Advanced replica-exchange sampling to study the flexibility and plasticity of peptides and proteins

Biochimica et Biophysica Acta - Proteins and Proteomics

Volumn 1834, Issue 5, 2013, Pages 847-853

  Ostermeir, Katja ^a   Zacharias, Martin ^a  

^a TECHNICAL UNIVERSITY OF MUNICH   (Germany)

Author keywords

Accelerated sampling; Conformational sampling; Force field calculation; Molecular dynamics simulation; Peptide and protein folding; Potential scaling

Indexed keywords

PEPTIDES AND PROTEINS;

ALLOSTERISM; CONFORMATIONAL TRANSITION; HIGH TEMPERATURE; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; PLASTICITY; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; REPLICATION STUDY; REVIEW; SIMULATION;

MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; PEPTIDES; PROTEIN CONFORMATION; PROTEINS; TEMPERATURE;

EID: 84876294309     PISSN: 15709639     EISSN: 18781454     Source Type: Journal    
DOI: 10.1016/j.bbapap.2012.12.016     Document Type: Review

References (99)

1. H.-L. Liu, and J.-P. Hsu Recent developments in structural proteomics for protein structure determination Proteomics 5 2005 2056 2068
2. R. Roy, S. Hohng, and H. Taekjip A practical guide to single-molecule FRET Nat. Methods 5 2008 507 516
3. M. Karplus, and J.A. McCammon Molecular dynamics simulations of biomolecules Nat. Struct. Biol. 9 2002 646 652
4. X. Daura, B. Jaun, D. Seebach, W.F. van Gunsteren, and A.E. Mark Reversible peptide folding in solution by molecular dynamics simulation J. Mol. Biol. 280 1998 925 932
5. K. Lindorff-Larsen, S. Piana, R.O. Dror, and D.E. Shaw How fast-folding proteins fold Science 334 2011 517 520
6. S. Piana, K. Lindorff-Larsen, and D.E. Shaw Protein folding kinetics and thermodynamics from atomistic simulation Proc. Natl. Acad. Sci. U. S. A. 109 2012 17845 17850
7. R.O. Dror, R.M. Dirks, J.P. Grossman, H. Xu, and D.E. Shaw Biomolecular simulation: a computational microscope for molecular biology Annu. Rev. Biophys. 41 2012 429 452
8. T. Kaihsu Conformational sampling for the impatient Biophys. Chem. 107 2004 213 220
9. S. Kirkpatrick, C.D. Gelatt, and M.P. Vecchi Jr. Optimization by simulated annealing Science 220 1983 671 680
10. P.J.M. Larrhoven, and E.H.L. Aarts Simulated Annealing: Theory and Applications 1987 Reidel Dordrecht (187 pp.)
11. A.T. Brunger, P.D. Adams, and L.M. Rice Annealing in crystallography: a powerful optimization tool Prog. Biophys. Mol. Biol. 72 1999 135 155
12. J. Kostrowicki, and H.A. Scheraga Application of the diffusion equation method for global optimization to oligopeptides J. Chem. Phys. 96 1992 7442
13. T. Huber, A.E. Torda, and W.F. van Gunsteren Structure optimization combining soft-core interaction functions, the diffusion equation method and molecular dynamics J. Phys. Chem. A 10 1997 5926 5930
14. K. Tappura, K.M. Lahtela-Kakkonen, and O. Teleman A new soft-core potential function for molecular dynamics applied to the prediction of protein loop conformations J. Comput. Chem. 21 2000 388 397
15. R.N. Riemann, and M. Zacharias Reversible scaling of dihedral angle barriers during molecular dynamics to improve structure prediction of cyclic peptides J. Pept. Sci. 63 2004 354 364
16. R.N. Riemann, and M. Zacharias Refinement of protein cores and protein-peptide interfaces using a potential scaling approach Protein Eng. Des. Sel. 18 2005 465 476
