Effect of ligand binding on the dynamics of trypsin. Comparison of different approaches

Journal of Molecular Graphics and Modelling

Volumn 49, Issue , 2014, Pages 99-109

  Ermakova, Elena ^a   Kurbanov, Rauf ^a  

^a KAZAN INSTITUTE OF BIOCHEMISTRY AND BIOPHYSICS   (Russian Federation)

Author keywords

GNM; Molecular dynamics; PCA; Signal transduction; Trypsin

Indexed keywords

BINDING ENERGY; COVARIANCE MATRIX; MOLECULAR DYNAMICS; PRINCIPAL COMPONENT ANALYSIS; SIGNAL TRANSDUCTION;

GAUSSIAN NETWORK MODEL; GNM; INTERACTION ENERGIES; MOLECULAR DYNAMICS SIMULATIONS; PCA; PROTEIN-LIGAND INTERACTIONS; SUBSTRATE-BINDING SITES; TRYPSIN;

LIGANDS;

LIGAND; TRYPSIN; TRYPSIN INHIBITOR; PROTEIN BINDING;

ARTICLE; CATALYSIS; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; ENZYME ACTIVITY; ENZYME STRUCTURE; ENZYME SUBSTRATE COMPLEX; HYDROGEN BOND; LIGAND BINDING; MOLECULAR DYNAMICS; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; PROTEIN INTERACTION; SIGNAL TRANSDUCTION; STATIC ELECTRICITY; BINDING SITE; CHEMISTRY; METABOLISM; PROTEIN SECONDARY STRUCTURE;

BINDING SITES; LIGANDS; MOLECULAR DYNAMICS SIMULATION; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; TRYPSIN;

EID: 84896334964     PISSN: 10933263     EISSN: 18734243     Source Type: Journal    
DOI: 10.1016/j.jmgm.2014.02.001     Document Type: Article

References (55)

