Molecular dynamics simulation of solvated azurin: Correlation between surface solvent accessibility and water residence times

Proteins: Structure, Function and Genetics

Volumn 39, Issue 1, 2000, Pages 56-67

  Luise, A ^a   Falconi, M ^a   Desideri, A ^a  

^a UNIVERSITY OF ROME TOR VERGATA   (Italy)

Author keywords

GROMOS force field; Hydration sites; Hydrophilicity; Protein solvent interactions; Solvent exposure; Surface shape

Indexed keywords

AZURIN; SOLVENT; WATER;

ARTICLE; HYDROGEN BOND; HYDROPHILICITY; MOLECULAR DYNAMICS; PRIORITY JOURNAL; SIMULATION; SOLVATION; SURFACE PROPERTY;

AZURIN; COMPUTER SIMULATION; MODELS, MOLECULAR; PROTEIN STRUCTURE, SECONDARY; SOFTWARE; SOLUTIONS; SOLVENTS; SURFACE PROPERTIES; WATER;

EID: 0033995767     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(20000401)39:1<56::AID-PROT6>3.0.CO;2-5     Document Type: Article

References (41)

1. Phillips Jr. G, Pettitt BM. Structure and dynamics of water around myoglobin. Protein Sci 1995;4:149-158.
2. Teeter MM. Water-protein interactions: theory and experiment. Annu Rev Biophys Biophys Chem 1991;20:577-600.
3. Karplus PA, Faerman C. Ordered water in macromolecular structure. Curr Opin Struct Biol 1994;4:770-776.
4. Burling FT, Weis WI, Flaherty KM, Brunger AT. Direct observation of protein solvation and discrete disorder with experimental crystallographic phases. Science 1996;271:72-77.
5. Kossiakoff AA, Sintchak MD, Shpungin J, Presta LG. Analysis of solvent structure in proteins using neutron D2O-H2O solvent maps: Pattern of primary and secondary hydration of trypsin. Proteins 1992;12:223-236.
6. Finer-Moore JS, Kossiakoff AA, Hurley JH, Earnest T, Stroud RM. Solvent structure in crystals of trypsin determined by X-ray and neutron diffraction. Proteins 1992;12:203-222.
7. Otting G, Liepinsh E, Wuthrich J. Protein hydration in aqueous solution. Science 1991;254:974-980.
8. Brunne RM, Liepinsh E, Otting G, Wutrich K, van Gunsteren WF. Hydration of proteins. A comparison of experimental residence times of water molecules solvating the bovine pancreatic trypsin inhibitor with theoretical model calculations. J Mol Biol 1993;231: 1040-1048.
9. Zanotti JM, Bellissent-Funel MC, Parello J. Hydration-coupled dynamics in proteins studied by neutron scattering and NMR: The case of the typical EF-hand calcium-binding parvalbumin. Biophys J 1999;76:2390-2411.
10. Bellissent-Funel MC, Lal J, Bradley KF, Chen SH. Neutron structure factors of in vivo deuterated amorphous protein C-phycocyanin. Biophys J 1993;64:1542-1549.
11. Bellissent-Funel MC, Zanotti JM, Chen SH. Slow dynamics of water molecules on the surface of a globular protein. Faraday Discuss 1996;103:281-294.
12. Komeiji Y, Uebayasi M, Someya J, Yamato I. A molecular dynamics study of solvent behavior around a protein. Proteins 1993;16: 268-277.
13. Abseher R, Schreiber H, Steinhauser O. The influence of a protein on water dynamics in its vicinity investigated by molecular dynamics simulation. Proteins 1996;25:366-378.
14. Bizzarri AR, Cannistraro S. Molecular dynamics simulation evidence of anomalous diffusion of plastocyanin hydration water. Phys Rev E 1996;53:3040-3043.
15. Makarov VA, Feig M, Andrews BK, Pettitt BM. Diffusion of solvent around biomolecular solutes: A molecular dynamics simulation study. Biophys J 1998;75:150-158.
16. Garcia AE, Stiller L. Computation of the mean residence time of water in the hydration shells of biomolecules. J Comput Chem 1993;14:1396-1406.
17. Levitt M, Sharon R. Accurate simulation of protein dynamics in solution. Proc Natl Acad Sci USA 1988;85:7557-7561.
