메뉴 건너뛰기




Volumn 78, Issue 9, 2010, Pages 2029-2040

Sub-angstrom modeling of complexes between flexible peptides and globular proteins

Author keywords

Linear binding motifs; Peptide docking; Peptide mediated interactions; Peptide protein interactions; Rosetta flexpepdock; Short peptides

Indexed keywords

GLOBULAR PROTEIN; PEPTIDE; CAPSID PROTEIN; MULTIPROTEIN COMPLEX; PROTEIN;

EID: 77953573815     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22716     Document Type: Article
Times cited : (346)

References (64)
  • 1
    • 0037453510 scopus 로고    scopus 로고
    • Assembly of cell regulatory systems through protein interaction domains
    • Pawson T, Nash P. Assembly of cell regulatory systems through protein interaction domains. Science 2003;300:445-452.
    • (2003) Science , vol.300 , pp. 445-452
    • Pawson, T.1    Nash, P.2
  • 2
    • 49549083915 scopus 로고    scopus 로고
    • Peptide-mediated interactions in biological systems: New discoveries and applications
    • Petsalaki E, Russell RB. Peptide-mediated interactions in biological systems: new discoveries and applications. Curr Opin Biotechnol 2008;19:344-350.
    • (2008) Curr Opin Biotechnol , vol.19 , pp. 344-350
    • Petsalaki, E.1    Russell, R.B.2
  • 3
    • 14644435825 scopus 로고    scopus 로고
    • Intrinsically unstructured proteins and their functions
    • Dyson HJ, Wright PE. Intrinsically unstructured proteins and their functions. Nat Rev Mol Cell Biol 2005;6:197-208.
    • (2005) Nat Rev Mol Cell Biol , vol.6 , pp. 197-208
    • Dyson, H.J.1    Wright, P.E.2
  • 4
    • 0036468397 scopus 로고    scopus 로고
    • Coupling of folding and binding for unstructured proteins
    • Dyson HJ, Wright PE. Coupling of folding and binding for unstructured proteins. Curr Opin Struct Biol 2002;12:54-60.
    • (2002) Curr Opin Struct Biol , vol.12 , pp. 54-60
    • Dyson, H.J.1    Wright, P.E.2
  • 6
    • 34249695447 scopus 로고    scopus 로고
    • Local structural disorder imparts plasticity on linear motifs
    • Fuxreiter M, Tompa P, Simon I. Local structural disorder imparts plasticity on linear motifs. Bioinformatics 2007;23:950-956.
    • (2007) Bioinformatics , vol.23 , pp. 950-956
    • Fuxreiter, M.1    Tompa, P.2    Simon, I.3
  • 9
    • 69949168453 scopus 로고    scopus 로고
    • A SPR strategy for high-throughput ligand screenings based on synthetic peptides mimicking a selected subdomain of the target protein: A proof of concept on HER2 receptor
    • Monfregola L, Vitale RM, Amodeo P, De Luca S. A SPR strategy for high-throughput ligand screenings based on synthetic peptides mimicking a selected subdomain of the target protein: a proof of concept on HER2 receptor. Bioorg Med Chem 2009;17:7015-7020.
    • (2009) Bioorg Med Chem , vol.17 , pp. 7015-7020
    • Monfregola, L.1    Vitale, R.M.2    Amodeo, P.3    De Luca, S.4
  • 10
    • 67349275522 scopus 로고    scopus 로고
    • Peptidic modulators of protein-protein interactions: Progress and challenges in computational design
    • Rubinstein M, Niv MY. Peptidic modulators of protein-protein interactions: progress and challenges in computational design. Biopolymers 2009;91:505-513.
    • (2009) Biopolymers , vol.91 , pp. 505-513
    • Rubinstein, M.1    Niv, M.Y.2
  • 11
    • 56449096489 scopus 로고    scopus 로고
    • Approved drug mimics of short peptide ligands from protein interaction motifs
    • Parthasarathi L, Casey F, Stein A, Aloy P, Shields DC. Approved drug mimics of short peptide ligands from protein interaction motifs. J Chem Inf Model 2008;48:1943-1948.
    • (2008) J Chem Inf Model , vol.48 , pp. 1943-1948
    • Parthasarathi, L.1    Casey, F.2    Stein, A.3    Aloy, P.4    Shields, D.C.5
  • 12
    • 65249171530 scopus 로고    scopus 로고
    • Design of protein-interaction specificity gives selective bZIP-binding peptides
    • Grigoryan G, Reinke AW, Keating AE. Design of protein-interaction specificity gives selective bZIP-binding peptides. Nature 2009;458: 859-864.