1. D. Long, and R. Bruschweiler Atomistic kinetic model for population shift and allostery in biomolecules J. Am. Chem. Soc. 133 2011 18999 19005
2. D. Kern, and E.R.P. Zuiderweg The role of dynamics in allosteric regulation Curr. Opin. Struct. Biol. 13 2003 748 757 (Pubitemid 37522151)
3. K.H. DuBay, J.P. Bothma, and P.L. Geissler Long-range intra-protein communication can be transmitted by correlated side-chain fluctuations alone PLoS Comput. Biol. 7 2011 e1002168
4. B. Alakent, S. Baskan, and P. Doruker Effect of ligand binding on the intraminimum dynamics of proteins J. Comput. Chem. 32 2011 483 496
5. N.M. Goodey, and S.J. Benkovic Allosteric regulation and catalysis emerge via a common route Nat. Chem. Biol. 4 2008 474 482 (Pubitemid 352019763)
6. K. Gunasekaran, B. Ma, and R. Nussinov Is allostery an intrinsic property of all dynamic proteins? Proteins: Struct. Funct. Genet. 57 2004 433 443 (Pubitemid 39390799)
7. I. Rivalta, M.M. Sultan, N.S. Lee, G.A. Manley, J.P. Loria, and V.S. Batista Allosteric pathways in imidazole glycerol phosphate synthase Proc. Natl. Acad. Sci. U. S. A. 109 2012 E1428 E1436
8. G.H. Peters, and R.P. Bywater Essential motions in a fungal lipase with bound substrate, covalently attached inhibitor and product J. Mol. Recognit. 15 2002 393 404 (Pubitemid 36101030)
9. D.-W. Li, D. Meng, and R. Bruschweiler Short-range coherence of internal protein dynamics revealed by high-precision in silico study J. Am. Chem. Soc. 131 2009 14610 14611
10. Z.N. Gerek, and S.B. Ozkan Change in allosteric network affects binding affinities of PDZ domains: analysis through perturbation response scanning PLoS Comput. Biol. 7 2011 e1002154
11. R.B. Fenwick, S. Esteban-Martín, B. Richter, D. Lee, K.F.A. Walter, D. Milovanovic, S. Becker, N.A. Lakomek, C. Griesinger, and X. Salvatella Weak long-range correlated motions in a surface patch of ubiquitin involved in molecular recognition J. Am. Chem. Soc. 133 2011 10336 10339
12. H.X. Kondo, N. Okimoto, G. Morimoto, and M. Taiji Free-energy landscapes of protein domain movements upon ligand binding J. Phys. Chem. B 115 2011 7629 7636
13. L.-W. Yang, and I. Bahar Coupling between catalytic site and collective dynamics: a requirement for mechanochemical activity of enzymes Structure 13 2005 893 904 (Pubitemid 40804392)
14. E. Marcos, R. Crehuet, and I. Bahar On the conservation of the slow conformational dynamics within the amino acid kinase family: NAGK the paradigm PLoS Comput. Biol. 6 2010 e1000738
15. J. Roy, and C.A. Laughton Long-timescale molecular-dynamics simulations of the major urinary protein provide atomistic interpretations of the unusual thermodynamics of ligand binding Biophys. J. 99 2010 218 226
16. L. Hedstrom Serine protease mechanism and specificity Chem. Rev. 102 2002 4501 4523
17. L. Hedstrom, L. Szilagyi, and W.J. Rutler Converting trypsin to chymotrypsin: the role of surface loops Science 255 1992 1249 1253
18. B. Wroblowsk, J.F. Díaz, J. Schlitter, and Y. Engelborghs Modelling pathways of a-chymotrypsin activation and deactivation Protein Eng. 10 1997 1163 1174 (Pubitemid 28046177)
19. E.L. Wu, K. Han, and J.Z.H. Zhang Selectivity of neutral/weakly basic P1 group inhibitors of thrombin and trypsin by a molecular dynamics study Chem. Eur. J. 14 2008 8704 8714
20. W. Ma, C. Tang, and L. Lai Specificity of trypsin and chymotrypsin: loop-motion-controlled dynamic correlation as a determinant Biophys. J. 89 2005 1183 1193 (Pubitemid 41099000)
21. M. Perakyla, and P.A. Kollman Why does trypsin cleave BPTI so slowly? J. Am. Chem. Soc. 122 2000 3436 3444 (Pubitemid 30211116)
22. R. Goncalves, N. Mateus, I. Pianet, M. Laguerre, and V. de Freitas Mechanisms of tannin-induced trypsin inhibition: a molecular approach Langmuir 27 2011 13122 13129
23. A.R. Rezaie, X. He, and C.T. Esmon Thrombomodulin increases the rate of thrombin inhibition by BPTI Biochemistry 37 1998 693 699 (Pubitemid 28123804)
24. P.F. Neuenschwander, S.R. Williamson, A. Nalian, and K.J. Baker-Deadmond Heparin modulates the 99-loop of factor IXa: effects on reactivity of protein with Kunitz-type inhibitor domains J. Biol. Chem. 281 2006 23066 23074
25. H.L.N. de Amorim, P.A. Netz, and J.A. Guimarães Thrombin allosteric modulation revisited: a molecular dynamics study J. Mol. Model. 16 2010 725 735
26. B.O. Brandsal, J. Aqvist, and A.O. Smalas Computational analysis of binding of P1 variants to trypsin Protein Sci. 10 2001 1584 1595 (Pubitemid 32667052)
27. O. Guvench, D.J. Price, and C.L. Brooks III Receptor rigidity and ligand mobility in trypsin-ligand complexes Proteins: Struct. Funct. Bioinform. 58 2005 407 417 (Pubitemid 40076054)
28. I. Bahar, A.R. Atilgan, M.C. Demirel, and B. Erman Vibrational dynamics of folded proteins: significance of slow and fast motions in relation to function and stability Phys. Rev. Lett. 80 1998 2733 2736 (Pubitemid 128621654)
29. 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
