Pump-probe molecular dynamics as a tool for studying protein motion and long range coupling

Proteins: Structure, Function and Genetics

Volumn 65, Issue 2, 2006, Pages 347-361

  Sharp, Kim ^a   Skinner, John J ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

Allostery; Correlation analysis; Molecular dynamics; Protein motion; Residue coupling

Indexed keywords

CALMODULIN; PDZ PROTEIN;

ALLOSTERISM; ARTICLE; FOURIER TRANSFORMATION; GENOMICS; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MUTATION; OSCILLATION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN SECONDARY STRUCTURE; PUMP PROBE MOLECULAR DYNAMICS;

CALMODULIN; MODELS, MOLECULAR; MOTION; MUTATION; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY;

EID: 33749029273     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21146     Document Type: Article

References (74)

1. Englander SW, Kallenbach NR. Hydrogen exchange and structural dynamics of proteins and nucleic acids. Q Rev Biophys 1983;16:521-655.
2. Palmer AG, Kroenke CD, Loria JP. Nuclear magnetic resonance methods for quantifying microsecond-to-millisecond motions in biological macromolecules. Methods Enzymol 2001;339:204-238.
3. Go N, Scheraga H. Dynamics of a small globular protein in terms of low frequency vibrational modes. J Chem Phys 1969;5:4751-4767.
4. Case DA. Normal mode analysis of protein dynamics. Curr Opin Struct Biol 1994;4:285-290.
5. Levy R, Srinivasen A, Olson W, McCammon JA. Quasi-harmonic method for studying very low frequency modes in proteins. Biopolymers 1984;23:1099-1112.
6. Levy R, Karplus M, Kushnick J, Perahia D. Evaluation of the configurational entropy for proteins: application to molecular dynamics simulations of an α helix. Macromolecules 1984;17: 1370-1374.
7. McCammon JA, Gelin B, Karplus M, Wolynes P. The hinge bending mode in lysozyme. Nature 1976;262:325,326.
8. Karplus M, Kushnick J. Method for estimating the configurational entropy of macromolecules, Macromolecules 1981;14:325-332.
9. Ichiye IT, Karplus M. Collective motions in proteins: a covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations. Proteins 1991;11:205-217.
10. Hayward S, Kitao A, Go N. Harmonicity and anharmonicity in protein dynamics: a normal mode analysis and principal component analysis. Proteins Struct Funct Genet 1995;23:177-186.
11. Amadei A, Linssen AB, Berendsen HJ. Essential dynamics of proteins. Proteins 1993;17:412-425.
12. Hünenberger PH, Mark AE, van Gunsteren WF. Fluctuation and cross-correlation analysis of protein motions observed in nanosecond molecular dynamics simulations. J Mol Biol 1995;252:492-503.
13. VanAalten D, DeGroot B, Findlay J, Berendsen H, Amadei A. A comparison of techniques for calculating essential dynamics. J Comp Chem 1997;18:169-181.
14. Abseher R, Nilges M. Are there non-trivial dynamic cross-correlations in proteins? J Mol Biol 1998;279:911-920.
15. Balsera MA, Wriggers W, Oono Y, Schulten K. Principal component analysis and long time protein dynamics. J Phys Chem 1996;100: 2567-2572.
16. Prabhu N, Lee A, Wand JW, Sharp KA. Dynamics and entropy of a calmodulin-peptide complex studied by NMR and molecular dynamics. Biochemistry 2002;42:562-570.
17. Tirion M. Large amplitude elastic motions in proteins from a single parameter, atomic analysis. Phys Rev Lett 1996;77:1905-1908.
18. Kim MK, Chirikjian GS, Jernigan RL. Elastic models of conformational transitions in macromolecules. J Mol Graph Model 2002;21:151-160.
19. Miyashita O, Onuchic JN, Wolynes PG. Nonlinear elasticity, protein quakes, and the energy landscapes of functional transitions in proteins. Proc Natl Acad Sci USA 2003;100:12570-12575.
20. Zheng W, Brooks B, Donaich S, Thirumalai D. Network of dynamically important residues in the open/closed transistion in polymerases is strongly conserved. Structure 2005;13:565-577.
21. Session R, Dauber-Osguthorpe P, Osguthorpe D. Filtering molecular dynamics trajectories to reveal low-frequency collective motions: phospholipase A2. J Mol Biol 1986;209:617-633.
22. Levitt M. Real-time interactive frequency filtering of molecular dynamics simulations. J Mol Biol 1991;220:1-4.