    • (2009) Nature , vol.458 , pp. 859-864
    • Grigoryan, G.1    Reinke, A.W.2    Keating, A.E.3
  • 14
    • 18144394737 scopus 로고    scopus 로고
    • Design and structure of peptide and peptidomimetic antagonists of protein-protein interaction
    • Sillerud LO, Larson RS. Design and structure of peptide and peptidomimetic antagonists of protein-protein interaction. Curr Protein Pept Sci 2005;6:151-169.
    • (2005) Curr Protein Pept Sci , vol.6 , pp. 151-169
    • Sillerud, L.O.1    Larson, R.S.2
  • 15
    • 57549106061 scopus 로고    scopus 로고
    • Peptides as protein binding site mimetics
    • Eichler J. Peptides as protein binding site mimetics. Curr Opin Chem Biol 2008;12:707-713.
    • (2008) Curr Opin Chem Biol , vol.12 , pp. 707-713
    • Eichler, J.1
  • 16
    • 64549115839 scopus 로고    scopus 로고
    • Protein structure prediction: When is it useful?
    • Zhang Y. Protein structure prediction: when is it useful? Curr Opin Struct Biol 2009;19:145-155.
    • (2009) Curr Opin Struct Biol , vol.19 , pp. 145-155
    • Zhang, Y.1
  • 17
    • 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
  • 18
    • 0037138380 scopus 로고    scopus 로고
    • Can we infer peptide recognition specificity mediated by SH3 domains?
    • Cesareni G, Panni S, Nardelli G, Castagnoli L. Can we infer peptide recognition specificity mediated by SH3 domains? FEBS Lett 2002; 513:38-44.
    • (2002) FEBS Lett , vol.513 , pp. 38-44
    • Cesareni, G.1    Panni, S.2    Nardelli, G.3    Castagnoli, L.4
  • 19
    • 26444604826 scopus 로고    scopus 로고
    • A flexible docking procedure for the exploration of peptide binding selectivity to known structures and homology models of PDZ domains
    • Niv MY, Weinstein H. A flexible docking procedure for the exploration of peptide binding selectivity to known structures and homology models of PDZ domains. J Am Chem Soc 2005;127:14072-14079.
    • (2005) J Am Chem Soc , vol.127 , pp. 14072-14079
    • Niv, M.Y.1    Weinstein, H.2
  • 20
    • 33646058599 scopus 로고    scopus 로고
    • Ab initio prediction of peptide-MHC binding geometry for diverse class i MHC allotypes
    • Bordner AJ, Abagyan R. Ab initio prediction of peptide-MHC binding geometry for diverse class I MHC allotypes. Proteins 2006;63: 512-526.
    • (2006) Proteins , vol.63 , pp. 512-526
    • Bordner, A.J.1    Abagyan, R.2
  • 21
    • 0030424581 scopus 로고    scopus 로고
    • Structure and function of the WW domain
    • 1996
    • Sudol M. Structure and function of the WW domain. Prog Biophys Mol Biol 1996;65:113-132, 1996.
    • (1996) Prog Biophys Mol Biol , vol.65 , pp. 113-132
    • Sudol, M.1
  • 23
    • 0026794581 scopus 로고
    • The three-dimensional structure of HLA-B27 at 2.1 A resolution suggests a general mechanism for tight peptide binding to MHC
    • Madden DR, Gorga JC, Strominger JL, Wiley DC. The three-dimensional structure of HLA-B27 at 2.1 A resolution suggests a general mechanism for tight peptide binding to MHC. Cell 1992;70:1035-1048.
    • (1992) Cell , vol.70 , pp. 1035-1048
    • Madden, D.R.1    Gorga, J.C.2    Strominger, J.L.3    Wiley, D.C.4
  • 24
    • 0032428378 scopus 로고    scopus 로고
    • Identification of protein-protein interfaces by decreased amide proton solvent accessibility
    • Mandell JG, Falick AM, Komives EA. Identification of protein-protein interfaces by decreased amide proton solvent accessibility. Proc Natl Acad Sci USA 1998;95:14705-14710.
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 14705-14710
    • Mandell, J.G.1    Falick, A.M.2    Komives, E.A.3
  • 27
    • 61449104961 scopus 로고    scopus 로고
    • Fragment-based identification of druggable hot spots of proteins using Fourier domain correlation techniques
    • Brenke R, Kozakov D, Chuang GY, Beglov D, Hall D, Landon MR, Mattos C, Vajda S. Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques. Bioinformatics 2009;25:621-627.
