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Volumn 80, Issue 2, 2012, Pages 591-601

Minimal ensembles of side chain conformers for modeling protein-protein interactions

Author keywords

Pre existing ensemble of conformers; Protein binding; Rotamer libraries; Side chain flexibility; Structure prediction

Indexed keywords

ARGININE; CYSTEINE; GLUCAGON; LEUKOTRIENE; SERINE; PROTEIN;

EID: 84855712140     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.23222     Document Type: Article
Times cited : (22)

References (40)
  • 1
    • 79953680719 scopus 로고    scopus 로고
    • Side-chain conformational changes upon protein-protein association
    • Ruvinsky AM, Kirys T, Tuzikov AV, Vakser IA. Side-chain conformational changes upon protein-protein association. J Mol Biol 2011; 408: 356-365.
    • (2011) J Mol Biol , vol.408 , pp. 356-365
    • Ruvinsky, A.M.1    Kirys, T.2    Tuzikov, A.V.3    Vakser, I.A.4
  • 2
    • 0001858251 scopus 로고
    • Application of a theory of enzyme specificity to protein synthesis
    • Koshland DE. Application of a theory of enzyme specificity to protein synthesis. Proc Natl Acad Sci USA 1958; 44: 98-104.
    • (1958) Proc Natl Acad Sci USA , vol.44 , pp. 98-104
    • Koshland, D.E.1
  • 3
    • 0029561993 scopus 로고
    • Spectroscopic calorimetric, and kinetic demonstration of conformational adaptation in peptide-antibody recognition
    • Leder L, Berger C, Bornhauser S, Wendt H, Ackermann F, Jelesarov I, Bosshard HR. Spectroscopic calorimetric, and kinetic demonstration of conformational adaptation in peptide-antibody recognition. Biochemistry 1995; 34: 16509-16518.
    • (1995) Biochemistry , vol.34 , pp. 16509-16518
    • Leder, L.1    Berger, C.2    Bornhauser, S.3    Wendt, H.4    Ackermann, F.5    Jelesarov, I.6    Bosshard, H.R.7
  • 4
    • 0031892160 scopus 로고    scopus 로고
    • Protein conformer selection by ligand binding observed with crystallography
    • Cao Y, Musah RA, Wilcox SK, Goodin DB, McRee DE. Protein conformer selection by ligand binding observed with crystallography. Protein Sci 1998; 7: 72-78.
    • (1998) Protein Sci , vol.7 , pp. 72-78
    • Cao, Y.1    Musah, R.A.2    Wilcox, S.K.3    Goodin, D.B.4    McRee, D.E.5
  • 7
    • 0033056708 scopus 로고    scopus 로고
    • Folding funnels, binding funnels, and protein function
    • Tsai CJ, Kumar S, Ma B, Nussinov R. Folding funnels, binding funnels, and protein function. Protein Sci 1999; 8: 1181-1190.
    • (1999) Protein Sci , vol.8 , pp. 1181-1190
    • Tsai, C.J.1    Kumar, S.2    Ma, B.3    Nussinov, R.4
  • 8
    • 70350340728 scopus 로고    scopus 로고
    • The role of dynamic conformational ensembles in biomolecular recognition
    • Boehr DD, Nussinov R, Wright PE. The role of dynamic conformational ensembles in biomolecular recognition. Nat Chem Biol 2009; 5: 789-796.
    • (2009) Nat Chem Biol , vol.5 , pp. 789-796
    • Boehr, D.D.1    Nussinov, R.2    Wright, P.E.3
  • 9
    • 0026320866 scopus 로고
    • The energy landscapes and motions of proteins
    • Frauenfelder H, Sligar SG, Wolynes PG. The energy landscapes and motions of proteins. Science 1991; 254: 1598-1603.
    • (1991) Science , vol.254 , pp. 1598-1603
    • Frauenfelder, H.1    Sligar, S.G.2    Wolynes, P.G.3
  • 10
    • 77957231785 scopus 로고    scopus 로고
    • Induced fit, conformational selection and independent dynamic segments: an extended view of binding events
    • Csermely P, Palotai R, Nussinov R. Induced fit, conformational selection and independent dynamic segments: an extended view of binding events. Trends Biochem Sci 2010; 35: 539-546.
    • (2010) Trends Biochem Sci , vol.35 , pp. 539-546
    • Csermely, P.1    Palotai, R.2    Nussinov, R.3
  • 11
    • 0031670902 scopus 로고    scopus 로고
    • Conformational switching in an aspartic proteinase
    • Lee AY, Gulnik SV, Erickson JW. Conformational switching in an aspartic proteinase. Nat Struct Biol 1998; 5: 866-871.
    • (1998) Nat Struct Biol , vol.5 , pp. 866-871
    • Lee, A.Y.1    Gulnik, S.V.2    Erickson, J.W.3
  • 13
    • 71449103005 scopus 로고    scopus 로고
    • Hidden alternative structures of proline isomerase essential for catalysis
    • Fraser JS, Clarkson MW, Degnan SC, Erion R, Kern D, Alber T. Hidden alternative structures of proline isomerase essential for catalysis. Nature 2009; 462: 669-673.