30. E. Eyal, L.W. Yang, and I. Bahar Anisotropic network model: systematic evaluation and a new web interface Bioinformatics 22 2006 2619 2627 (Pubitemid 44642600)
31. A. Amadei, A.B.M. Linssen, and H.J.C. Berendsen Essential dynamics of proteins Proteins 17 1993 412
32. L. Skjaerven, A. Martinez, and N. Reuter Principal component and normal mode analysis of proteins; a quantitative comparison using the GroEL subunit Proteins 79 2011 232 243
33. Y. Kong, and M. Karplus The signaling pathway of rhodopsin Structure 15 2007 611 623 (Pubitemid 46702686)
34. Y. Kong, and M. Karplus Signaling pathways of PDZ2 domain: A molecular dynamics interaction correlation analysis Proteins: Struct. Funct. Genet. 74 2009 145 154
35. F.C. Bernstein, T.F. Koetzle, G.J.B. Williams, E.F. Meyer, M.D. Brice, J.R. Rogers, O. Kennard, T. Shimanouchi, and M. Tatsumi The protein data bank: a computer-based archival file for macromolecular structures J. Mol. Biol. 112 1977 535 542 (Pubitemid 8109216)
36. J.J.P. Stewart Optimization of parameters for semiempirical methods I. Method J. Comput. Chem. 10 1989 209 220
37. J.C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R.D. Skeel, L. Kale, and K. Schulten Scalable molecular dynamics with NAMD J. Comput. Chem. 26 2005 1781 1802 (Pubitemid 43078511)
38. A.D. MacKerell, D. Bashford, M. Bellott, R.L. Dunbrack, J.D. Evanseck, M.J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F.T.K. Lau, C. Mattos, S. Michnick, T. Ngo, D.T. Nguyen, B. Prodhom, W.E. Reiher, B. Roux, M. Schlenkrich, J.C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M. Karplus All-atom empirical potential for molecular modeling and dynamics studies of proteins J. Phys. Chem. B 102 1998 3586 3616 (Pubitemid 128576688)
39. K. Vanommeslaeghe, E. Hatcher, C. Acharya, S. Kundu, S. Zhong, J. Shim, E. Darian, O. Guvench, P. Lopes, I. Vorobyov, and A.D. Mackerell Jr. CHARMM general force field: a force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields J. Comput. Chem. 33 2012 2451 2468
40. W. Humphrey, A. Dalke, and K. Schulten VMD - Visual Molecular Dynamics J. Molec. Graphics 14.1 1996 33 38
41. B.R. Brooks, R.E. Bruccoleri, B.D. Olafson, D.J. States, S. Swaminathan, and M. Karplus CHARMM: a program for macromolecular energy, minimization, and dynamics calculations J. Comput. Chem. 4 1983 187 217
42. A. Bakan, L.M. Meireles, and I. Bahar ProDy: protein dynamics inferred from theory and experiments Bioinformatics 27 2011 1575 1577
43. P.A. Kollman, I. Massova, C. Reyes, B. Kuhn, S. Huo, L. Chong, M. Lee, T. Lee, Y. Duan, W. Wang, O. Donini, P. Cieplak, J. Srinivasan, D.A. Case, and T.E. 3rd Cheatham Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models Acc. Chem. Res. 33 2000 889 897 (Pubitemid 32056774)
44. T. Hou, J. Wang, Y. Li, and W. Wang Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations J. Chem. Inf. Model. 51 2011 69 82
45. D.P. Oehme, R.T.C. Brownlee, and D.J.D. Wilson Effect of atomic charge, solvation, entropy, and ligand protonation state on MM-PB(GB)SA binding energies of HIV protease J. Comput. Chem. 33 2012 2566 2580
46. A. Sethi, J. Eargle, A.A. Blacka, and Z. Luthey-Schulten Dynamical networks in tRNA: protein complexes Proc. Natl. Acad. Sci. U. S. A. 106 2009 6620 6625
47. B.A. Katz, J. Finer-Moore, R. Mortezaei, D.H. Rich, and R.M. Stroud Episelection: Novel Ki - nanomolar inhibitors of serine proteases selected by binding or chemistry on an enzyme surface Biochemistry 34 1995 8264 8280
48. Zh. Chi, R. Liu, and H. Zhang Noncovalent interaction of oxytetracycline with the enzyme trypsin Biomacromolecules 11 2010 2454 2459
49. S.H. Hung, and L. Hedstrom Converting trypsin to elastase: substitution of the S1 site and adjacent loops reconstitutes esterase specificity but not amidase activity Protein Eng. 11 1998 669 673 (Pubitemid 28389157)
50. M. Gur, E. Zomot, and I. Bahar Global motions exhibited by proteins in micro- to milliseconds simulations concur with anisotropic network model predictions J. Chem. Phys. 139 2013 121912
51. Z.N. Gerek, and S.B. Ozkan Change in allosteric network affects binding affinities of PDZ domains: analysis through perturbation response scanning PLoS Comput. Biol. 7 2011 e1002154
52. del Sol, H. Fujihashi, D. Amoros, and R. Nussinov Residues crucial for maintaining short paths in network communication mediate signaling in proteins Mol. Syst. Biol. 2 2006 0019
53. A. Ghosh, and S. Vishveshwara A study of communication pathways in methionyl- tRNA synthetase by molecular dynamics simulations and structure network analysis Proc. Natl. Acad. Sci. U. S. A. 104 2007 15711 15716 (Pubitemid 350035365)
54. N.M. Glykos Software news and updates. CARMA: a molecular dynamics analysis program J. Comp. Chem. 27 2006 1765 1768 (Pubitemid 44476671)
55. M.M. Girvan Newman, Community structure in social and biological networks Proc. Natl. Acad. Sci. U. S. A. 99 2002 7821 7826