18. Muegge I, Knapp EW. Residence times and lateral diffusion of water at protein surfaces: application to BPTI. J Phys Chem 1995;99:1371-1374.
19. Rocchi C, Bizzarri AR, Cannistraro S. Water residence times around copper plastocyanin: a molecular dynamics simulation approach. Chem Phys 1997;214:261-276.
20. Kovacs H, Mark AE, van Gunsteren WF. Solvent structure at a hydrophobic protein surface. Proteins 1997;27:395-404.
21. Bonvin AMJJ, Sunnerhagen M, Otting G, van Gunsteren WF. Water molecules in DNA recognition II: a molecular dynamics view of the structure and hydration of the trp operator. J Mol Biol 1998;282:859-873.
22. Frenkel D, Smit B. Understanding molecular simulation. From algorithms to applications. San Diego: Academic Press; 1996. 347 p.
23. Alper HE, Bassolino-Klimas D, Stouch TR. The limiting behavior of water hydrating phospholipid monolayer: A computer simulation study. J Chem Phys 1993;99:5547-5559.
24. Smith W, Forester TR. DL_POLY_2.0: A general-purpose parallel molecular dynamics simulation package. J Mol Graph 1996;14: 136-141.
25. Melchionna S, Luise A, Venturoli M, Cozzini S. DLPROTEIN: A molecular dynamics package to simulate biomolecules. In: Voli M, editor. Science and supercomputing at CINECA - 1997 report. Supercomputing Group, CINECA; 1998. p 496-505.
26. van Gunsteren WF, Berendsen HJC. Groningen Molecular Simulation (GROMOS) Library Manual. Groningen: Biomos; 1987.
27. Melchionna S, Falconi M, Desideri A. Effect of temperature and hydration on protein fluctuations: molecular dynamics simulation of Cu, Zn superoxide dismutase at six different temperatures. Comparison with neutron scattering data. J Chem Phys 1998;108: 6033-6041.
28. Berendsen HJC, Grigera JR, Straatsma TP. The missing term in effective pair potentials. J Phys Chem 1987;91:6269-6271.
29. Nar H, Messerschmidt A, Huber R, Van De Kamp M, Canters GW. Crystal structure analysis of oxidized pseudomonas aeruginosa azurin at ph 5.5 and pH 9.0. A pH-induced conformational transition involves a peptide bond flip. J Mol Biol 1991;221:765-772.
30. Bernstein F, Koetzle T, Williams G, et al. The protein data bank: a computer-based archival file for macromolecular structures. J Mol Biol 1977;112:535-542.
31. Melchionna S, Ciccotti G. Atomic stress isobaric scaling for systems subjected to holonomic constraints. J Chem Phys 1997;106: 195-200.
32. Ryckaert JP, Ciccotti G, Berendsen HJC. Numerical integration of the cartesian equations of motions of a system with constraints: molecular dynamics of N-alkanes. J Comp Phys 1977;23:327-341.
33. Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
34. Kneller GR. Superposition of molecular structures using quaternions. Mol Sim 1991;7:113-119.
35. Lee B, Richards FM. The interpretation of protein structures: estimation of static accessibility. J Mol Biol 1971;55:379-400.
36. Impey RW, Madden PA, McDonald IR. Hydration and mobility of ions in solution. J Phys Chem 1983;87:5071-5083.
37. Kuhn LA, Swanson CA, Pique ME, Tainer JA, Getzoff ED. Atomic and residue hydrophylicity in the context of folded protein structure. Proteins 1995;23:536-547.
38. Levitt M, Park BH. Water: now you see it, now you don't. Structure 1993;15:223-226.
39. Kuhn LA, Siani MA, Pique ME, Fisher CL, Getzoff ED, Tainer JA. The interdependence of protein surface topography and bound water molecules revealed by surface accessibility and fractal density measures. J Mol Biol 1992;228:13-22.
40. Wade RC, Mazor MH, McCammon JA, Quiocho FA. A molecular dynamics study of thermodynamic and structural aspects of the hydration of cavities in proteins. Biopolymers 1991;1:919-931.
41. Kraulis J. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J Appl Cryst 1991;24:946-950.