17. O.F. Lange, L.V. Schäfer, and H. Grubmüller Flooding in GROMACS: accelerated barrier crossings in molecular dynamics J. Comput. Chem. 27 2006 1693 1702
18. A. Laio, and M. Parrinello Escaping free energy minima Proc. Natl. Acad. Sci. U. S. A. 99 2002 12562 12566
19. C. Simmerling, J.L. Miller, and P.A. Kollman Combined locally enhanced sampling and particle mesh Ewald as a strategy to locate the experimental structure of a nonhelical nucleic acid J. Am. Chem. Soc. 120 1998 7149 7158
20. D. Hamelberg, J. Mongan, and J.A. McCammon Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules J. Chem. Phys. 120 2004 11919
21. R.H. Swendsen, and J.S. Wang Replica Monte Carlo simulations of spin glasses Phys. Rev. Lett. 57 1986 2607 2609
22. T. Okabe, M. Kawata, Y. Okamoto, and M. Mikami Replica-exchange Monte Carlo method for the isobaric-isothermal ensemble Chem. Phys. Lett. 335 2001 435 439
23. Y. Okamoto Generalized-ensemble algorithms: enhanced sampling techniques for Monte Carlo and molecular dynamics simulations J. Mol. Graph. Model. 22 2004 425 439
24. T. Kaihsu Conformational sampling for the impatient Biophys. Chem. 107 2004 213 218
25. C. Predescu, M. Predescu, and C.V.J. Ciobanu On the efficiency of exchange in parallel tempering Monte Carlo simulations J. Phys. Chem. B 109 2005 4189 4196
26. Y. Sugita, and Y. Okamoto Replica-exchange molecular dynamics method for protein folding Chem. Phys. Lett. 314 1999 141 151
27. D.M. Zuckerman, and E. Lyman A second look at canonical sampling of biomolecules using replica exchange simulation J. Chem. Theory Comput. 2 2006 1200 1202
28. J. Machta Strengths and weaknesses of parallel tempering Phys. Rev. E 80 2009 056706
29. H. Nymeyer How efficient is replica exchange molecular dynamics? An analytic approach Chem. Theory Comput. 4 2008 626 636
30. R. Denschlag, M. Lingenheil, and P. Tavan Efficiency reduction and pseudo-convergence in replica exchange sampling of peptide folding-unfolding equilibria Chem. Phys. Lett. 458 2008 244 248
31. W. Nadler, J.H. Meinke, and U.H.E. Hansmann Folding proteins by first-passage-times-optimized replica exchange Phys. Rev. E 78 2008 061905
32. D. Gront, and A. Kolinski Efficient scheme for optimization of parallel tempering Monte Carlo method Phys. Condens. Matter 19 2007 036225
33. M.J. Abraham, and J.E. Gready Ensuring mixing efficiency of replica-exchange molecular dynamics simulations J. Chem. Theory Comput. 4 2008 1119 1128
34. S. Trebst, M. Troyer, and U.H.E. Hansmann Optimized parallel tempering simulations of proteins J. Chem. Phys. 124 2006 174903
35. W. Nadler, and U.H.E. Hansmann Optimized explicit-solvent replica exchange molecular dynamics from scratch J. Phys. Chem. B 112 2008 10386 10387
36. F. Calvo All-exchanges parallel tempering J. Chem. Phys. 123 2005 124106
37. P. Brenner, C.R. Sweet, D. VonHandorf, and J.A. Izaguirre Accelerating the replica exchange method through an efficient all-pairs exchange J. Chem. Phys. 126 2007 074103
38. X. Periole, and A.E. Mark Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent J. Chem. Phys. 126 2007 1014903
39. D.J. Sindhikara, Y. Meng, and A.E. Roitberg Exchange frequency in replica exchange molecular dynamics J. Chem. Phys. 128 2008 024103
40. D.J. Sindhikara, J. Daniel, D.J. Emerson, and A. Roitberg Exchange often and properly in replica exchange molecular dynamics J. Chem. Theory Comput. 6 2010 2804 2808