    • (2009) Bioinformatics , vol.25 , pp. 621-627
    • Brenke, R.1    Kozakov, D.2    Chuang, G.Y.3    Beglov, D.4    Hall, D.5    Landon, M.R.6    Mattos, C.7    Vajda, S.8
  • 28
    • 74549149999 scopus 로고    scopus 로고
    • Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure
    • Capra JA, Laskowski RA, Thornton JM, Singh M, Funkhouser TA. Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure. PLoS Comput Biol 2009;5: e1000585.
    • (2009) PLoS Comput Biol , vol.5
    • Capra, J.A.1    Laskowski, R.A.2    Thornton, J.M.3    Singh, M.4    Funkhouser, T.A.5
  • 29
    • 72749083363 scopus 로고    scopus 로고
    • Interaction of the disordered yersinia effector protein YopE with its cognate chaperone SycE
    • Hu X, Lee MS, Wallqvist A. Interaction of the disordered Yersinia effector protein YopE with its cognate chaperone SycE. Biochemistry 2009;48:11158-11160.
    • (2009) Biochemistry , vol.48 , pp. 11158-11160
    • Hu, X.1    Lee, M.S.2    Wallqvist, A.3
  • 30
    • 33748276474 scopus 로고    scopus 로고
    • Protein-ligand docking: Current status and future challenges
    • Sousa SF, Fernandes PA, Ramos MJ. Protein-ligand docking: current status and future challenges. Proteins 2006;65:15-26.
    • (2006) Proteins , vol.65 , pp. 15-26
    • Sousa, S.F.1    Fernandes, P.A.2    Ramos, M.J.3
  • 31
    • 53249111802 scopus 로고    scopus 로고
    • A new peptide docking strategy using a mean field technique with mutually orthogonal Latin square sampling
    • Arun Prasad P, Gautham N. A new peptide docking strategy using a mean field technique with mutually orthogonal Latin square sampling. J Comput Aided Mol Des 2008;22:815-829.
    • (2008) J Comput Aided Mol des , vol.22 , pp. 815-829
    • Arun Prasad, P.1    Gautham, N.2
  • 32
    • 0036084259 scopus 로고    scopus 로고
    • Efficient docking of peptides to proteins without prior knowledge of the binding site
    • Hetenyi C, van der Spoel D. Efficient docking of peptides to proteins without prior knowledge of the binding site. Protein Sci 2002; 11:1729-1737.
    • (2002) Protein Sci , vol.11 , pp. 1729-1737
    • Hetenyi, C.1    Van Der Spoel, D.2
  • 33
    • 4344589929 scopus 로고    scopus 로고
    • Modeling the structure of bound peptide ligands to major histocompatibility complex
    • Tong JC, Tan TW, Ranganathan S. Modeling the structure of bound peptide ligands to major histocompatibility complex. Protein Sci 2004;13:2523-2532.
    • (2004) Protein Sci , vol.13 , pp. 2523-2532
    • Tong, J.C.1    Tan, T.W.2    Ranganathan, S.3
  • 34
    • 30744455459 scopus 로고    scopus 로고
    • Structural prediction of peptides bound to MHC class I
    • Fagerberg T, Cerottini JC, Michielin O. Structural prediction of peptides bound to MHC class I. J Mol Biol 2006;356:521-546.
    • (2006) J Mol Biol , vol.356 , pp. 521-546
    • Fagerberg, T.1    Cerottini, J.C.2    Michielin, O.3
  • 35
    • 70350010160 scopus 로고    scopus 로고
    • All-atom monte carlo approach to proteinpeptide binding
    • Staneva I, Wallin S. All-Atom Monte Carlo Approach to ProteinPeptide Binding. J Mol Biol 2009;393:1118-1128.
    • (2009) J Mol Biol , vol.393 , pp. 1118-1128
    • Staneva, I.1    Wallin, S.2
  • 37
    • 71049127018 scopus 로고    scopus 로고
    • Identification of structural mechanisms of HIV-1 protease specificity using computational peptide docking: Implications for drug resistance
    • Chaudhury S, Gray JJ. Identification of structural mechanisms of HIV-1 protease specificity using computational peptide docking: implications for drug resistance. Structure 2009;17:1636-1648.
    • (2009) Structure , vol.17 , pp. 1636-1648
    • Chaudhury, S.1    Gray, J.J.2
  • 38
    • 3142745414 scopus 로고    scopus 로고
    • Structural mining self-consistent design on flexible protein-peptide docking and transferable binding affinity potential
    • Liu Z, Dominy BN, Shakhnovich EI. Structural mining: self-consistent design on flexible protein-peptide docking and transferable binding affinity potential. J Am Chem Soc 2004;126:8515-8528.
