High-density hydration layer of lysozymes" Molecular dynamics decomposition of solution scattering data

Journal of Chemical Information and Modeling

Volumn 45, Issue 6, 2005, Pages 1593-1599

  Merzel, Franci ^a   Smith, Jeremy C ^a,b  

^a NATIONAL INSTITUTE OF CHEMISTRY   (Slovenia)

^b UNIVERSITY OF HEIDELBERG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

DATA ACQUISITION; DECOMPOSITION; HYDRATION; MOLECULAR DYNAMICS; NEUTRON SCATTERING; PERTURBATION TECHNIQUES; X RAY ANALYSIS;

BULK WATER; PROTEIN STRUCTURE; WATER DENSITY; WATER DIPOLES;

PROTEINS;

LYSOZYME; OXYGEN; PROTEIN; SOLVENT; WATER;

ALGORITHM; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; HYDROGEN BOND; SOLUTION AND SOLUBILITY;

ALGORITHMS; HYDROGEN BONDING; MODELS, MOLECULAR; MURAMIDASE; OXYGEN; PROTEINS; SOLUTIONS; SOLVENTS; WATER;

EID: 28944441392     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci0502000     Document Type: Conference Paper

References (26)

1. Pettitt, B. M.; Makarov, V. A.; Andrews, B. K. Protein hydration density" theory, simulations and crystallography. Curr. Opin. Struct. Biol. 1998, 8, 218-221.
2. Teeter, M. M. Water-protein interactions - theory and experiment. Annu. Rev. Biophys. Biophys. Chem. 1991, 20, 577-600.
3. Carugo, O.; Bordo, D. How many water molecules can be detected by protein crystallography? Acta Crystallogr., Sect. D 1999, 55, 479-483.
4. Schoenborn, B. P.; Garcia, A.; Knott, R. Hydration in protein crystallography. Prog. Biophys. Mol. Biol. 1995, 64, 105-119.
5. Denisov, V. P.; Halle, B. Protein hydration dynamics in aqueous solution. Faraday Discuss. 1996, 103, 227-244.
6. Wiesner, S.; Kurian, E.; Prendergast, F. G.; Halle, B. Water molecules in the binding cavity of intestinal fatty acid binding protein" Dynamic characterization by water O-17 and H-2 magnetic relaxation dispersion. J. Mol. Biol. 1999, 256, 233-246.
7. Leach, A. R.; Molecular Modelling" Principles and Applications; Addison-Wesley Longman" Essex, England, 1996.
8. Janežič, D.; Praprotnik, M.; Merzel, F. Molecular dynamics integration and molecular vibrational theory. I. New symplectic integrators. J. Chem. Phys. 2005, 122, 174101 (article number).
9. Praprotnik, M.; Janežič, D. Molecular dynamics integration and molecular vibrational theory. II. Simulation of nonlinear molecules. J. Chem. Phys. 2005, 122, 174102 (article number).
10. Praprotnik, M.; Janežič, D. Molecular dynamics integration and molecular vibrational theory. III. The infrared spectrum of water. J. Chem. Phys. 2005, 122, 174103 (article number).
11. 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.
12. Makarov, V. A.; Andrews, B. K.; Smith, P. E.; Pettitt, B. M. Residence times of water molecules in the hydration sites of myoglobin Biophys. J. 2000, 79, 2966-2974.
13. Luise, A.; Falconi, M.; Desideri, A. Molecular dynamics simulation of solvated azurin" Correlation between surface solvent accessibility and water residence times Proteins 2000, 39, 56-67.
14. Brooks, B. R.; Janežič, D.; Karplus, M. Harmonic-analysis of large systems. 1. Methodology. J. Comput. Chem. 1995, 16, 1522-1542.
15. Janežič, D.; Brooks, B. R. Harmonic-analysis of large systems. 2. Comparison of different protein models. J. Comput. Chem. 1995, 16, 1543-1553.
16. Janežič, D.; Venable, R. M.; Brooks, B. R. Harmonic-analysis of large systems. 3. Comparison with molecular-dynamics. J. Comput. Chem. 1995, 16, 1554-1566.
17. Higgins, J. S.; Benoit, H. C. Polymers and Neutron Scattering; Calendron Press" Oxford, U. K., 1994.
18. Svergun, D.; Richard, S.; Koch, M. H.; Sayers, Z.; Kuprin, S.; Zaccai, G. Protein hydration in solution" Experimental observation by X-ray and neutron scattering. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 2267-2272.
19. Merzel, F.; Smith, J. C. Is the first hydration shell of lysozyme of higher density than bulk water? Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 5378-5383.
20. Merzel, F.; Smith, J. C. SASSIM" a method for calculating small-angle X-ray and neutron scattering and the associated molecular envelope from explicit-atom models of solvated proteins. Acta Crystallogr., Sect. D 2002, 58, 242-249.
21. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. CHARMM - a program for macro-molecular energy, minimization, and dynamics calculations. J. Comput. Chem. 1983, 4, 187-217.
22. Vaney, M. C.; Maignan, S.; RiesKautt, M.; Ducruix, A. High-resolution structure (1.33 angstrom) of a HEW lysozyme tetragonal crystal grown in the APCF apparatus. Data and structural comparison with a crystal grown under microgravity from SpaceHab-01 mission. Acta Crystallogr., Sect. D 1996, 52, 505-517.
23. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 1983, 79, 926-935.
24. Lebedev, V. I. The 59th order of algebraic accuracy quadrature formula for sphere. Dokl. Akad. Nauk 1994, 338, 454-456.
25. Luzar, A.; Chandler, D. Structure and hydrogen-bond dynamics of water-dimethyl sulfoxide mixtures by computer simulations. J. Chem. Phys. 1993, 98, 8160-8173.
26. Gerstein, M.; Chothia, C. Packing at the protein-water interface. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 10167-10172.