23. Dauber-Osguthorpe P, Maunder C, Osguthorpe D. Molecular dynamics: deciphering the data. J Comput Aided Des 1996;10:177-185.
24. Phillips S, Essex J, Edge C. Digitally filtered molecular dynamics: the frequency specific control of molecular dynamics simulations. J Phys Chem 2000;112:2586-2597.
25. Bowman JM, Zhang X, Brown A. Normal-mode analysis without the Hessian: a driven molecular-dynamics approach. J Chem Phys 2003;119:646-650.
26. Kaledin M, Brown A, Kaledin AL, Bowman JM. Normal mode analysis using the driven molecular dynamics method. II. An application to biological macromolecules. J Chem Phys 2004;121:5646-5653.
27. Akke M, Bruschweiler R, Palmer A. NMR order parameters and free energy. J Am Chem Soc 1993;115:9832,9833.
28. Chatfield D, Szabo A, Brooks BR. Molecular dynamics of S. nuclease: comparison of simulation with 15N and 13O relaxation data. J Am Chem Soc 1998;120:5301-5311.
29. Wong KB, Daggett V. Barstar has a highly dynamic hydrophobic core: evidence from molecular dynamics simulations and nuclear magnetic resonance relaxation data. Biochemistry 1998;11:11182-11192.
30. Zabell APR, Post CB. Docking multiple conformations of a flexible ligand into a protein binding site using NMR restraints. Proteins Struct Funct Genet 2002;46:295-307.
31. Ma J, Karplus M. The allosteric mechanism of the chaperonin GroEL: a dynamic analysis. Proc Natl Acad Sci USA 1998;95: 8502-8507.
32. Cooper A, Dryden DTF. Allostery without conformational change. A plausible model. Eur Biophys J 1984;11:103-109.
33. Perutz M. Mechanisms of cooperativity and allosteric regulation in proteins. Q Rev Biophys 1989;22:139-237.
34. Perutz MF, Fermi G, Luisi B, Shaanan B, Liddington RC. Stereochemistry of cooperative mechanisms in hemoglobin. Acc Chem Res 1987;20:309-321.
35. Freire E. The propagation of binding interactions to remote sites in proteins. Proc Natl Acad Sci USA 1999;96:10118-10122.
36. Sun H, Yin D, Coffeen LA, Shea MA, Squier TC. Mutation of Tyr138 disrupts the structural coupling between the opposing domains in vertebrate calmodulin. Biochemistry 2001;40:9605-9617.
37. Jaren OR, Kranz JK, Sorensen BR, Wand AJ, Shea MA. Calcium-induced conformational switching of Paramecium calmodulin provides evidence for domain coupling. Biochemistry 2002;41:14158-14166.
38. Sorensen BR, Faga LA, Hultman R, Shea MA. An interdomain linker increases the thermostability and decreases the calcium affinity of the calmodulin N-domain. Biochemistry 2002;41:15-20.
39. Faga LA, Sorensen BR, VanScyoc WS, Shea MA. Basic interdomain boundary residues in calmodulin decrease calcium affinity of sites I and II by stabilizing helix-helix interactions. Proteins Struct Funct Genet 2003;50:381-391.
40. Lockless S, Ranganathan R. Evolutionarily conserved pathways of energetic connectivity in protein families. Science 1999;286: 295-299.
41. Fuentes E, Channing J, Lee AL. Ligand dependent dynamics and intramolecular signaling in a PDZ domain. J Mol Biol 2004; 335:1105-1115.
42. Suel G, Lockless S, Wall M, Ranganathan R. Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nat Struct Biol 2003;10:59-69.
43. Clarkson M, Lee AL. Long range dynamic effects of point mutations propagate through side chains in the serine protease inhibitor Eglin c. Biochemistry 2004;43:12448-12458.
44. Igumenova T, Lee AL, Wand AJ. Backbone and side chain dynamics of mutant calmodulin-peptide complexes. Biochemistry 2005;44:12627-12639.
45. Lee AL, Kinnear SA, Wand AJ. Redistribution and loss of side chain entropy upon formation of a calmodulin-peptide complex. Nat Struct Biol 2000;7:72-77.
46. Lee AL, Wand AJ. Microscopic origins of entropy, heat capacity and the glass transition in proteins. Nature 2001;411:501-504.
47. Lee AL, Sharp KA, Kranz JK, Song X, Wand AJ. Temperature dependence of the internal dynamics of a calmodulin-peptide complex. Biochemistry 2002;41:13814-13825.
48. Mayer K, Earley M, Gupta S, Pichumani K, Regan L, Stone M. Covariation of backbone motion throughout a small protein domain. Nat Struct Biol 2003;10:962-965.