41. N.V. Buchete, and G. Hummer Peptide folding kinetics from replica exchange molecular dynamics Phys. Rev. E 77 2002 030902
42. E. Rosta, and G. Hummer Error and efficiency of simulated tempering simulations J. Chem. Phys. 132 2010 034102
43. E. Rosta, N.V. Buchete, and G. Hummer Thermostat artifacts in replica exchange molecular dynamics simulations J. Chem. Theory Comput. 131 2009 1393 1399
44. M. Lingenheil, R. Denschlag, G. Mathias, and P. Tavan Efficiency of exchange schemes in replica exchange Chem. Phys. Lett. 478 2009 80 84
45. W. Zheng, M. Andrec, E. Gallicchio, and R.M. Levy Simple continuous and discrete models for simulating replica exchange simulations of protein folding J. Phys. Chem. B 112 2008 6083 6093
46. W. Zheng, M. Andrec, E. Gallicchio, and R.M. Levy Simulating replica exchange simulations of protein folding with a kinetic network model Proc. Natl. Acad. Sci. U. S. A. 104 2007 15340 15345
47. A. Onufriev, D. Bashford, and D.A. Case Exploring protein native states and large-scale conformational changes with a modified generalized Born model Proteins 55 2004 383 394
48. Y. Chebaro, X. Dong, R. Laghaei, P. Derreumaux, and N. Mousseau Replica exchange molecular dynamics simulations of coarse-grained proteins in implicit solvent J. Phys. Chem. B 113 2009 267 274
49. H. Nymeyer, and A.E. Garcia Simulation of the folding equilibrium of α-helical peptides: a comparison of the generalized Born approximation with explicit solvent Proc. Natl. Acad. Sci. U. S. A. 100 2003 13934 13939
50. R. Zhou Free energy landscape of protein folding in water: explicit vs. implicit solvent Proteins Struct. Funct. Bioinform. 53 2003 148 161
51. W. Xu, T. Lai, Y. Yang, and Y. Mu Reversible folding simulation by hybrid Hamiltonian replica exchange J. Chem. Phys. 128 2008 175105
52. X. Cheng, G. Cui, V. Hornak, and C. Simmerling Modified replica exchange simulation methods for local structure refinement J. Phys. Chem. B 109 2005 8220 8230
53. M.B. Kubitzki, and B.L. de Groot Molecular Dynamics simulations using temperature-enhanced essential dynamics replica exchange Biophys. J. 92 2007 4262 4270
54. X. Wu, M. Hodoscek, and B.R. Brooks Replica exchanging self-guided Langevin dynamics for efficient and accurate conformational sampling J. Chem. Phys. 137 2012 044106
55. P. Liu, B. Kim, R.A. Friesner, and B.A. Berne Replica exchange with solute tempering: a method for sampling biological systems in explicit water Proc. Natl. Acad. Sci. 102 2005 13749 13754
56. X. Li, R.A. Latour, and S.J. Stuart TIGER2: an improved algorithm for temperature intervals with global exchange of replicas J. Chem. Phys. 130 2009 174106
57. A.J. Lee, and S.W. Rick Improving replica exchange using driven scaling J. Chem. Phys. 131 2009 174113
58. A.J. Ballard, and C. Jarzynski Replica exchange with nonequilibrium switches Proc. Natl. Acad. Sci. 106 2009 12224 12229
59. A. Okur, D.R. Roe, G. Cui, V. Hornak, and C. Simmerling Improving convergence of replica-exchange simulations through coupling to a high-temperature structure reservoir J. Chem. Theory Comput. 3 2007 557 568
60. J.Z. Ruscio, N.L. Fawzi, and T. Head-Gordon How hot? Systematic convergence of the replica exchange method using multiple reservoirs J. Comput. Chem. 31 2010 620 627
61. A.E. Roitberg, A. Okur, and C. Simmerling Coupling of replica exchange simulations to a non-Boltzmann structure reservoir J. Phys. Chem. B 111 2007 2415 2418
