Information-driven modeling of protein-peptide complexes

Methods in Molecular Biology

Volumn 1268, Issue , 2015, Pages 221-239

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

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; BINDING SITE; COMPLEX FORMATION; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; MOLECULAR DOCKING; MOLECULAR DYNAMICS; MOLECULAR MODEL; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CONFORMATION; WEB BROWSER; ALGORITHMS; CHEMISTRY; METABOLISM; METHODS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MOLECULAR DOCKING SIMULATION; PROTEIN INTERACTION MAPPING; SOFTWARE;

PEPTIDES; PROTEIN BINDING; PROTEINS;

ALGORITHMS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MOLECULAR DOCKING SIMULATION; PEPTIDES; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; PROTEINS; SOFTWARE;

EID: 84955125857     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-2285-7_10     Document Type: Article

References (37)

1. Tzakos AG, Fuchs P, van Nuland NA 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
2. Musi V, Birdsall B, Fernandez-Ballester G 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
3. Huang BX, Kim H-Y (2006) Interdomain conformational changes in Akt activation revealed by chemical cross-linking and tandem mass spectrometry. Mol Cell Proteomics 5:1045–1053
4. Casares S, Ab E, Eshuis H et al (2007) The high-resolution NMR structure of the R21A Spc-SH3:P41 complex: understanding the determinants of binding affi nity by comparison with Abl-SH3. BMC Struct Biol 7:22
5. Gelis I, Bonvin AM, Keramisanou D et al (2007) Structural basis for signal-sequence recognition by the translocase motor SecA as determined by NMR. Cell 131:756–769
6. Schneider T, Kruse T, Wimmer R et al (2010) Plectasin, a fungal defensin, targets the bacterial cell wall precursor Lipid II. Science 328: 1168–1172
7. Wodak SJ, Janin J (1978) Computer analysis of protein-protein interaction. J Mol Biol 124:323–342
8. Strynadka NCJ, Eisenstein M, Katchalski- Katzir E et al (1996) Molecular docking programs successfully predict the binding of a β-lactamase inhibitory protein to TEM-1 β-lactamase. Nat Struct Mol Biol 3:233–239
9. Petsalaki E, Russell RB (2008) Peptidemediated interactions in biological systems: new discoveries and applications. Curr Opin Biotechnol 19:344–350
10. Stein A, Aloy P (2008) Contextual specifi city in peptide-mediated protein interactions. PLoS One 3:e2524
11. London N, Movshovitz-Attias D, Schueler- Furman O (2010) The structural basis of peptide- protein binding strategies. Structure 18:188–199
12. London N, Raveh B, Schueler-Furman O (2013) Peptide docking and structure-based characterization of peptide binding: from knowledge to know-how. Curr Opin Struct Biol 23:894–902
13. Petsalaki E, Stark A, Garcia-Urdiales E, Russell RB (2009) Accurate prediction of peptide binding sites on protein surfaces. PLoS Comput Biol 5:e1000335
14. Antes I (2010) DynaDock: a new molecular dynamics-based algorithm for protein-peptide docking including receptor fl exibility. Proteins 78:1084–1104
15. Raveh B, London N, Schueler-Furman O (2010) Sub-angstrom modeling of complexes between fl exible peptides and globular proteins. Proteins 78:2029–2040
16. Ben-Shimon A, Eisenstein M (2010) Computational mapping of anchoring spots on protein surfaces. J Mol Biol 402:259–277
17. Dagliyan O, Proctor EA, D’Auria KM et al (2011) Structural and dynamic determinants of protein-peptide recognition. Structure 19: 1837–1845
18. Raveh B, London N, Zimmerman L, Schueler- Furman O (2011) Rosetta FlexPepDock abinitio: simultaneous folding, docking and refi nement of peptides onto their receptors. PLoS One 6:e18934
19. Donsky E, Wolfson HJ (2011) PepCrawler: a fast RRT-based algorithm for high-resolution refi nement and binding affi nity estimation of peptide inhibitors. Bioinformatics 27: 2836–2842
20. Lavi A, Ngan CH, Movshovitz-Attias D et al (2013) Detection of peptide-binding sites on protein surfaces: the fi rst step toward the modeling and targeting of peptide-mediated interactions. Proteins 81:2096–2105
21. Verschueren E, Vanhee P, Rousseau F et al (2013) Protein-peptide complex prediction through fragment interaction patterns. Structure 21:789–797
22. De Vries SJ, van Dijk AD, Krzeminski M et al (2007) HADDOCK versus HADDOCK: new features and performance of HADDOCK2.0 on the CAPRI targets. Proteins 69:726–733
23. Trellet M, Melquiond ASJ, Bonvin AMJJ (2013) A unifi ed conformational selection and induced fi t approach to protein-peptide docking. PLoS One 8:e58769
24. 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
25. Brünger AT, Adams PD, Clore GM et al (1998) Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr 54:905–921
26. Brunger AT (2007) Version 1.2 of the crystallography and NMR system. Nat Protoc 2: 2728–2733
27. Jorgensen WL, Tirado-Rives J (1988) The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. J Am Chem Soc 110:1657–1666
28. Moreira IS, Fernandes PA, Ramos MJ (2010) Protein-protein docking dealing with the unknown. J Comput Chem 31:317–342
29. Lensink MF, Wodak SJ (2013) Docking, scoring, and affi nity prediction in CAPRI. Proteins 81:2082–2095
30. Diella F, Haslam N, Chica C et al (2008) Understanding eukaryotic linear motifs and their role in cell signaling and regulation. Front Biosci 13:6580–6603
31. Van Dijk ADJ, Boelens R, Bonvin AMJJ (2005) Data-driven docking for the study of biomolecular complexes. FEBS J 272:293–312
32. Melquiond ASJ, Bonvin AMJJ (2010) Datadriven docking: using external information to spark the biomolecular rendez-vous. In: Protein-protein complexes: analysis, modelling and drug design. Edited by M. Zacharrias, Imperial College Press, London, p 183–209
33. Jorgensen WL, Chandrasekhar J, Madura JD et al (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926–935
34. Janin J, Henrick K, Moult J 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. Schrodinger L (2010) The PyMOL molecular graphics system, version 1.3r1
37. Claude J-B, Suhre K, Notredame C et al (2004) CaspR: a web server for automated molecular replacement using homology modelling. Nucleic Acids Res 32:W606–W609