    • (2004) J Am Chem Soc , vol.126 , pp. 8515-8528
    • Liu, Z.1    Dominy, B.N.2    Shakhnovich, E.I.3
  • 39
    • 77951223167 scopus 로고    scopus 로고
    • DynaDock: A new molecular dynamics-based algorithm for protein-peptide docking including receptor flexibility
    • Antes I. DynaDock: A new molecular dynamics-based algorithm for protein-peptide docking including receptor flexibility. Proteins 2010;78:1084-1104.
    • (2010) Proteins , vol.78 , pp. 1084-1104
    • Antes, I.1
  • 40
    • 50649095790 scopus 로고    scopus 로고
    • Macromolecular modeling with rosetta
    • Das R, Baker D. Macromolecular modeling with rosetta. Annu Rev Biochem 2008;77:363-382.
    • (2008) Annu Rev Biochem , vol.77 , pp. 363-382
    • Das, R.1    Baker, D.2
  • 41
    • 0023430366 scopus 로고
    • Monte Carlo-minimization approach to the multiple-minima problem in protein folding
    • Li Z, Scheraga HA. Monte Carlo-minimization approach to the multiple-minima problem in protein folding. Proc Natl Acad Sci USA 1987;84:6611-6615.
    • (1987) Proc Natl Acad Sci USA , vol.84 , pp. 6611-6615
    • Li, Z.1    Scheraga, H.A.2
  • 44
    • 70349229596 scopus 로고    scopus 로고
    • Dynamic interactions of proteins in complex networks: A more structured view
    • Stein A, Pache RA, Bernado P, Pons M, Aloy P. Dynamic interactions of proteins in complex networks: a more structured view. FEBS J 2009;276:5390-5405.
    • (2009) FEBS J , vol.276 , pp. 5390-5405
    • Stein, A.1    Pache, R.A.2    Bernado, P.3    Pons, M.4    Aloy, P.5
  • 45
    • 0042710087 scopus 로고    scopus 로고
    • Computational alanine scanning to probe protein-protein interactions a novel approach to evaluate binding free energies
    • Massova I, Kollman PA. Computational alanine scanning to probe protein-protein interactions: a novel approach to evaluate binding free energies. J Am Chem Soc 1999;121:8133-8143.
    • (1999) J Am Chem Soc , vol.121 , pp. 8133-8143
    • Massova, I.1    Kollman, P.A.2
  • 46
    • 3242879771 scopus 로고    scopus 로고
    • Computational alanine scanning of protein-protein interfaces
    • Kortemme T, Kim DE, Baker D. Computational alanine scanning of protein-protein interfaces. Sci STKE 2004;2004:12.
    • (2004) Sci STKE 2004 , pp. 12
    • Kortemme, T.1    Kim, D.E.2    Baker, D.3
  • 47
    • 0036291145 scopus 로고    scopus 로고
    • Predicting changes in the stability of proteins and protein complexes a study of more than 1000 mutations
    • Guerois R, Nielsen JE, Serrano L. Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J Mol Biol 2002;320:369-387.
    • (2002) J Mol Biol , vol.320 , pp. 369-387
    • Guerois, R.1    Nielsen, J.E.2    Serrano, L.3
  • 48
    • 75849126506 scopus 로고    scopus 로고
    • The structural basis of peptide-protein binding strategies
    • London N, Movshovitz-Attias D, Schueler-Furman O. The structural basis of peptide-protein binding strategies. Structure 2009; 18: 188-199.
    • (2009) Structure , vol.18 , pp. 188-199
    • London, N.1    Movshovitz-Attias, D.2    Schueler-Furman, O.3
  • 49
    • 0014592230 scopus 로고
    • Computed circular dichroism spectra for the evaluation of protein conformation
    • Greenfield N, Fasman GD. Computed circular dichroism spectra for the evaluation of protein conformation. Biochemistry 1969;8:4108-4116.
    • (1969) Biochemistry , vol.8 , pp. 4108-4116
    • Greenfield, N.1    Fasman, G.D.2
  • 50
    • 45649084560 scopus 로고    scopus 로고
    • Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction
    • Smith CA, Kortemme T. Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction. J Mol Biol 2008;380:742-756.
    • (2008) J Mol Biol , vol.380 , pp. 742-756
    • Smith, C.A.1    Kortemme, T.2
  • 51
    • 0037406075 scopus 로고    scopus 로고
    • Cyclic coordinate descent: A robotics algorithm for protein loop closure
    • Canutescu AA, Dunbrack RL, Jr. Cyclic coordinate descent: a robotics algorithm for protein loop closure. Protein Sci 2003;12:963-972.
