Global transitions of proteins explored by a multiscale hybrid methodology: Application to adenylate kinase

Biophysical Journal

Volumn 105, Issue 7, 2013, Pages 1643-1652

  Gur, Mert ^a   Madura, Jeffry D ^b   Bahar, Ivet ^a  

^a UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

^b DUQUESNE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENYLATE KINASE;

ALGORITHM; AMINO ACID SEQUENCE; ANIMAL; ANISOTROPY; ARTICLE; CHEMISTRY; MOLECULAR DYNAMICS; MOLECULAR GENETICS;

ADENYLATE KINASE; ALGORITHMS; AMINO ACID SEQUENCE; ANIMALS; ANISOTROPY; MOLECULAR DYNAMICS SIMULATION; MOLECULAR SEQUENCE DATA;

EID: 84885111575     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2013.07.058     Document Type: Article

References (52)

1. A.R. Atilgan, and S.R. Durell I. Bahar Anisotropy of fluctuation dynamics of proteins with an elastic network model Biophys. J. 80 2001 505 515
2. I. Bahar, and T.R. Lezon E. Eyal Global dynamics of proteins: bridging between structure and function Annu. Rev. Biophys 39 2010 23 42
3. Z. Yang, P. Májek, and I. Bahar Allosteric transitions of supramolecular systems explored by network models: application to chaperonin GroEL PLOS Comput. Biol. 5 2009 e1000360
4. E. Darve, D. Rodríguez-Gómez, and A. Pohorille Adaptive biasing force method for scalar and vector free energy calculations J. Chem. Phys. 128 2008 144120
5. C. Chipot, and J. Hénin Exploring the free-energy landscape of a short peptide using an average force J. Chem. Phys. 123 2005 244906
6. A. Amadei, A.B. Linssen, and H.J. Berendsen Essential dynamics of proteins Proteins 17 1993 412 425
7. M. Gur, and B. Erman Quasi-harmonic fluctuations of two bound peptides Proteins 80 2012 2769 2779
8. M.M. Teeter, and D.A. Case Harmonic and quasiharmonic descriptions of crambin J. Phys. Chem. 94 1990 8091 8097
9. K.A. Henzler-Wildman, and M. Lei D. Kern A hierarchy of timescales in protein dynamics is linked to enzyme catalysis Nature 450 2007 913 916
10. Y.E. Shapiro, and E. Meirovitch Activation energy of catalysis-related domain motion in E. coli adenylate kinase J. Phys. Chem. B 110 2006 11519 11524
11. J.A. Hanson, and K. Duderstadt H. Yang Illuminating the mechanistic roles of enzyme conformational dynamics Proc. Natl. Acad. Sci. USA 104 2007 18055 18060
12. Y. Wang, and L. Gan J. Wang Exploring the dynamic functional landscape of adenylate kinase modulated by substrates J. Chem. Theory Comput. 9 2013 84 95
13. H.F. Lou, and R.I. Cukier Molecular dynamics of apo-adenylate kinase: a distance replica exchange method for the free energy of conformational fluctuations J. Phys. Chem. B 110 2006 24121 24137
14. D. Bhatt, and D.M. Zuckerman Heterogeneous path ensembles for conformational transitions in semi-atomistic models of adenylate kinase J. Chem. Theory Comput. 6 2010 3527 3539
15. 15N-NMR relaxation data Proteins 57 2004 468 480
16. J.B. Brokaw, and J.W. Chu On the roles of substrate binding and hinge unfolding in conformational changes of adenylate kinase Biophys. J. 99 2010 3420 3429
17. C. Snow, G.Y. Qi, and S. Hayward Essential dynamics sampling study of adenylate kinase: comparison to citrate synthase and implication for the hinge and shear mechanisms of domain motions Proteins 67 2007 325 337
18. N. Kantarci-Carsibasi, T. Haliloglu, and P. Doruker Conformational transition pathways explored by Monte Carlo simulation integrated with collective modes Biophys. J. 95 2008 5862 5873
19. M.D. Daily, and H. Yu Q. Cui Allosteric activation transitions in enzymes and biomolecular motors: insights from atomistic and coarse-grained simulations Top. Curr. Chem. 337 2013 139 164 (Epub ahead of print)
20. M.D. Daily, G.N. Phillips Jr., and Q. Cui Many local motions cooperate to produce the adenylate kinase conformational transition J. Mol. Biol. 400 2010 618 631
21. M.D. Daily, G.N. Phillips Jr., and Q. Cui Interconversion of functional motions between mesophilic and thermophilic adenylate kinases PLOS Comput. Biol. 7 2011 e1002103
22. K. Arora, and C.L. Brooks 3rd Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism Proc. Natl. Acad. Sci. USA 104 2007 18496 18501
23. P.C. Whitford, and O. Miyashita J.N. Onuchic Conformational transitions of adenylate kinase: switching by cracking J. Mol. Biol. 366 2007 1661 1671
24. P.C. Whitford, S. Gosavi, and J.N. Onuchic Conformational transitions in adenylate kinase. Allosteric communication reduces misligation J. Biol. Chem. 283 2008 2042 2048