62. S. Kannan, and M. Zacharias Simulated annealing coupled replica exchange molecular dynamics - an efficient conformational sampling method J. Struct. Biol. 166 2009 288 294
63. H. Fukunishi, O. Watanabe, and S. Takada On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: application to protein structure prediction J. Chem. Phys. 116 2002 9058
64. R. Affentranger, I. Tavernelli, and E.E. Di Iorio A novel Hamiltonian replica exchange MD protocol to enhance protein conformational space sampling J. Chem. Theory Comput. 2 2006 217 228
65. J. Hritz, and C. Oostenbrink Hamiltonian replica exchange molecular dynamics using soft-core interactions J. Chem. Phys. 128 2008 144121
66. X. Huang, M. Hagen, B. Kim, R. Friesner, R. Zhou, and B.J. Berne Replica exchange with solute tempering: efficiency in large scale systems J. Phys. Chem. B 111 2007 5405 5410
67. L. Lingle, R.A. Friesner, and B.J. Berne Replica exchange with solute scaling: a more efficient version of replica exchange with solute tempering (REST2) J. Phys. Chem. B 115 2011 9431 9438
68. P. Liu, H. Ru, Z. Xuhui, R. Zhou, and B.J. Berne Hydrophobic aided replica exchange: an efficient algorithm for protein folding in explicit solvent J. Phys. Chem. B 110 2006 19018 19022
69. S.L.C. Moors, S. Michielssens, and A. Ceulemans Improved replica exchange method for native-state protein sampling J. Chem. Theory Comput. 7 2011 1012 1020
70. M. Fajer, D. Hamelberg, and J.A. McCammon Replica-exchange accelerated molecular dynamics (REXAMD) applied to thermodynamic integration J. Chem. Theory Comput. 4 2008 1565 1569
71. S.G. Itoh, Hisashi Okumura, and Yuko Okamoto Replica-exchange method in van der Waals radius space: overcoming steric restrictions for biomolecules J. Chem. Phys. 132 2010 134105
72. S. Kannan, and M. Zacharias Enhanced sampling of peptide and protein conformations using replica exchange simulations with a peptide backbone biasing-potential Proteins 66 2007 697 706
73. S. Kannan, and M. Zacharias Folding simulations of Trp-cage mini protein in explicit solvent using biasing potential replica-exchange molecular dynamics simulations Proteins Struct. Funct. Bioinform. 76 2009 448 460
74. S. Kannan, and M. Zacharias Application of biasing-potential replica-exchange simulations for loop modeling and refinement of proteins in explicit solvent Proteins Struct. Funct. Bioinform. 78 2010 2809 2819
75. Y. Mu Dissociation aided and side chain sampling enhanced Hamiltonian replica exchange J. Chem. Phys. 130 2009 164107
76. J. Curuksu, and M. Zacharias Enhanced conformational sampling of nucleic acids by a new Hamiltonian replica exchange molecular dynamics approach J. Chem. Phys. 130 2009 104110
77. E. Lyman, and D.M. Zuckerman Resolution exchange simulation with incremental coarsening J. Chem. Theory Comput. 2 2006 656 666
78. M. Zacharias Combining elastic network analysis and molecular dynamics simulations by Hamiltonian replica exchange J. Chem. Theory Comput. 4 2008 477 487
79. S. Piana, and A. Laio A bias-exchange approach to protein folding J. Phys. Chem. B 111 2007 4553 4559
80. P. Cossio, F. Marinelli, A. Laio, and F. Pietrucci Optimizing the performance of bias-exchange metadynamics: folding a 48-residue LysM domain using a coarse-grained model J. Phys. Chem. B 114 2010 3259 3265
81. C.J. Woods, M.A. King, and J.W. Essex The development of replica-exchange-based free-energy methods J. Phys. Chem. B 107 2003 13703 13710
