A Unified Conformational Selection and Induced Fit Approach to Protein-Peptide Docking

PLoS ONE

Volumn 8, Issue 3, 2013, Pages

  Trellet, Mikael ^a,b   Melquiond, Adrien S J ^a   Bonvin, Alexandre M J J ^a  

^a UTRECHT UNIVERSITY   (Netherlands)

^b UFR 919 Laboratoire d'Informatique Pour la Mécanique et les Sciences de l'Ingénieur   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA HELIX; ARTICLE; BINDING SITE; CLUSTER ANALYSIS; CLUSTER BASED SCORING; CONFORMATIONAL SELECTION; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; CRYSTAL STRUCTURE; EXTENDED CONFORMATION; MOLECULAR DOCKING; POLYPROLINE II CONFORMATION; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN PEPTIDE DOCKING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; QUALITY CONTROL; SCORING SYSTEM;

BENCHMARKING; CLUSTER ANALYSIS; DATABASES, PROTEIN; MOLECULAR DOCKING SIMULATION; PEPTIDES; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEINS; SUBSTRATE SPECIFICITY;

EID: 84874871709     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0058769     Document Type: Article

References (59)

1. Petsalaki E, Russell RB, (2008) Peptide-mediated interactions in biological systems: new discoveries and applications. Curr Opin Biotechnol 19: 344-350.
2. Bordner AJ, Abagyan R, (2006) Ab initio prediction of peptide-MHC binding geometry for diverse class I MHC allotypes. Proteins 63: 512-526.
3. Hahn S, Kim D, (2012) Transient protein-protein interaction of the SH3-peptide complex via closely located multiple binding sites. PLoS One 7: e32804.
4. Lee HJ, Zheng JJ, (2010) PDZ domains and their binding partners: structure, specificity, and modification. Cell Commun Signal 8: 8.
5. Naider F, Anglister J, (2009) Peptides in the treatment of AIDS. Curr Opin Struct Biol 19: 473-482.
6. Vaara M, (2009) New approaches in peptide antibiotics. Curr Opin Pharmacol 9: 571-576.
7. Fjell CD, Hiss JA, Hancock REW, Schneider G, (2012) Designing antimicrobial peptides: form follows function. Nature Reviews Drug Discovery 11: 37-51.
8. Wimley WC, Hristova K, (2011) Antimicrobial peptides: successes, challenges and unanswered questions. J Membr Biol 239: 27-34.
9. Maes M, Loyter A, Friedler A, (2012) Peptides that inhibit HIV-1 integrase by blocking its protein-protein interactions. FEBS J 279: 2795-2809.
10. Madine J, Doig AJ, Middleton DA, (2008) Design of an N-methylated peptide inhibitor of alpha-synuclein aggregation guided by solid-state NMR. J Am Chem Soc 130: 7873-7881.
11. Yamin G, Ruchala P, Teplow DB, (2009) A peptide hairpin inhibitor of amyloid beta-protein oligomerization and fibrillogenesis. Biochemistry 48: 11329-11331.
12. Frydman-Marom A, Shaltiel-Karyo R, Moshe S, Gazit E, (2011) The generic amyloid formation inhibition effect of a designed small aromatic beta-breaking peptide. Amyloid 18: 119-127.
13. Svensen N, Walton JG, Bradley M, (2012) Peptides for cell-selective drug delivery. Trends Pharmacol Sci 33: 186-192.
14. Shtatland T, Guettler D, Kossodo M, Pivovarov M, Weissleder R, (2007) PepBank-a database of peptides based on sequence text mining and public peptide data sources. BMC Bioinformatics 8: 280.
15. Vanhee P, Reumers J, Stricher F, Baeten L, Serrano L, et al. (2009) PepX: a structural database of non-redundant protein-peptide complexes. Nucleic Acids Res 38: D545-551.
16. Rubinstein M, Niv MY, (2009) Peptidic modulators of protein-protein interactions: progress and challenges in computational design. Biopolymers 91: 505-513.