25. O. Beckstein, and E.J. Denning T.B. Woolf Zipping and unzipping of adenylate kinase: atomistic insights into the ensemble of open↠"closed transitions J. Mol. Biol. 394 2009 160 176
26. M.B. Kubitzki, and B.L. de Groot The atomistic mechanism of conformational transition in adenylate kinase: A TEE-REX molecular dynamics study Structure 16 2008 1175 1182
27. 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
28. Y. Matsunaga, and H. Fujisaki A. Kidera Minimum free energy path of ligand-induced transition in adenylate kinase PLOS Comput. Biol. 8 2012 e1002555
29. E. Eyal, L.W. Yang, and I. Bahar Anisotropic network model: systematic evaluation and a new web interface Bioinformatics 22 2006 2619 2627
30. A. Bakan, L.M. Meireles, and I. Bahar ProDy: protein dynamics inferred from theory and experiments Bioinformatics 27 2011 1575 1577
31. C.W. Müller, and G.J. Schlauderer G.E. Schulz Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding Structure 4 1996 147 156
32. C.W. Müller, and G.E. Schulz Structure of the complex between adenylate kinase from Escherichia coli and the inhibitor Ap5A refined at 1.9 Å resolution. A model for a catalytic transition state J. Mol. Biol. 224 1992 159 177
33. W.L. Jorgensen, and J. Chandrasekhar M.L. Klein Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 79 1983 926 935
34. A.D. MacKerell, and D. Bashford M. Karplus All-atom empirical potential for molecular modeling and dynamics studies of proteins J. Phys. Chem. B 102 1998 3586 3616
35. M. Schaefer, and C. Bartels M. Karplus Effective atom volumes for implicit solvent models: comparison between Voronoi volumes and minimum fluctuation volumes J. Comput. Chem. 22 2001 1857 1879
36. B.R. Brooks, and R.E. Bruccoleri M. Karplus Charmm: a program for macromolecular energy, minimization, and dynamics calculations J. Comput. Chem. 4 1983 187 217
37. P.E. Marszalek, and H. Lu J.M. Fernandez Mechanical unfolding intermediates in titin modules Nature 402 1999 100 103
38. R.V. Swift, and J.A. McCammon Catalytically requisite conformational dynamics in the mRNA-capping enzyme probed by targeted molecular dynamics Biochemistry 47 2008 4102 4111
39. E. Paci, and M. Karplus Forced unfolding of fibronectin type 3 modules: an analysis by biased molecular dynamics simulations J. Mol. Biol. 288 1999 441 459
40. J. Schlitter, and M. Engels A. Wollmer Targeted molecular-dynamics simulation of conformational change: application to the Tâ†"R transition in insulin Mol. Simul. 10 1993 291 308
41. Y. Arkun, and M. Gur Combining optimal control theory and molecular dynamics for protein folding PLoS ONE 7 2012 e29628
42. B. Isin, and K. Schulten I. Bahar Mechanism of signal propagation upon retinal isomerization: insights from molecular dynamics simulations of rhodopsin restrained by normal modes Biophys. J. 95 2008 789 803
43. J. Ma, and M. Karplus Molecular switch in signal transduction: reaction paths of the conformational changes in ras p21 Proc. Natl. Acad. Sci. USA 94 1997 11905 11910
44. Z. Zhang, Y. Shi, and H. Liu Molecular dynamics simulations of peptides and proteins with amplified collective motions Biophys. J. 84 2003 3583 3593
45. O. Miyashita, J.N. Onuchic, and P.G. Wolynes Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins Proc. Natl. Acad. Sci. USA 100 2003 12570 12575
46. E. Bae, and G.N. Phillips Jr. Roles of static and dynamic domains in stability and catalysis of adenylate kinase Proc. Natl. Acad. Sci. USA 103 2006 2132 2137
47. J.W. Chu, and G.A. Voth Coarse-grained free energy functions for studying protein conformational changes: a double-well network model Biophys. J. 93 2007 3860 3871
48. J.C. Phillips, and R. Braun K. Schulten Scalable molecular dynamics with NAMD J. Comput. Chem. 26 2005 1781 1802
49. A.D. Mackerell Jr., M. Feig, and C.L. Brooks 3rd Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations J. Comput. Chem. 25 2004 1400 1415
50. T. Darden, D. York, and L. Pedersen Particle mesh Ewald. An N·log(N) method for Ewald sums in large systems J. Chem. Phys. 98 1993 10089 10092
51. G.J. Martyna, D.J. Tobias, and M.L. Klein Constant pressure molecular dynamics algorithms J. Chem. Phys. 101 1994 4177 4189
52. S.E. Feller, and Y.H. Zhang B.R. Brooks Constant pressure molecular dynamics simulation - the Langevin piston method J. Chem. Phys. 103 1995 4613 4621