Insights into protein flexibility: The relationship between normal modes and conformational change upon protein-protein docking

Proceedings of the National Academy of Sciences of the United States of America

Volumn 105, Issue 30, 2008, Pages 10390-10395

  Dobbins, Sara E ^a   Lesk, Victor I ^a   Sternberg, Michael J E ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

Conformational selection; Elastic network model; Induced fit; Protein interactions; Protein recognition

Indexed keywords

DOCKING PROTEIN;

ARTICLE; COMPLEX FORMATION; CONFORMATIONAL TRANSITION; MOTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION;

COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; MODELS, STATISTICAL; MOLECULAR CONFORMATION; OSCILLOMETRY; PERIPLASMIC PROTEINS; PLIABILITY; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN INTERACTION MAPPING; PROTEINS;

EID: 48749126860     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0802496105     Document Type: Article

References (55)

1. Betts MJ, Sternberg MJE (1999) An analysis of conformational changes on protein-protein association: Implications for predictive docking. Protein Eng 12:271-283.
2. Huber R, Bennett WS, Jr (1983) Functional significance of flexibility in proteins. Biopolymers 22:261-279.
3. Fischer E (1894) Einfluss der Configuration auf die Wirkung der Enzyme. Ber Dtsch Chem Ges 27:3189-3232.
4. Koshland DE (1958) Application of a theory of enzyme specificity to protein synthesis. Proc Natl Acad Sci USA 44:98-104.
5. Henzler-Wildman KA, et al. (2007) A hierarchy of timescales in protein dynamics is linked to enzyme catalysis. Nature 450:913-916.
6. Gutteridge A, Thornton JM (2005) Conformational changes observed in enzyme crystal structures upon substrate binding. J Mol Biol 346:21-28.
7. Watt ED, Shimada H, Kovrigin EL, Loria JP (2007) The mechanism of rate-limiting motions in enzyme function. Proc Natl Acad Sci USA 104:11981-11986.
8. 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.
9. Grunberg R, Nilges M, Leckner J (2006) Flexibility and conformational entropy in protein-protein binding. Structure (London) 14:683-693.
10. Mintseris J, et al. (2005) Protein-protein docking benchmark 2.0: An update. Proteins 60:214-216.
11. Fernandez-Recio J, Totrov M, Abagyan R (2002) Soft protein-protein docking in internal coordinates. Protein Sci 11:280-291.
12. Goldstein H (2002) Classical Mechanics (Addison-Wesley, Reading, MA).
13. Moore WH, Krimm S (1976) Vibrational analysis of peptides, polypeptides, and proteins. II. beta-poly(L-alanine) and beta-poly(L-anaylglycine). Biopolymers 15:2465-2483.
14. Tasumi M, Takeuchi H, Ataka S, Dwivedi AM, Krimm S (1982) Normal vibrations of proteins: glucagon. Biopolymers 21:711-714.
15. Brooks B, Karplus M (1983) Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor. Proc Natl Acad Sci USA 80:6571-6575.
16. Noguti T, Go N (1982) Collective variable description of small-amplitude conformational fluctuations in a globular protein. Nature 296:776-778.
17. Levitt M, Sander C, Stern PS (1983) Normal-mode dynamics of a protein: bovine pancreatic trypsin inhibitor. Int J Quant Chem Quant Biol Symp 10:181-199.
18. Tirion MM (1996) Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys Rev Lett 77:1905-1908.
19. Elber R, Karplus M (1987) Multiple conformational states of proteins: A molecular dynamics analysis of myoglobin. Science 235:318-321.
20. Frauenfelder H, Parak F, Young RD (1988) Conformational substates in proteins. Annu Rev Biophys Biophys Chem 17:451-479.
21. Kitao A, Hayward S, Go N (1998) Energy landscape of a native protein: Jumping-among-minima model. Proteins 33:496-517.
22. Alexandrov V, et al. (2005) Normal modes for predicting protein motions: A comprehensive database assessment and associated web tool. Protein Sci 14:633-643.
23. Hinsen K (1998) Analysis of domain motions by approximate normal mode calculations. Proteins 33:417-429.
24. Delarue M, Sanejouand YH (2002) Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: the elastic network model. J Mol Biol 320:1011-1024.
25. Hayward S, Kitao A, Berendsen HJ (1997) Model-free methods of analyzing domain motions in proteins from simulation: a comparison of normal mode analysis and molecular dynamics simulation of lysozyme. Proteins 27:425-437.