    • (2003) Protein Sci , vol.12 , pp. 963-972
    • Canutescu, A.A.1    Dunbrack Jr., R.L.2
  • 52
    • 68349104348 scopus 로고    scopus 로고
    • Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling
    • Mandell DJ, Coutsias EA, Kortemme T. Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling. Nat Methods 2009;6:551-552.
    • (2009) Nat Methods , vol.6 , pp. 551-552
    • Mandell, D.J.1    Coutsias, E.A.2    Kortemme, T.3
  • 54
    • 76649139794 scopus 로고    scopus 로고
    • Computational approaches to identifying and characterizing protein binding sites for ligand design
    • Henrich S, Salo-Ahen OM, Huang B, Rippmann FF, Cruciani G, Wade RC. Computational approaches to identifying and characterizing protein binding sites for ligand design. J Mol Recognit 2009;23:209-219.
    • (2009) J Mol Recognit , vol.23 , pp. 209-219
    • Henrich, S.1    Salo-Ahen, O.M.2    Huang, B.3    Rippmann, F.F.4    Cruciani, G.5    Wade, R.C.6
  • 55
    • 1842326139 scopus 로고    scopus 로고
    • Bayesian statistical analysis of protein side-chain rotamer preferences
    • Dunbrack RL, Jr., Cohen FE. Bayesian statistical analysis of protein side-chain rotamer preferences. Protein Sci 1997;6:1661-1681.
    • (1997) Protein Sci , vol.6 , pp. 1661-1681
    • Dunbrack Jr., R.L.1    Cohen, F.E.2
  • 56
    • 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
  • 57
    • 17744364070 scopus 로고    scopus 로고
    • Improved side-chain modeling for protein-protein docking
    • Wang C, Schueler-Furman O, Baker D. Improved side-chain modeling for protein-protein docking. Protein Sci 2005;14:1328-1339.
    • (2005) Protein Sci , vol.14 , pp. 1328-1339
    • Wang, C.1    Schueler-Furman, O.2    Baker, D.3
  • 58
    • 21644459373 scopus 로고    scopus 로고
    • Progress in protein-protein docking: Atomic resolution predictions in the capri experiment using RosettaDock with an improved treatment of side-chain flexibility
    • Schueler-Furman O, Wang C, Baker D. Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility. Proteins 2005;60:187-194.
    • (2005) Proteins , vol.60 , pp. 187-194
    • Schueler-Furman, O.1    Wang, C.2    Baker, D.3
  • 59
    • 84964389892 scopus 로고
    • Variable metric method for minimization
    • Davidon WC. Variable metric method for minimization. SIAM, Journal on Optim 1991;1:1-17.
    • (1991) SIAM Journal on Optim , vol.1 , pp. 1-17
    • Davidon, W.C.1
  • 60
    • 0034641749 scopus 로고    scopus 로고
    • Native protein sequences are close to optimal for their structures
    • Kuhlman. B, Baker D. Native protein sequences are close to optimal for their structures. Proc Natl Acad Sci USA 2000;97:10383-10388.
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 10383-10388
    • Kuhlman, B.1    Baker, D.2
  • 62
    • 0029619259 scopus 로고
    • Knowledge-based protein secondary structure assignment
    • Frishman D, Argos P. Knowledge-based protein secondary structure assignment. Proteins 1995;23:566-579.
    • (1995) Proteins , vol.23 , pp. 566-579
    • Frishman, D.1    Argos, P.2
  • 63
    • 1642540577 scopus 로고    scopus 로고
    • Evaluation of docking performance comparative data on docking algorithms
    • Kontoyianni M, McClellan LM, Sokol GS. Evaluation of docking performance: comparative data on docking algorithms. J Med Chem 2004;47:558-565.
    • (2004) J Med Chem , vol.47 , pp. 558-565
    • Kontoyianni, M.1    McClellan, L.M.2    Sokol, G.S.3
  • 64
    • 0033670439 scopus 로고    scopus 로고
    • MaxSub: An automated measure for the assessment of protein structure prediction quality
    • Siew N, Elofsson A, Rychlewski L, Fischer D. MaxSub: an automated measure for the assessment of protein structure prediction quality. Bioinformatics 2000;16:776-785.
    • (2000) Bioinformatics , vol.16 , pp. 776-785
    • Siew, N.1    Elofsson, A.2    Rychlewski, L.3    Fischer, D.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.