Modeling the hydration layer around proteins: HyPred

Biophysical Journal

Volumn 99, Issue 5, 2010, Pages 1611-1619

  Virtanen, Jouko J ^a,c   Makowski, Lee ^d   Sosnick, Tobin R ^a,b   Freed, Karl F ^a,c  

^a UNIVERSITY OF CHICAGO   (United States)

^b UNIVERSITY OF CHICAGO   (United States)

^c UNIVERSITY OF CHICAGO   (United States)

^d ARGONNE NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77956593725     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2010.06.027     Document Type: Article

References (40)

1. Denisov, V. P., B. H. Jonsson, and B. Halle. 1999. Hydration of denatured and molten globule proteins. Nat. Struct. Biol. 6:253-260.
2. Langhorst, U., J. Backmann., J. Steyaert. 2000. Analysis of a water mediated protein-protein interactions within RNase T1. Biochemistry. 39:6586-6593.
3. Tarek, M., and D. J. Tobias. 1999. Environmental dependence of the dynamics of protein hydration water. J. Am. Chem. Soc. 121:9740-9741.
4. Chen, C., B. W. Beck., B. M. Pettitt. 2006. Solvent participation in Serratia marcescens endonuclease complexes. Proteins. 62:982-995.
5. Dubins, D. N., R. Filfil., T. V. Chalikian. 2000. Role of water in protein-ligand interactions: volumetric characterization of the binding of 2′-CMP and 3′-CMP to ribonuclease A. J. Phys. Chem. B. 104:390-401.
6. Tame, J. R., S. H. Sleigh., J. E. Ladbury. 1996. The role of water in sequence-independent ligand binding by an oligopeptide transporter protein. Nat. Struct. Biol. 3:998-1001.
7. Mehl, A. F., B. Demeler, and A. Zraikat. 2007. A water mediated electrostatic interaction gives thermal stability to the "tail" region of the GrpE protein from E. coli. Protein J. 26:239-245.
8. Yang, Y., M. Berrondo., D. Busath. 2004. The importance of water molecules in ion channel simulations. J. Phys. Condens. Matter. 16: S2145-S2148.
9. Ernst, J. A., R. T. Clubb., G. M. Clore. 1995. Demonstration of positionally disordered water within a protein hydrophobic cavity by NMR. Science. 267:1813-1817.
10. Syvitski, R. T., Y. Li., G. N. La Mar. 2002. 1H NMR detection of immobilized water molecules within a strong distal hydrogen-bonding network of substrate-bound human heme oxygenase-1. J. Am. Chem. Soc. 124:14296-14297.
11. Tsui, V., I. Radhakrishnan., D. A. Case. 2000. NMR and molecular dynamics studies of the hydration of a zinc finger-DNA complex. J. Mol. Biol. 302:1101-1117.
12. Higo, J., and M. Nakasako. 2002. Hydration structure of human lysozyme investigated by molecular dynamics simulation and cryogenic x-ray crystal structure analyses: on the correlation between crystal water sites, solvent density, and solvent dipole. J. Comput. Chem. 23:1323-1336.
13. Jiang, J. S., and A. T. Brünger. 1994. Protein hydration observed by x-ray diffraction. Solvation properties of penicillopepsin and neuraminidase crystal structures. J. Mol. Biol. 243:100-115.
14. Svergun, D. I., S. Richard., G. Zaccai. 1998. Protein hydration in solution: experimental observation by x-ray and neutron scattering. Proc. Natl. Acad. Sci. USA. 95:2267-2272.
15. McDowell, R. S., and A. A. Kossiakoff. 1995. A comparison of neutron diffraction and molecular dynamics structures: hydroxyl group and water molecule orientations in trypsin. J. Mol. Biol. 250:553-570.
16. Savage, H., and A. Wlodawer. 1986. Determination of water structure around biomolecules using x-ray and neutron diffraction methods. Methods Enzymol. 127:162-183.
