinement of the solution structure of squash trypsin inhibitor. J Mol Biol 219(3):499-510
    • (1991) J Mol Biol , vol.219 , Issue.3 , pp. 499-510
    • Nilges, M.1    Habazettl, J.2    Brunger, A.T.3    Holak, T.A.4
  • 32
    • 0027245080 scopus 로고
    • Crystal structure of the SH3 domain in human Fyn; comparison of the three-dimensional structures of SH3 domains in tyrosine kinases and spectrin
    • Noble ME, Musacchio A, Saraste M, Courtneidge SA, Wierenga RK (1993) Crystal structure of the SH3 domain in human Fyn; comparison of the three-dimensional structures of SH3 domains in tyrosine kinases and spectrin. EMBO J 12(7):2617-2624 (Pubitemid 23218310)
    • (1993) EMBO Journal , vol.12 , Issue.7 , pp. 2617-2624
    • Noble, M.E.M.1    Musacchio, A.2    Sarasate, M.3    Courtneidge, S.A.4    Wierenga, R.K.5
  • 34
    • 68049093935 scopus 로고    scopus 로고
    • The INPHARMA technique for pharmacophore mapping: A theoretical guide to the method
    • Orts J, Griesinger C, Carlomagno T (2009) The INPHARMA technique for pharmacophore mapping: A theoretical guide to the method. J Magn Reson 200(1):64-73
    • (2009) J Magn Reson , vol.200 , Issue.1 , pp. 64-73
    • Orts, J.1    Griesinger, C.2    Carlomagno, T.3
  • 35
    • 84856548602 scopus 로고    scopus 로고
    • An NMR-based scoring function improves the accuracy of binding pose predictions by docking by two orders of magnitude
    • Orts J, Bartoschek S, Griesinger C, Monecke P, Carlomagno T (2012) An NMR-based scoring function improves the accuracy of binding pose predictions by docking by two orders of magnitude. J Biomol NMR 52(1):23-30
    • (2012) J Biomol NMR , vol.52 , Issue.1 , pp. 23-30
    • Orts, J.1    Bartoschek, S.2    Griesinger, C.3    Monecke, P.4    Carlomagno, T.5
  • 39
    • 0344791680 scopus 로고    scopus 로고
    • Influence of internal dynamics on accuracy of protein NMR structures: Derivation of realistic model distance data from a long molecular dynamics trajectory
    • DOI 10.1006/jmbi.1998.2323
    • Schneider TR, Brunger AT, Nilges M (1999) Influence of internal dynamics on accuracy of protein NMR structures: Derivation of realistic model distance data from a long molecular dynamics trajectory. J Mol Biol 285(2):727-740 (Pubitemid 29041804)
    • (1999) Journal of Molecular Biology , vol.285 , Issue.2 , pp. 727-740
    • Schneider, T.R.1    Brunger, A.T.2    Nilges, M.3
  • 40
    • 35948943745 scopus 로고    scopus 로고
    • Validation of molecular dynamics simulations of biomolecules using NMR spin relaxation as benchmarks: An application to the AMBER99SB force field
    • Showalter SA, Brueschweiler R (2007) Validation of molecular dynamics simulations of biomolecules using NMR spin relaxation as benchmarks: An application to the AMBER99SB force field. J Chem Theory Comput 3(3):961-975
    • (2007) J Chem Theory Comput , vol.3 , Issue.3 , pp. 961-975
    • Showalter, S.A.1    Brueschweiler, R.2
  • 41
    • 36448947240 scopus 로고    scopus 로고
    • Toward quantitative interpretation of methyl side-chain dynamics from NMR by molecular dynamics simulations
    • DOI 10.1021/ja075976r
    • Showalter SA, Johnson E, Rance M, Bruschweiler R (2007) Toward quantitative interpretation of methyl side-chain dynamics from NMR by molecular dynamics simulations. J Am Chem Soc 129(46):14146-14147 (Pubitemid 350171419)
    • (2007) Journal of the American Chemical Society , vol.129 , Issue.46 , pp. 14146-14147
    • Showalter, S.A.1    Johnson, E.2    Rance, M.3    Bruschweiler, R.4
  • 43
    • 0023644679 scopus 로고
    • Structure of ubiquitin refined at 1.8 A resolution
    • Vijay-Kumar S, Bugg CE, Cook WJ (1987) Structure of ubiquitin refined at 1.8 A resolution. J Mol Biol 194(3):531-544
    • (1987) J Mol Biol , vol.194 , Issue.3 , pp. 531-544
    • Vijay-Kumar, S.1    Bugg, C.E.2    Cook, W.J.3
  • 47
    • 0033614004 scopus 로고    scopus 로고
    • Asparagine and glutamine: Using hydrogen atom contacts in the choice of side-chain amide orientation
    • DOI 10.1006/jmbi.1998.2401
    • Word JM, Lovell SC, Richardson JS, Richardson DC (1999) Asparagine and glutamine: Using hydrogen atom contacts in the choice of side-chain amide orientation. J Mol Biol 285(4): 1735-1747 (Pubitemid 29060467)
    • (1999) Journal of Molecular Biology , vol.285 , Issue.4 , pp. 1735-1747
    • Word, J.M.1    Lovell, S.C.2    Richardson, J.S.3    Richardson, D.C.4
  • 48
    • 0027480327 scopus 로고
    • The adipocyte lipid-binding protein at 1.6-A resolution. Crystal structures of the apoprotein and with bound saturated and unsaturated fatty acids
    • Xu Z, Bernlohr DA, Banaszak LJ (1993) The adipocyte lipid-binding protein at 1.6-A resolution. Crystal structures of the apoprotein and with bound saturated and unsaturated fatty acids. J Biol Chem 268(11):7874-7884 (Pubitemid 23120364)
    • (1993) Journal of Biological Chemistry , vol.268 , Issue.11 , pp. 7874-7884
    • Xu, Z.1    Bernlohr, D.A.2    Banaszak, L.J.3
  • 49
    • 0001571821 scopus 로고
    • Protein indirect relaxation effects in exchange-transferred NOESY by a rate-matrix analysis
    • Zheng J, Post CB (1993) Protein indirect relaxation effects in exchange-transferred NOESY by a rate-matrix analysis. J Magn Reson 101:262-270
    • (1993) J Magn Reson , vol.101 , pp. 262-270
    • Zheng, J.1    Post, C.B.2


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