82. I.V. Khavrutskii, A. Wallqvist, and Anders Improved binding free energy predictions from single-reference thermodynamic integration augmented with Hamiltonian replica exchange J. Chem. Theory Comput. 7 2011 3001 3011
83. D.K. Shenfeld, H. Xu, Huafeng, M.P. Eastwood, R.O. Dror, and D.E. Shaw Minimizing thermodynamic length to select intermediate states for free-energy calculations and replica-exchange simulations Phys. Rev. E 80 2009 046705
84. M.P. Luitz, M. Zacharias, Role of tyrosine hot-spot residues at the interface of colicin E9 and immunity protein 9: a comparative free energy simulation study. Proteins (in press), http://dx.doi.org/10.1002/prot.24203.
85. Y. Meng, D. Sabri Dashti, and A.E. Roitberg Computing alchemical free energy differences with Hamiltonian replica exchange molecular dynamics (H-REMD) simulations J. Chem. Theory Comput. 7 2011 2721 2727
86. T. Rodinger, P.L. Howell, and R. Pomès Calculation of absolute protein-ligand binding free energy using distributed replica sampling J. Chem. Phys. 129 2008 155102 155114
87. W. Jiang, M. Hodoscek, and B. Roux Computation of absolute hydration and binding free energy with free energy perturbation distributed replica-exchange molecular dynamics J. Chem. Theory Comput. 5 2009 2583 2588
88. W. Jiang, and B. Roux Free energy perturbation Hamiltonian replica-exchange molecular dynamics (FEP/H-REMD) for absolute ligand binding free energy calculations J. Chem. Theory Comput. 6 2010 2559 2565
89. M. Lapelosa, E. Gallicchio, and R.M. Levy Conformational transitions and convergence of absolute binding free energy calculations J. Chem. Theory Comput. 8 2012 47 60
90. Y. Sugita, A. Kitao, and Y. Okamoto Multidimensional replica-exchange method for free-energy calculations J. Chem. Phys. 113 2000 6042 6045
91. K. Lindorff-Larsen, N. Trbovic, P. Maragakis, S. Piana, and D.E. Shaw Structure and dynamics of an unfolded protein examined by molecular dynamics simulation J. Am. Chem. Soc. 134 2012 3787 3791
92. C.K. Fisher, and C.M. Stultz Constructing ensembles for intrinsically disordered proteins Curr. Opin. Struct. Biol. 21 2011 426 431
93. M. Cecchini, F. Rao, M. Seeber, and A. Caflisch Replica exchange molecular dynamics simulations of amyloid peptide aggregation J. Chem. Phys. 121 2004 10748
94. M. Han, and U.H.E. Hansmann Replica exchange molecular dynamics of the thermodynamics of fibril growth of Alzheimer's A beta [sub 42] peptide J. Chem. Phys. 135 2010 065101
95. P. Anand, F.S. Nandel, and U.H.E. Hansmann The Alzheimer's beta amyloid (A beta[sub 1-39]) monomer in an implicit solvent J. Chem. Phys. 128 2008 165102
96. 16-22 dimer and trimer Phys. Chem. Chem. Phys. 13 2011 9778 9788
97. Y. Chebaro, N. Mousseau, and P. Derreumaux Structures and thermodynamics of Alzheimer's Amyloid-A (16-35) monomer and dimer by replica exchange molecular dynamics simulations: implication for full-length A fibrillation J. Phys. Chem. B 113 2009 7668 7675
98. A. Baumketner, and J.-E. Shea The structure of the Alzheimer amyloid β 10-35 peptide probed through replica-exchange molecular dynamics simulations in explicit solvent J. Mol. Biol. 366 2007 275 285
99. R. Laghaei, N. Mousseau, and G. Wei Structure and thermodynamics of amylin dimer studied by Hamiltonian-temperature replica exchange molecular dynamics simulations J. Phys. Chem. B 115 2011 3146 3154