17. Cesareni G, Panni S, Nardelli G, Castagnoli L, (2002) Can we infer peptide recognition specificity mediated by SH3 domains? FEBS Lett 513: 38-44.
18. Niv MY, Weinstein H, (2005) A flexible docking procedure for the exploration of peptide binding selectivity to known structures and homology models of PDZ domains. J Am Chem Soc 127: 14072-14079.
19. Zhou Y, Abagyan R, (1998) How and why phosphotyrosine-containing peptides bind to the SH2 and PTB domains. Fold Des 3: 513-522.
20. Stigler RD, Hoffmann B, Abagyan R, Schneider-Mergener J, (1999) Soft docking an L and a D peptide to an anticholera toxin antibody using internal coordinate mechanics. Structure 7: 663-670.
21. Hetenyi C, van der Spoel D, (2002) Efficient docking of peptides to proteins without prior knowledge of the binding site. Protein Sci 11: 1729-1737.
22. Dagliyan O, Proctor EA, D'Auria KM, Ding F, Dokholyan NV, (2011) Structural and dynamic determinants of protein-peptide recognition. Structure 19: 1837-1845.
23. Raveh B, London N, Schueler-Furman O, (2010) Sub-angstrom modeling of complexes between flexible peptides and globular proteins. Proteins 78: 2029-2040.
24. London N, Raveh B, Cohen E, Fathi G, Schueler-Furman O, (2011) Rosetta FlexPepDock web server-high resolution modeling of peptide-protein interactions. Nucleic Acids Res 39: W249-253.
25. Raveh B, London N, Zimmerman L, Schueler-Furman O, (2011) Rosetta FlexPepDock ab-initio: simultaneous folding, docking and refinement of peptides onto their receptors. PLoS One 6: e18934.
26. Dominguez C, Boelens R, Bonvin AM, (2003) HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J Am Chem Soc 125: 1731-1737.
27. de Vries SJ, van Dijk AD, Krzeminski M, van Dijk M, Thureau A, et al. (2007) HADDOCK versus HADDOCK: new features and performance of HADDOCK2.0 on the CAPRI targets. Proteins 69: 726-733.
28. Tzakos AG, Fuchs P, van Nuland NA, Troganis A, Tselios T, et al. (2004) NMR and molecular dynamics studies of an autoimmune myelin basic protein peptide and its antagonist: structural implications for the MHC II (I-Au)-peptide complex from docking calculations. Eur J Biochem 271: 3399-3413.
29. Musi V, Birdsall B, Fernandez-Ballester G, Guerrini R, Salvatori S, et al. (2006) New approaches to high-throughput structure characterization of SH3 complexes: the example of Myosin-3 and Myosin-5 SH3 domains from S. cerevisiae. Protein Sci 15: 795-807.
30. Gelis I, Bonvin AM, Keramisanou D, Koukaki M, Gouridis G, et al. (2007) Structural basis for signal-sequence recognition by the translocase motor SecA as determined by NMR. Cell 131: 756-769.
31. Schneider T, Kruse T, Wimmer R, Wiedemann I, Sass V, et al. (2010) Plectasin, a fungal defensin, targets the bacterial cell wall precursor Lipid II. Science 328: 1168-1172.
32. Casares S, Ab E, Eshuis H, Lopez-Mayorga O, van Nuland NA, et al. (2007) The high-resolution NMR structure of the R21A Spc-SH3: P41 complex: understanding the determinants of binding affinity by comparison with Abl-SH3. BMC Struct Biol 7: 22.
33. Karaca E, Melquiond AS, de Vries SJ, Kastritis PL, Bonvin AM, (2010) Building macromolecular assemblies by information-driven docking: introducing the HADDOCK multibody docking server. Mol Cell Proteomics 9: 1784-1794.
34. Janin J, Henrick K, Moult J, Eyck LT, Sternberg MJ, et al. (2003) CAPRI: a Critical Assessment of PRedicted Interactions. Proteins 52: 2-9.
35. Lensink MF, Wodak SJ, (2010) Docking and scoring protein interactions: CAPRI 2009. Proteins 78: 3073-3084.