    • (2009) Nature , vol.462 , pp. 669-673
    • Fraser, J.S.1    Clarkson, M.W.2    Degnan, S.C.3    Erion, R.4    Kern, D.5    Alber, T.6
  • 14
    • 33645834303 scopus 로고    scopus 로고
    • New tools provide new insights in NMR studies of protein dynamics
    • Mittermaier A, Kay LE. New tools provide new insights in NMR studies of protein dynamics. Science 2006; 312: 224-228.
    • (2006) Science , vol.312 , pp. 224-228
    • Mittermaier, A.1    Kay, L.E.2
  • 15
    • 0027160197 scopus 로고
    • Backbone-dependent rotamer library for proteins. Application to side chain prediction
    • Dunbrack RL, Karplus M. Backbone-dependent rotamer library for proteins. Application to side chain prediction. J Mol Biol 1993; 230: 543-574.
    • (1993) J Mol Biol , vol.230 , pp. 543-574
    • Dunbrack, R.L.1    Karplus, M.2
  • 16
    • 0036667731 scopus 로고    scopus 로고
    • Rotamer libraries in the 21st century
    • Dunbrack RL. Rotamer libraries in the 21st century. Curr Opin Struct Biol 2002; 12: 431-440.
    • (2002) Curr Opin Struct Biol , vol.12 , pp. 431-440
    • Dunbrack, R.L.1
  • 17
    • 0034996721 scopus 로고    scopus 로고
    • Approaches to solving the rigid receptor problem by identifying a minimal set of flexible residues during ligand docking
    • Anderson AC, O'Neil RH, Surti TS, Stroud RM. Approaches to solving the rigid receptor problem by identifying a minimal set of flexible residues during ligand docking. Chem Biol 2001; 8: 445-457.
    • (2001) Chem Biol , vol.8 , pp. 445-457
    • Anderson, A.C.1    O'Neil, R.H.2    Surti, T.S.3    Stroud, R.M.4
  • 18
    • 0034656949 scopus 로고    scopus 로고
    • Side-chain flexibility in proteins upon ligand binding
    • Najmanovich R, Kuttner J, Sobolev V, Edelman M. Side-chain flexibility in proteins upon ligand binding. Proteins 2000; 39: 261-268.
    • (2000) Proteins , vol.39 , pp. 261-268
    • Najmanovich, R.1    Kuttner, J.2    Sobolev, V.3    Edelman, M.4
  • 19
    • 0035141353 scopus 로고    scopus 로고
    • Dynamical view of the positions of key side chains in protein-protein recognition
    • Kimura SR, Brower RC, Vajda S, Camacho CJ. Dynamical view of the positions of key side chains in protein-protein recognition. Biophys J 2001; 80: 635-642.
    • (2001) Biophys J , vol.80 , pp. 635-642
    • Kimura, S.R.1    Brower, R.C.2    Vajda, S.3    Camacho, C.J.4
  • 21
    • 7944225979 scopus 로고    scopus 로고
    • Protein-protein interactions: hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: implications for docking
    • Li X, Keskin O, Ma B, Nussinov R, Liang J. Protein-protein interactions: hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: implications for docking. J Mol Biol 2004; 344: 781-795.
    • (2004) J Mol Biol , vol.344 , pp. 781-795
    • Li, X.1    Keskin, O.2    Ma, B.3    Nussinov, R.4    Liang, J.5
  • 22
    • 15244355250 scopus 로고    scopus 로고
    • The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking
    • Smith GR, Sternberg MJ, Bates PA. The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking. J Mol Biol 2005; 347: 1077-1101.
    • (2005) J Mol Biol , vol.347 , pp. 1077-1101
    • Smith, G.R.1    Sternberg, M.J.2    Bates, P.A.3
  • 23
    • 0038161052 scopus 로고    scopus 로고
    • Protein-protein docking with simultaneous optimization of rigid-body displacement and side chain conformations
    • Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D. Protein-protein docking with simultaneous optimization of rigid-body displacement and side chain conformations. J Mol Biol 2003; 331: 281-299.
    • (2003) J Mol Biol , vol.331 , pp. 281-299
    • Gray, J.J.1    Moughon, S.2    Wang, C.3    Schueler-Furman, O.4    Kuhlman, B.5    Rohl, C.A.6    Baker, D.7
  • 27
    • 0012227656 scopus 로고    scopus 로고
    • A comprehensive analytical treatment of continuum electrostatics
    • Schaefer M, Karplus M. A comprehensive analytical treatment of continuum electrostatics. J Phys Chem 1996; 100: 1578-1599.
    • (1996) J Phys Chem , vol.100 , pp. 1578-1599
    • Schaefer, M.1    Karplus, M.2
  • 28
    • 2942704296 scopus 로고    scopus 로고
    • Statistically based reduced representation of amino acid side chains