49. Lange O, Grubmuller H, deGroot B. Molecular dynamics simulations protein G challenge NMR-derived correlated backbone motions. Angew Chem Int Ed 2005;44:3394-3399.
50. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: a program for macromolecular energy, minimization and dynamics calculations. J Comp Chem 1983;4: 187.
51. Press W, Flannery B, Teukolsky S, Vetterling W. Numerical recipes. Cambridge: Cambridge University Press; 1986.
52. van Kampen NG. Stochastic processes in physics and chemistry. Amsterdam: Elsevier; 1992.
53. MacKerell AD, Brooks B, Brooks CL, Nilsson L, Roux B, Won Y, Karplus M. CHARMM: the energy function and its parameterization with an overview of the program. In: Schleyer PVR, editor. The encyclopedia of computational chemistry, Vol. 1. Chichester: Wiley; 1998. pp 271-277.
54. Sridharan S, Nicholls A, Sharp KA. A rapid method for calculating derivatives of solvent accessible surface areas of molecules. J Comp Chem 1995;16:1038-1044.
55. Ryckaert JP, Ciccotti G, Berendsen HJC. Integration of the Cartesian equation of motions of a system with constraints: molecular dynamics of n-alkanes. Numerical J Comp Chem 1977;23: 327-341.
56. Meador W, Means A, Quiocho F. Target enzyme recognition by calmodulin: 2.4 angstroms structure of a calmodulin-peptide. Science 1992;257:1251.
57. Yap KL, Kim J, Truong K, Sherman M, Yuan T, Ikura M. Calmodulin target database. J Struct Funct Genomics 2001;1:8-14.
58. Babu YS, Bugg CE, Cook WJ. Structure of calmodulin refined at 2.2 A resolution. J Mol Biol 1988;204:191-204.
59. Pedigo S, Shea MA. Discontinuous equilibrium titrations of cooperative calcium binding to calmodulin monitored by 1-D 1H-nuclear magnetic resonance spectroscopy. Biochemistry 1995;34:10676-10689.
60. Wintrode P, Privalov P. Energetics of target peptide recognition by calmodulin: a calorimetric study. J Mol Biol 1997;266:1050-1062.
61. Kranz JK, Flynn PF, Fuentes EJ, Wand AJ. Dissection of the pathway of molecular recognition by calmodulin. Biochemistry 2002;41:2599-2608.
62. Vanscyoc WS, Shea MA. Phenylalanine fluorescence studies of calcium binding to N-domain fragments of Paramecium calmodulin mutants show increased calcium affinity correlates with increased disorder. Protein Sci 2001;10:1758-1768.
63. Doyle DA, Lee A, Lewis J, Kim E, Sheng M, MacKinnon R. Crystal structures of a complexed and peptide-free membrane protein-binding domain: molecular basis of peptide recognition by PDZ. Cell 1996;85:1067-1076.
64. Songyang Z, Fanning AS, Fu C, Xu J, Marfatia SM, Chishti AH, Crompton A, Chan AC, Anderson JM, Cantley LC. Recognition of unique carboxyl-terminal motifs by distinct PDZ domains. Science 1997;275:73-77.
65. Dadarlat VM, Post CB. Adhesive-cohesive model for protein compressibility: an alternative perspective on stability. Proc Natl Acad Sci USA 2003;100:14778-14783.
66. Lide DR, editor. CRC handbook of chemistry and physics, 71st ed. Boca Raton: CRC; 1990.
67. Becker O, Karplus M. Temperature echoes in molecular dynamics simulations of proteins. Phys Rev Lett 1993;70:3514-3517.
68. Ota N, Agard D. Intramolecular signaling pathways revealed by anisotropic thermal diffusion. J Mol Biol 2005;351:345-354.
69. Paci E, Karplus M. Unfolding proteins by external forces and temperature: the importance of topology and energetics. Proc Natl Acad Sci USA 2000;97:6521-6526.
70. Snow CD, Qiu LD, Deguo, Gai F, Hagen SJ, Pande VS. Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy. Proc Natl Acad Sci USA 2004;101:4077-4082.
71. Lu H, Isralewitz B, Krammer A, Vogel V, Schulten K. Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation. Biophys J 1998;75:662-671.
72. Yu X, Leitner DM. Heat flow in proteins: computation of thermal transport coefficients. J Chem Phys 2005;122:1-11.
73. Cusack S, Smith J, Finney J, Tidor B, Karplus M. Inelastic neutron scattering analysis of picosecond internal protein dynamics. Comparison of harmonic theory with experiment. J Mol Biol 1988;202:903-908.
74. Balog E, Becker T, Oettl M, Lechner R, Daniel R, Finney J, Smith JC. Direct determination of vibrational density of states change on ligand binding to a protein. Phys Rev Lett 2004;93:1-4.