Flexible protein-protein docking

Current Opinion in Structural Biology

Volumn 16, Issue 2, 2006, Pages 194-200

  Bonvin, Alexandre MJJ ^a  

^a UTRECHT UNIVERSITY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

DOCKING PROTEIN;

COMPLEX FORMATION; COMPUTER MODEL; CONFORMATIONAL TRANSITION; HARDNESS; MOTION; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; REVIEW; SURFACE PROPERTY;

BINDING SITES; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN INTERACTION MAPPING; PROTEINS;

EID: 33645961330     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.sbi.2006.02.002     Document Type: Review

References (51)

1. Méndez R., Leplae R., Lensink M.F., and Wodak S.J. Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures. Proteins 60 (2005) 150-169. This paper gives an overview of the current state of the art in protein-protein docking, as assessed from recent rounds of the blind docking experiment CAPRI. The characteristics (see in particular Table III) and performance of the various docking approaches are discussed, together with aspects of flexibility treatment.
2. Brooijmans N., and Kuntz I.D. Molecular recognition and docking algorithms. Annu Rev Biophys Biomol Struct 32 (2003) 335-373
3. Erickson J.A., Jalaie M., Robertson D.H., Lewis R.A., and Vieth M. Lessons in molecular recognition: the effects of ligand and protein flexibility on molecular docking accuracy. J Med Chem 47 (2004) 45-55
4. O'Hearn S.D., Kusalik A.J., and Angel J.F. MolCom: a method to compare protein molecules based on 3-D structural and chemical similarity. Protein Eng 16 (2003) 169-178
5. Jacobs D.J., Rader A.J., Kuhn L.A., and Thorpe M.F. Protein flexibility predictions using graph theory. Proteins 44 (2001) 150-165
6. Tirion M.M. Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys Rev Lett 77 (1996) 1905-1908
7. de Groot B.L., van Aalten D.M., Scheek R.M., Amadei A., Vriend G., and Berendsen H.J. Prediction of protein conformational freedom from distance constraints. Proteins 29 (1997) 240-251
8. Alexandrov V., Lehnert U., Echols N., Milburn D., Engelman D., and Gerstein M. Normal modes for predicting protein motions: a comprehensive database assessment and associated Web tool. Protein Sci 14 (2005) 633-643
9. Barrett C.P., Hall B.A., and Noble M.E.M. Dynamite: a simple way to gain insight into protein motions. Acta Crystallogr D Biol Crystallogr 60 (2004) 2280-2287
10. Tai K. Conformational sampling for the impatient. Biophys Chem 107 (2004) 213-220
11. Lei M., Zavodszky M.I., Kuhn L.A., and Thorpe M.F. Sampling protein conformations and pathways. J Comput Chem 25 (2004) 1133-1148
12. Suhre K., and Sanejouand Y.-H. ElNémo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Res 32 (2004) W610-W614
13. Barrett C.P., and Noble M.E.M. Dynamite extended: two new services to simplify protein dynamic analysis. Bioinformatics 21 (2005) 3174-3175
14. Palma P.N., Krippahl L., Wampler J.E., and Moura J.J.G. BiGGER: a new (soft) docking algorithm for predicting protein interactions. Proteins 39 (2000) 372-384
15. Heifetz A., and Eisenstein M. Effect of local shape modifications of molecular surfaces on rigid-body protein-protein docking. Protein Eng 16 (2003) 179-185
16. Ma B., Elkayam T., Wolfson H., and Nussinov R. Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces. Proc Natl Acad Sci USA 100 (2003) 5772-5777
17. Smith G.R., Sternberg M.J.E., and Bates P.A. 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 347 (2005) 1077-1101. MD simulations in water of a set of 41 proteins are used to analyze the impact of flexibility on docking using 3D-Dock. Various approaches are compared: grid smoothing and ensemble docking from conformations obtained by clustering or principal components analysis. Grid smoothing does not lead to improvements, whereas ensemble docking is shown to enhance the results. An interesting observation is that interface core residues show a tendency to be less mobile than the remainder of the surface.
