Protein-water interactions in ribonuclease A and angiogenin: A molecular dynamics study

Proteins: Structure, Function and Genetics

Volumn 55, Issue 4, 2004, Pages 915-923

  Sanjeev, B S ^a   Vishveshwara, Saraswathi ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

Author keywords

Invariant waters; Maximum residence time; Protein water networks

Indexed keywords

ANGIOGENIN; PROTEIN; RIBONUCLEASE A; WATER;

ARTICLE; ENZYME MECHANISM; HYDRATION; HYDROGEN BOND; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN INTERACTION; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS;

BINDING SITES; COMPUTER SIMULATION; HYDROGEN BONDING; MODELS, MOLECULAR; RIBONUCLEASE, PANCREATIC; WATER;

EID: 2542633488     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20114     Document Type: Article

References (40)

1. Westhof E, editor. Topics in molecular and structure biology: water and biological macromolecules. London: MacMillan Press Ltd.; 1993.
2. Levitt M, Park BH. Water: now you see it, now you don't. Structure 1993;1:223-226.
3. Zhang XJ, Matthews BW. Conservation of solvent-binding sites in 10 crystal forms of T4 lysozyme. Protein Sci 1994;3:1031-1039.
4. Simmerling CL, Elber R. Computer determination of peptide conformations in water: different roads to structure. Proc Natl Acad Sci USA 1995;92:3190-3193.
5. Sadasivan C, Nagendra HG, Vijayan M. Plasticity, hydration and accessibility in ribonuclease A. The structure of a new crystal form and its low-humidity variant. Acta Crystallogr D Biol Crystallogr 1998;54:1343-1352.
6. Biswal BK, Sukumar N, Vijayan M. Hydration, mobility, and accessibility of lysozyme: structures of a pH 6.5 orthorhombic form and its low-humidity variant and a comparative study involving 20 crystallographically independent molecules. Acta Crystallogr D Biol Crystallogr 2000;56:1110-1119.
7. Prasad BV, Suguna K. Role of water molecules in the structure and function of aspartic proteinases. Acta Crystallogr D Biol Crystallogr 2002;58:250-259.
8. Tarek M, Tobias DJ. The dynamics of protein hydration water: a quantitative comparison of molecular dynamics simulations and neutron-scattering experiments. Biophys J 2000;79:3244-3257.
9. Chatake T, Ostermann A, Kurihara K, Parak FG, Niimura N. Hydration in proteins observed by high-resolution neutron crystallography. Proteins 2003;50:516-523.
10. Austin RH, Roberson MW, Mansky P. Far-infrared perturbation of reaction rates in myoglobin at low temperatures. Phys Rev Lett 1989;62:1912-1915.
11. Massi F, Straub JE. Structural and dynamical analysis of the hydration of the Alzheimer's beta-amyloid peptide. J Comp Chem 2002;24:143-153.
12. Bizzarri AR, Cannistraro S. Molecular dynamics of water at the protein-solvent interface. J Phys Chem B 2002;106:6617-6633.
13. Makarov V, Pettitt BM. Solvation and hydration of proteins and nucleic acids: a theoretical view of simulation and experiment. Acc Chem Res 2002;35:376-384.
14. Kombo DC, Young MA, Beveridge DL. Molecular dynamics simulation accurately predicts the experimentally-observed distributions of the (C, N, O) protein atoms around water molecules and sodium ions. Proteins 2000;39:212-215.
15. Denisov VP, Halle B. Protein hydration dynamics in aqueous solution. Faraday discuss 1996;103:227-244.
16. Rocchi C, Bizzarri AR, Cannistraro S. Water residence times around copper plastocyanin: a molecular dynamics simulation approach. Chem Phys 1997;214:261-276.
17. Bizzarri AR, Cannistraro S. Molecular dynamics simulation evidence of anamolous diffusion of protein hydration water. Phys Rev E 1996;53:R3040-R3043.
18. Bizzarri AR, Cannistraro S. Anamolous and anisotropic diffusion of plastocyanin hydration water. Europhys Lett 1997;37:201-206.
19. Makarov VA, Andrews BK, Smith PE, Pettit BM. Residence times of water molecules in the hydration sites of myoglobin. Biophys J 2000;79:2966-2974.
20. Muegge I, Knapp EW. Residence times and lateral diffusion of water at protein surfaces: application to BPTI. J Phys Chem 1995;99:1371-1374.
21. Garcia AE, Stiller L. Computation of the mean residence time of water in the hydration shells of biomolecules. J Comp Chem 1993;14:1396-1406.
22. Roe SM, Teeter MM. Patterns for prediction of hydration around polar residues in proteins. J Mol Biol 1993;229:419-427.
23. Madhusudhan MS, Vishveshwara S. Deducing hydration sites of a protein from molecular dynamics simulations. J Biomol Struct Dyn 2001;19:105-114.
24. Madhusudhan MS, Sanjeev BS, Vishveshwara S. Computer modeling and molecular dynamics simulations of ligand bound complexes of bovine angiogenin: dinucleotide topology at the active site of RNase a family proteins. Proteins 2001;45:30-39.
25. Vishveshwara S, Madhusudhan MS, Maizel Jr JV. Short-strong hydrogen bonds and a low barrier transition state for the proton transfer reaction in RNase A catalysis: a quantum chemical study. Biophys Chem 2001;89:105-117.
26. Wlodawer A, Svensson LA, Sjolin L, Gilliland GL. Structure of phosphate-free ribonuclease A refined at 1.26 Å. Biochemistry 1988;27:2705-2717.
27. Leonidas DD, Shapiro R, Allen SC, Subbarao GV, Veluraja K, Acharya KR. Refined crystal structures of native human angiogenin and two active site variants: implications for the unique functional properties of an enzyme involved in neovascularisation during tumour growth. J Mol Biol 1999;285:1209-1233.
28. AMBER, Version 7, University of California, San Francisco; 2002
29. Cheatham III TE, Cieplak P, Kollman PA. A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat. J Biomol Struct Dyn 2002;16:845-861
30. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. Comparison of simple potential functions for simulating liquid water. J Chem Phys 1983;79:926-935.
31. Darden TA, York DM, Pedersen LG. Particle mesh Ewald: An N. log (N) Method for Ewald sums in large systems. J Chem Phys 1993;98:10089-10092.
32. Schoenborn BP, Garcia A, Knott R. Hydration in protein crystallography. Prog. Biophys Mol Biol 1995;64:105-119.
33. Blake CCF, Pulford WCA, Artymuik PJ. X-ray study of water in crystals of lysozyme. J Mol Biol 1983;167:693-723.
34. Baker EN, Hubbard RE. Hydrogen bonding in globular proteins. Prog Biophys Mol Biol 1984;44:97-179.
35. Narsingh D. Graph theory with applications to engineering and computer science. New York: Prentice-Hall; 1974. p 274-276.
36. NACCESS, Version 2.1.1, Department of Biochemistry and Molecular Biology, University College London; 1996.
37. Brunne RM, Liepish E, Otting G, Wuthrich K, van Gunsteren WF. Hydration of proteins: a comparison of residence times of water molecules solvating the bovine pancreatic trysin inhibitor with theoretical model calculations. J Mol Biol 1993;231:1040-1048.
38. Kovacs H, Mark AE, van Gunsteren WF. Solvent structure at a hydrophobic protein surface. Proteins 1997;27:395-404.
39. Rupley JA, Careri G. Protein hydration and function. Adv Protein Chem 1991;41:37-172.
40. Kraulis PJ. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 1991;24: 946-950.