    • Rainey JK, Goh MC. Statistically based reduced representation of amino acid side chains. J Chem Inf Comput Sci 2004; 44: 817-830.
    • (2004) J Chem Inf Comput Sci , vol.44 , pp. 817-830
    • Rainey, J.K.1    Goh, M.C.2
  • 29
    • 34548317146 scopus 로고    scopus 로고
    • FireDock: fast interaction refinement in molecular docking
    • Andrusier N, Nussinov R, Wolfson HJ. FireDock: fast interaction refinement in molecular docking. Proteins 2007; 69: 139-159.
    • (2007) Proteins , vol.69 , pp. 139-159
    • Andrusier, N.1    Nussinov, R.2    Wolfson, H.J.3
  • 30
    • 0000267310 scopus 로고
    • Versuch einer mathematischen theorie der koagulationskinetik kolloider loeschungen
    • Smoluchowski MV. Versuch einer mathematischen theorie der koagulationskinetik kolloider loeschungen. Z Phys Chem 1917; 92: 129-168.
    • (1917) Z Phys Chem , vol.92 , pp. 129-168
    • Smoluchowski, M.V.1
  • 32
    • 65249099497 scopus 로고    scopus 로고
    • Fundamental aspects of protein-protein association kinetics
    • Schreiber G, Haran G, Zhou HX. Fundamental aspects of protein-protein association kinetics. Chem Rev 2009; 109: 839-860.
    • (2009) Chem Rev , vol.109 , pp. 839-860
    • Schreiber, G.1    Haran, G.2    Zhou, H.X.3
  • 33
    • 0034049350 scopus 로고    scopus 로고
    • Kinetics of desolvation-mediated protein-protein binding
    • Camacho CJ, Kimura SR, DeLisi C, Vajda S. Kinetics of desolvation-mediated protein-protein binding. Biophys J 2000; 78: 1094-1105.
    • (2000) Biophys J , vol.78 , pp. 1094-1105
    • Camacho, C.J.1    Kimura, S.R.2    DeLisi, C.3    Vajda, S.4
  • 34
    • 2442640122 scopus 로고    scopus 로고
    • Realistic protein-protein association rates from a simple diffusional model neglecting long-range interactions, free energy barriers, and landscape ruggedness
    • Schlosshauer M, Baker D. Realistic protein-protein association rates from a simple diffusional model neglecting long-range interactions, free energy barriers, and landscape ruggedness. Protein Sci 2004; 13: 1660-1669.
    • (2004) Protein Sci , vol.13 , pp. 1660-1669
    • Schlosshauer, M.1    Baker, D.2
  • 35
    • 64549106038 scopus 로고    scopus 로고
    • Convergence and combination of methods in protein-protein docking
    • Vajda S, Kozakov D. Convergence and combination of methods in protein-protein docking. Curr Opin Struct Biol 2009; 19: 164-170.
    • (2009) Curr Opin Struct Biol , vol.19 , pp. 164-170
    • Vajda, S.1    Kozakov, D.2
  • 36
    • 0031581852 scopus 로고    scopus 로고
    • Molecular docking to ensembles of protein structures
    • Knegtel RM, Kuntz ID, Oshiro CM. Molecular docking to ensembles of protein structures. J Mol Biol 1997; 266: 424-440.
    • (1997) J Mol Biol , vol.266 , pp. 424-440
    • Knegtel, R.M.1    Kuntz, I.D.2    Oshiro, C.M.3
  • 37
    • 0031965676 scopus 로고    scopus 로고
    • Flexible ligand docking using conformational ensembles
    • Lorber DM, Shoichet BK. Flexible ligand docking using conformational ensembles. Protein Sci 1998; 7: 938-950.
    • (1998) Protein Sci , vol.7 , pp. 938-950
    • Lorber, D.M.1    Shoichet, B.K.2
  • 38
    • 0033974667 scopus 로고    scopus 로고
    • Accommodating protein flexibility in computational drug design
    • Carlson HA, McCammon JA. Accommodating protein flexibility in computational drug design. Mol Pharmacol 2000; 57: 213-218.
    • (2000) Mol Pharmacol , vol.57 , pp. 213-218
    • Carlson, H.A.1    McCammon, J.A.2
  • 39
    • 41949132916 scopus 로고    scopus 로고
    • Flexible ligand docking to multiple receptor conformations: a practical alternative
    • Totrov M, Abagyan R. Flexible ligand docking to multiple receptor conformations: a practical alternative. Curr Opin Struct Biol 2008; 18: 178-184.
    • (2008) Curr Opin Struct Biol , vol.18 , pp. 178-184
    • Totrov, M.1    Abagyan, R.2
  • 40
    • 33846000313 scopus 로고    scopus 로고
    • Ensemble docking of multiple protein structures: considering protein structural variations in molecular docking
    • Huang SY, Zou X. Ensemble docking of multiple protein structures: considering protein structural variations in molecular docking. Proteins 2007; 66: 399-421.
    • (2007) Proteins , vol.66 , pp. 399-421
    • Huang, S.Y.1    Zou, X.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.