26. Gibrat JF, Go N (1990) Normal mode analysis of human lysozyme: study of the relative motion of the two domains and characterization of the harmonic motion. Proteins 8:258-279.
27. Kong Y, Ma J, Karplus M, Lipscomb WN (2006) The allosteric mechanism of yeast chorismate mutase: A dynamic analysis. J Mol Biol 356:237-247.
28. Levitt M, Sander C, Stern PS (1985) Protein normal-mode dynamics: Trypsin inhibitor, crambin, ribonuclease and lysozyme. J Mol Biol 181:423-447.
29. Marques O, Sanejouand YH (1995) Hinge-bending motion in citrate synthase arising from normal mode calculations. Proteins 23:557-560.
30. Shrivastava IH, Bahar I (2006) Common mechanism of pore opening shared by five different potassium channels. Biophys J 90:3929-3940.
31. Gerstein M, Krebs W (1998) A database of macromolecular motions. Nucleic Acids Res 26:4280-4290.
32. Tama F, Sanejouand YH (2001) Conformational change of proteins arising from normal mode calculations. Protein Eng 14:1-6.
33. Krebs WG, et al. (2002) Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic. Proteins 48:682-695.
34. Tobi D, Bahar I (2005) Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state. Proc Natl Acad Sci USA 102:18908-18913.
35. Lindahl E, Delarue M (2005) Refinement of docked protein-ligand and protein-DNA structures using low frequency normal mode amplitude optimization. Nucleic Acids Res 33:4496-4506.
36. May A, Zacharias M (2008) Energy minimization in low-frequency normal modes to efficiently allow for global flexibility during systematic protein-protein docking. Proteins 70:794-809.
37. Cavasotto CN, Kovacs JA, Abagyan RA (2005) Representing receptor flexibility in ligand docking through relevant normal modes. J Am Chem Soc 127:9632-9640.
38. Schneidman-Duhovny D, Inbar Y, Nussinov R, Wolfson HJ (2005) Geometry-based flexible and symmetric protein docking. Proteins 60:224-231.
39. Ming D, Cohn JD, Wall ME (2008) Fast dynamics perturbation analysis for prediction of protein functional sites. BMC Struct Biol 8:5.
40. Cui Q, Bahar I (2006) Normal Mode Analysis: Theory and Applications to Biological and Chemical Systems (Chapman & Hall, London).
41. Brooks B, Janezic D, Karplus M (1995) Harmonic analysis of large systems. I. Methodology. J Comput Chem 16:1522-1542.
42. Califano S (1976) Vibrational States (Wiley Interscience, New York).
43. Hayward S, Berendsen HJ (1998) Systematic analysis of domain motions in proteins from conformational change: New results on citrate synthase and T4 lysozyme. Proteins 30:144-154.
44. Islam SA, Luo J, Sternberg MJE (1995) Identification and analysis of domains in proteins. Protein Eng 8:513-525.
45. Smith GR, Sternberg MJE, Bates PA (2005) 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 347:1077-1101.
46. Rajamani D, Thiel S, Vajda S, Camacho CJ (2004) Anchor residues in protein-protein interactions. Proc Natl Acad Sci USA 101:11287-11292.
47. Mustard D, Ritchie DW (2005) Docking essential dynamics eigenstructures. Proteins Struct Funct Bioinf 60:269-274.
48. Janin J (2002) Welcome to CAPRI: a critical assessment of predicted interactions. Proteins Struct Funct Genetics 47:257.
49. Luque I, Freire E (2000) Structural stability of binding sites: Consequences for binding affinity and allosteric effects. Proteins Suppl 4:63-71.
50. Yang LW, Bahar I (2005) Coupling between catalytic site and collective dynamics: A requirement for mechanochemical activity of enzymes. Structure (London) 13:893-904.
51. Li X, Keskin O, Ma B, Nussinov R, Liang J (2004) Protein-protein interactions: Hot spots and structurally conserved residues often locate in complemented pockets that preorganized in the unbound states: Implications for docking. J Mol Biol 344:781-795.
52. Suhre K, Sanejouand Y-H (2004) ElNemo: A normal mode web server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Res 32:W610-W614.
53. Song G, Jernigan RL (2006) An enhanced elastic network model to represent the motions of domain-swapped proteins. Proteins 63:197-209.
54. Bruschweiler R (1995) Collective protein dynamics and nuclear spin relaxation. J Chem Phys 102:3396-3403.
55. Lesk VI, Sternberg MJE (2008) 3D-Garden: A system for modelling protein-protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm. Bioinformatics 10.1093/bioinformatics/btn093.