18. Rajamani D., Thiel S., Vajda S., and Camacho C.J. Anchor residues in protein-protein interactions. Proc Natl Acad Sci USA 101 (2004) 11287-11292. MD simulations in water of a set of 11 proteins in their unbound form reveal that the sidechains of residues critical to complex formation, the so-called hot-spot or anchor residues, sample bound conformations during the simulations. These usually correspond to surface sidechains that bury the largest surface area upon complex formation.
19. Li X., Keskin O., Ma B., Nussinov R., and 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 344 (2004) 781-795
20. Dominguez C., Bonvin A.M.J.J., Winkler G.S., van Schaik F.M.A., Timmers H.T.M., and Boelens R. Structural model of the UbcH5B/CNOT4 complex revealed by combining NMR, mutagenesis, and docking approaches. Structure 12 (2004) 633-644
21. Grünberg R., Leckner J., and Nilges M. Complementarity of structure ensembles in protein-protein binding. Structure 12 (2004) 2125-2136. Ensembles of structures obtained from MD simulations with restraints along the principal components of motion are used for cross docking with HEX. The results for a set of 17 complexes indicate improved performance in terms of the number of near-native solutions, but a more difficult scoring; various combinations of starting structures can lead to high scoring solutions. The recognition process is discussed in terms of conformation selection.
22. Smith G.R., Fitzjohn P.W., Page C.S., and Bates P.A. Incorporation of flexibility into rigid-body docking: applications in rounds 3-5 of CAPRI. Proteins 60 (2005) 263-268
23. Camacho C.J. Modeling side-chains using molecular dynamics improve recognition of binding region in CAPRI targets. Proteins 60 (2005) 245-251
24. van Dijk A.D.J., de Vries S.J., Dominguez C., Chen H., Zhou H.-X., and Bonvin A.M.J.J. Data-driven docking: HADDOCK's adventures in CAPRI. Proteins 60 (2005) 232-238. Successful CAPRI predictions were obtained using a multilevel representation of flexibility: ensemble docking from conformations obtained by short MD simulations is combined with subsequent explicit sidechain and backbone flexible refinement by torsion angle MD. Flexibility is shown to have the most impact on the fraction of native contacts.
25. Zavodszky M.I., Lei M., Thorpe M.F., Day A.R., and Kuhn L.A. Modeling correlated main-chain motions in proteins for flexible molecular recognition. Proteins 57 (2004) 243-261. The flexibility of proteins is analyzed using the geometry-based approach FIRST, combined with conformational sampling with ROCK. The resulting conformations are subsequently used in ensemble docking. This approach is applied to the docking of the cyclophilin A-cyclosporin complex.
26. Amadei A., Linssen A.B.M., and Berendsen H.J.C. Essential dynamics of proteins. Proteins 17 (1994) 412-425
27. Mustard D., and Ritchie D.W. Docking essential dynamics eigenstructures. Proteins 60 (2005) 269-274
28. Li L., and Weng Z. RDOCK: refinement of rigid-body protein docking predictions. Proteins 53 (2003) 693-707
29. Fernández-Recio J., Totrov M., and Abagyan R. ICM-DISCO docking by global energy optimization with fully flexible side-chains. Proteins 52 (2003) 113-117
30. Dominguez C., Boelens R., and Bonvin A.M.J.J. HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J Am Chem Soc 125 (2003) 1731-1737
31. Zacharias M. Protein-protein docking with a reduced protein model accounting for side-chain flexibility. Protein Sci 12 (2003) 1271-1282
32. Zacharias M. Rapid protein-ligand docking using soft modes from molecular dynamics simulations to account for protein deformability: binding of FK506 to FKBP. Proteins 54 (2004) 759-767
33. Gray J.J., Moughon S., Wang C., Schueler-Furman O., Kuhlman B., Rohl C.A., and Baker D. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Biol 331 (2003) 281-299
34. Wang C., Schueler-Furman O., and Baker D. Improved side-chain modeling for protein-protein docking. Protein Sci 14 (2005) 1328-1339. RosettaDock's flexible sidechain modeling based on backbone-dependent rotamer libraries is extended by off-rotamer optimization using short EM steps during the MC search. This is shown to improve both accuracy and discrimination between native and non-native solutions.
