Ligand-induced conformational change of a protein reproduced by a linear combination of displacement vectors obtained from normal mode analysis

Biophysical Chemistry

Volumn 159, Issue 2-3, 2011, Pages 257-266

  Wako, Hiroshi ^a   Endo, Shigeru ^b  

^a WASEDA UNIVERSITY   (Japan)

^b KITASATO UNIVERSITY   (Japan)

Author keywords

Apo form protein; Conformational change; Conformational sampling; Holo form protein; Ligand binding; Normal mode analysis

Indexed keywords

1 DEOXY DEXTRO XYLULOSE 5 PHOSPHATE REDUCTOISOMERASE; BINDING PROTEIN; DIMER; ISOMERASE; LEUCINE BINDING PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; ELASTIC NETWORK MODEL; LIGAND BINDING; MOLECULAR DOCKING; MOLECULAR DYNAMICS; MOLECULAR MODEL; NORMAL MODE ANALYSIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION;

APOPROTEINS; DATABASES, PROTEIN; LIGANDS; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN MULTIMERIZATION; PROTEINS;

EID: 80053348799     PISSN: 03014622     EISSN: 18734200     Source Type: Journal    
DOI: 10.1016/j.bpc.2011.07.004     Document Type: Article

References (38)

1. E. Fischer Einfluss der configuration auf die wirkung der enzyme Ber. Dtsch. Chem. Ges. 27 1894 2985 2993
2. D.E. Koshland Jr. Application of a theory of enzyme specificity to protein synthesis Proc. Natl. Acad. Sci. U.S.A. 44 1958 98 104
3. R. Najmanovich, J. Kuttner, V. Sobolev, and M. Edelman Side-chain flexibility in proteins upon ligand binding Proteins 39 2000 261 268 (Pubitemid 30226508)
4. M.I. Zavodszky, and L.A. Kuhn Side-chain flexibility in protein-ligand binding: the minimal rotation hypothesis Protein Sci. 14 2005 1104 1114 (Pubitemid 40389381)
5. S. Karthikeyan, Q. Zhou, A.L. Osterman, and H. Zhang Ligand-binding induced conformational changes in riboflavin kinase: structural basis for the ordered mechanism Biochemistry 42 2003 12532 12538 (Pubitemid 37337543)
6. M.G. Malkowski, P.D. Martin, J.C. Guzik, and B.F. Edwards The co-crystal structure of unliganded bovine α-thrombin and prethrombin-2: movement of the Tyr-Pro-Pro-Trp segment and active site residues upon ligand binding Protein Sci. 6 1997 1438 1448
7. L. Kraft, G.A. Sprenger, and Y. Lindqvist Conformational changes during the catalytic cycle of gluconate kinase as revealed by X-ray crystallography J. Mol. Biol. 318 2002 1057 1069 (Pubitemid 35007368)
8. U. Magnusson, B. Salopek-Sondi, L.A. Luck, and S.L. Mowbray X-ray structures of the leucine-binding protein illustrate conformational changes and the basis of ligand specificity J. Biol. Chem. 279 2004 8747 8752 (Pubitemid 38295931)
9. G. Benison, P.A. Karplus, and E. Barbar The interplay of ligand binding and quaternary structure in the diverse interactions of dynein light chain LC8 J. Mol. Biol. 384 2008 954 966
10. J.-P. Xiong, T. Stehle, R. Zhang, A. Joachimiak, M. Frech, S.L. Goodman, and M.A. Arnaout Crystal structure of the extracellular segment of integrin αVβ3 in complex with an Arg-Gly-Asp ligand Science 296 2002 151 155 (Pubitemid 34280076)
11. M. Brylinski, and J. Skolnick What is the relationship between the global structures of apo and holo proteins? Proteins 70 2008 363 377
12. W.G. Krebs, V. Alexandrov, C.A. Wilson, N. Echols, H. Yu, and M. Gerstein Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic Proteins 48 2002 682 695 (Pubitemid 34925457)
13. V. Alexandrov, U. Lehnert, N. Echols, D. Milburn, D. Engelman, and M. Gerstein Normal modes for predicting protein motions: a comprehensive database assessment and associated web tool Protein Sci. 14 2005 633 643 (Pubitemid 40283901)
14. S.E. Dobbins, V.I. Lesk, and J.E. Sternberg Insights into protein flexibility: the relationship between normal modes and conformational change upon protein-protein docking Proc. Natl. Acad. Sci. U.S.A. 105 2008 10390 10395
15. F. Tama, and Y.-H. Sanejouand Conformational change of proteins arising from normal mode calculations Protein Eng. 14 2001 1 6 (Pubitemid 32318932)
16. D. Tobi, and I. Bahar Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state Proc. Natl. Acad. Sci. U.S.A. 102 2005 18908 18913 (Pubitemid 43049540)
17. M.L. Teodoro, and L.E. Kavraki Conformational flexibility models for the receptor in structure based drug design Curr. Pharm. Des. 9 2003 1635 1648 (Pubitemid 36966031)