17. Makarov, V., B. M. Pettitt, and M. Feig. 2002. Solvation and hydration of proteins and nucleic acids: a theoretical view of simulation and experiment. Acc. Chem. Res. 35:376-384.
18. Feig, M., and B. M. Pettitt. 1999. Modeling high-resolution hydration patterns in correlation with DNA sequence and conformation. J. Mol. Biol. 286:1075-1095.
19. Lounnas, V., B. M. Pettitt, and G. N. Phillips, Jr. 1994. A global model of the protein-solvent interface. Biophys. J. 66:601-614.
20. Makarov, V. A., B. K. Andrews, and B. M. Pettitt. 1998. Reconstructing the protein-water interface. Biopolymers. 45:469-478.
21. Rudnicki, W. R., and B. M. Pettitt. 1997. Modeling the DNA-solvent interface. Biopolymers. 41:107-119.
22. Dudowicz, J., K. F. Freed, and M. Y. Shen. 2003. Hydration structure of Met-encephalin: a molecular dynamics study. J. Chem. Phys. 118:1989-1995.
23. Vijay-Kumar, S., C. E. Bugg., W. J. Cook. 1987. Comparison of the three-dimensional structures of human, yeast, and oat ubiquitin. J. Biol. Chem. 262:6396-6399.
24. Diamond, R. 1974. Real-space refinement of the structure of hen egg-white lysozyme. J. Mol. Biol. 82:371-391.
25. Maurus, R., C. M. Overall., G. D. Brayer. 1997. A myoglobin variant with a polar substitution in a conserved hydrophobic cluster in the heme binding pocket. Biochim. Biophys. Acta. 1341:1-13.
26. Phillips, J. C., R. Braun., K. Schulten. 2005. Scalable molecular dynamics with NAMD. J. Comput. Chem. 26:1781-1802.
27. MacKerell, Jr., A. D., D. Bashford., M. Karplus. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B. 102:3586-3616.
28. Mahoney, M. W. J., and L. William. 2000. A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions. J. Chem. Phys. 112:8910-8922.
29. Jorgensen, W. L., J. Chandrasekhar., M. L. Klein. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935.
30. Pettitt, B. M., V. A. Makarov, and B. K. Andrews. 1998. Protein hydration density: theory, simulations and crystallography. Curr. Opin. Struct. Biol. 8:218-221.
31. Schymkowitz, J. W., F. Rousseau., L. Serrano. 2005. Prediction of water and metal binding sites and their affinities by using the Fold-X force field. Proc. Natl. Acad. Sci. USA. 102:10147-10152.
32. Roe, S. M., and M. M. Teeter. 1993. Patterns for prediction of hydration around polar residues in proteins. J. Mol. Biol. 229:419-427.
33. Schneider, B., D. M. Cohen., H. M. Berman. 1993. A systematic method for studying the spatial distribution of water molecules around nucleic acid bases. Biophys. J. 65:2291-2303.
34. Madhusudhan, M. S., and S. Vishveshwara. 2001. Deducing hydration sites of a protein from molecular dynamics simulations. J. Biomol. Struct. Dyn. 19:105-114.
35. Makarov, V. A., B. K. Andrews., B. M. Pettitt. 2000. Residence times of water molecules in the hydration sites of myoglobin. Biophys. J. 79:2966-2974.
36. Hummer, G., A. E. García, and D. M. Soumpasis. 1995. Hydration of nucleic acid fragments: comparison of theory and experiment for highresolution crystal structures of RNA, DNA, and DNA-drug complexes. Biophys. J. 68:1639-1652.
37. Zhang, X. J., and B. W. Matthews. 1994. Conservation of solventbinding sites in 10 crystal forms of T4 lysozyme. Protein Sci. 3:1031-1039.
38. Reference deleted in proof.
39. Lazaridis, T., and M. E. Paulaitis. 1992. Entropy of hydrophobic hydration: a new statistical mechanical formulation. J. Phys. Chem. 96:3847-3855.
40. Eisenberg, D., and A. D. McLachlan. 1986. Solvation energy in protein folding and binding. Nature. 319:199-203.