36. de Vries SJ, van Dijk M, Bonvin AM, (2010) The HADDOCK web server for data-driven biomolecular docking. Nat Protoc 5: 883-897.
37. Fischer E, (1894) Einfluss der configuration auf die Wirkung der enzyme. Berichte der Deutchen Chemischen Gesellschaft 27: 2985-2993.
38. Koshland DE Jr, (1959) Enzyme flexibility and enzyme action. J Cell Comp Physiol 54: 245-258.
39. Kumar S, Ma B, Tsai CJ, Sinha N, Nussinov R, (2000) Folding and binding cascades: dynamic landscapes and population shifts. Protein Sci 9: 10-19.
40. Rubin MM, Changeux JP, (1966) On the nature of allosteric transitions: implications of non-exclusive ligand binding. J Mol Biol 21: 265-274.
41. Monod J, Wyman J, Changeux JP, (1965) On the Nature of Allosteric Transitions: A Plausible Model. J Mol Biol 12: 88-118.
42. Hammes GG, Chang YC, Oas TG, (2009) Conformational selection or induced fit: a flux description of reaction mechanism. Proc Natl Acad Sci U S A 106: 13737-13741.
43. Csermely P, Palotai R, Nussinov R, (2010) Induced fit, conformational selection and independent dynamic segments: an extended view of binding events. Trends Biochem Sci 35: 539-546.
44. Changeux JP, Edelstein S, (2011) Conformational selection or induced fit? 50 years of debate resolved. F1000 Biol Rep 3: 19.
45. Weikl TR, von Deuster C, (2009) Selected-fit versus induced-fit protein binding: kinetic differences and mutational analysis. Proteins 75: 104-110.
46. London N, Movshovitz-Attias D, Schueler-Furman O, (2010) The structural basis of peptide-protein binding strategies. Structure 18: 188-199.
47. Diella F, Haslam N, Chica C, Budd A, Michael S, et al. (2008) Understanding eukaryotic linear motifs and their role in cell signaling and regulation. Front Biosci 13: 6580-6603.
48. Pons C, D'Abramo M, Svergun DI, Orozco M, Bernado P, et al. (2010) Structural characterization of protein-protein complexes by integrating computational docking with small-angle scattering data. J Mol Biol 403: 217-230.
49. Antes I, (2010) DynaDock: A new molecular dynamics-based algorithm for protein-peptide docking including receptor flexibility. Proteins 78: 1084-1104.
50. Karaca E, Bonvin AM, (2011) A multidomain flexible docking approach to deal with large conformational changes in the modeling of biomolecular complexes. Structure 19: 555-565.
51. Stein A, Aloy P, (2008) Contextual specificity in peptide-mediated protein interactions. PLoS One 3: e2524.
52. Trabuco LG, Lise S, Petsalaki E, Russell RB, (2012) PepSite: prediction of peptide-binding sites from protein surfaces. Nucleic Acids Res 40: W423-427.
53. Ben-Shimon A, Eisenstein M, (2010) Computational mapping of anchoring spots on protein surfaces. J Mol Biol 402: 259-277.
54. Heinig M, Frishman D, (2004) STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins. Nucleic Acids Res 32: W500-502.
55. Hubbard SJ, Thornton JM (1993) NACCESS. 2.1.1 ed. Manchester.
56. Schrodinger LLC (2010) The PyMOL Molecular Graphics System, Version 1.3r1.
57. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, et al. (2000) The Protein Data Bank. Nucleic Acids Res 28: 235-242.
58. Wassenaar TA, van Dijk M, Loureiro-Ferreira N, van der Schot G, de Vries SJ, et al. (2011) WeNMR: structural biology on the grid. CEUR. [1]-[8] %@ 1613-0073.
59. Mendez R, Leplae R, De Maria L, Wodak SJ, (2003) Assessment of blind predictions of protein-protein interactions: current status of docking methods. Proteins 52: 51-67.