18. M. Totrov, and R. Abagyan Flexible ligand docking to multiple receptor conformations: a practical alternative Curr. Opin. Struct. Biol. 18 2008 178 184
19. C.N. Cavasotto, J. Kovacs, and R.A. Abagyan Representing receptor flexibility in ligand docking through relevant normal modes J. Am. Chem. Soc. 127 2005 9632 9640 (Pubitemid 40934775)
20. H. Wako, and N. Go Algorithm for rapid calculation of hessian of conformational energy function of proteins by supercomputer J. Comp. Chem. 8 1987 625 635
21. H. Wako, S. Endo, K. Nagayama, and N. Go FEDER/2: program for static and dynamic conformational energy analysis of macro-molecules in dihedral angle space Comp. Phys. Comm. 19 1995 233 251
22. K. Hinsen Analysis of domain motions by approximate normal mode calculations Proteins 33 1998 417 429 (Pubitemid 28516346)
23. A.R. Atilgan, S.R. Durell, R.L. Jernigan, M.C. Demirel, O. Keskin, and I. Bahar Anisotropy of fluctuation dynamics of proteins with an elastic network model Biophys. J. 80 2001 505 515
24. I. Bahar, and A.J. Rader Coarse-grained normal mode analysis in structural biology Curr. Opin. Struct. Biol. 15 2005 1 7
25. D. Seeliger, and B.L. de Groot Conformational transitions upon ligand binding: holo-structure prediction from apo conformations PLOS Comp. Biol. 6 2010 e1000634
26. H. Wako, M. Kato, and S. Endo ProMode: a database of normal mode analyses on protein molecules with a full-atom model Bioinformatics 20 2004 2035 2043 (Pubitemid 39236555)
27. A. Mac Sweeney, R. Lange, R.P.M. Fernandes, H. Schulz, G.E. Dale, A. Douangamath, P.J. Proteau, and C. Oefner The crystal structure of E. coli 1-deoxy-d-xylulose-5-phosphate reductoisomerase in a ternary complex with the antimalarial compound fosmidomycin and NADPH reveals a tight-binding closed enzyme conformation J. Mol. Biol. 345 2005 115 127 (Pubitemid 39572829)
28. K. Reuter, S. Sanderbrand, H. Jomaa, J. Wiesner, I. Steinbrecher, E. Beck, M. Hintz, G. Klebe, and M.T. Stubbs Crystal structure of 1-deoxy-d-xylulose-5-phosphate reductoisomerase, a crucial enzyme in the non-mevalonate pathway of isoprenoid biosynthesis J. Biol. Chem. 277 2002 5378 5384 (Pubitemid 34968584)
29. S.D. Lahiri, G. Zhang, D. Dunaway-Mariano, and K.N. Allen The pentacovalent phosphorus intermediate of a phosphoryl transfer reaction Science 299 2003 2067 2071 (Pubitemid 36383733)
30. G. Zhang, J. Dai, L. Wang, D. Dunaway-Mariano, L.W. Tremblay, and K.N. Allen Catalytic cycling in β-phosphoglucomutase: a kinetic and structural analysis Biochemistry 44 2005 9404 9416 (Pubitemid 40962039)
31. R.A. Laskowski PDBsum new things Nucleic Acids Res. 37 2009 D355 D359
32. F.K. Winkler, D.W. Banner, C. Oefner, D. Tsernoglou, R.S. Brown, S.P. Heathman, R.K. Bryan, P.D. Martin, K. Petratos, and K.S. Wilson The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments EMBO J. 12 1993 1781 1795 (Pubitemid 23157693)
33. P. Maragakis, and M. Karplus Large amplitude conformational change in proteins explored with a plastic network model: adenylate kinase J. Mol. Biol. 352 2005 807 822 (Pubitemid 41267070)
34. H. Ishida, Y. Jochi, and A. Kidera Dynamic structure of subtilisin-eglin c complex studied by normal mode analysis Proteins 32 1998 324 333 (Pubitemid 28360829)
35. M. Ikeguchi, J. Ueno, M. Sato, and A. Kidera Protein structural change upon ligand binding: linear response theory Phys. Rev. Lett. 94 2005 078102
36. H. Park, J.L. Hilsenbeck, H.J. Kim, W.A. Shuttleworth, Y.H. Park, J.N. Evans, and C.H. Kang Structural studies of Streptococcus pneumonia EPSP synthase in unliganded state, tetrahedral intermediate-bound state and S3P-GLP-bound state Mol. Microbiol. 51 2004 963 971 (Pubitemid 38270792)
37. B.W. Poland, Z. Hou, C. Bruns, H.J. Fromm, and R.B. Honzatko Refined crystal structures of guanine nucleotide complexes of adenylosuccinate synthetase from Escherichia coli J. Biol. Chem. 271 1996 15407 15413 (Pubitemid 26225309)
38. A.L. Milac, N.V. Buchete, T.A. Fritz, G. Hummer, and L.A. Tabak Substrate-induced conformational changes and dynamics of UDP-N- acetylgalactosamine: polypeptide N-acetylgalactosaminyltransferase-2 J. Mol. Biol. 373 2007 439 451 (Pubitemid 47445582)