35. Jiang L., Kuhlman B., Kortemme T.A., and Baker D. A "solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfaces. Proteins 58 (2005) 893-904
36. Schueler-Furman O., Wang C., and 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 60 (2005) 187-194
37. Daily M.D., Masica D., Sivasubramanian A., Somarouthu S., and Gray J.J. CAPRI rounds 3-5 reveal promising successes and future challenges for RosettaDock. Proteins 60 (2005) 181-186
38. Liu Z., Dominy B.N., and Shakhnovich E.I. Structural mining: self-consistent design on flexible protein-peptide docking and transferable binding affinity potential. J Am Chem Soc 126 (2004) 8515-8528
39. Fitzjohn P.W., and Bates P.A. Guided docking: first step to locate potential binding sites. Proteins 52 (2003) 28-32
40. Ehrlich L.P., Nilges M., and Wade R.C. The impact of protein flexibility on protein-protein docking. Proteins 58 (2005) 126-133
41. May A., and Zacharias M. Accounting for global protein deformability during protein-protein and protein-ligand docking. Biochim Biophys Acta 1754 (2005) 225-231. This review addresses aspects of protein deformability in docking. It demonstrates for both protein-ligand and protein-protein docking how displacements along pre-calculated collective degrees of motion can be introduced as additional degrees of freedom during docking.
42. Tama F., Miyashita O., and Brooks III C.L. Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network mode analysis. J Mol Biol 337 (2004) 985-999
43. Hinsen K., Reuter N., Navaza J., Stokes D.L., and Lacapère J.-J. Normal mode-based fitting of atomic structure into electron density maps: application to sarcoplasmic reticulum Ca-ATPase. Biophys J 88 (2005) 818-827
44. Lindahl E., and Delarue M. Refinement of docked protein-ligand and protein-DNA structures using low frequency normal mode amplitude optimization. Nucleic Acids Res 33 (2005) 4496-4506
45. Bastard K., Thureau A., Lavery R., and Prévost C. Docking macromolecules with flexible segments. J Comput Chem 24 (2003) 1910-1920
46. Bastard K, Prévost C, Zacharias M: Accounting for loop flexibility during protein-protein docking. Proteins 2005, in press. The problem of loop flexibility in docking is addressed using a multicopy mean-field approach implemented in ATTRACT. The weight of each loop copy is adapted during docking by rigid-body EM based on its interaction energy following a Boltzmann criterion.
47. Rohl C.A., Strauss C.E.M., Chivian D., and Baker D. Modeling structurally variable regions in homologous proteins with Rosetta. Proteins 55 (2004) 656-677
48. Graille M., Heurgué-Hamard V., Champ S., Mora L., Scrima N., Ulryck N., van Tilbeurgh H., and Buckingham R.H. Molecular basis for bacterial class I release factor methylation by PrmC. Mol Cell 20 (2005) 917-927
49. Schneidman-Duhovny D., Inbar Y., Nussinov R., and Wolfson H.J. Geometry-based flexible and symmetric protein docking. Proteins 60 (2005) 224-231. The challenge of dealing with large conformational changes in docking is addressed by dissecting proteins into subdomains after having identified hinge regions. Fast pairwise docking of subdomains is then performed by surface patch matching using PatchDock and the resulting solutions are combined to reconstruct the complete complex based on a graph theory algorithm. This approach, implemented in FlexDock, is extremely fast and was able to reproduce the large conformational changes that occur in calmodulin upon peptide binding.
50. Wolfson H.J., Shatsky M., Schneidman-Duhovny D., Dror O., Shulman-Peleg A., Ma B., and Nussinov R. From structure to function: methods and applications. Curr Protein Pept Sci 6 (2005) 171-183. This review discusses, among others, methods to identify flexible and hinge regions in proteins, and their application to hinge-based flexible docking. The described approaches are applied to the modeling of the s-Src protein kinase complexed with a proline-rich peptide.
51. Ben-Zeev E., Kowalsman N., Ben-Shimon A., Segal D., Atarot T., Noivirt O., Shay T., and Eisenstein M. Docking to single-domain and multiple-domain proteins: old and new challenges. Proteins 60 (2005) 195-201