Solvation and hydration of proteins and nucleic acids: A theoretical view of simulation and experiment

Accounts of Chemical Research

Volumn 35, Issue 6, 2002, Pages 376-384

  Makarov, Vladimir ^a   Pettitt, B Montgomery ^a   Feig, Michael ^b  

^a University of Houston ^*  (United States)

^b SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

SOLVENT; NUCLEIC ACID; PROTEIN; WATER;

ARTICLE; CRYSTAL STRUCTURE; HYDRATION; MACROMOLECULE; MOLECULAR DYNAMICS; PROTEIN ANALYSIS; PROTEIN DNA INTERACTION; SOLVATION; THERMODYNAMICS; WATER TRANSPORT; X RAY ANALYSIS; X RAY CRYSTALLOGRAPHY; X RAY DIFFRACTION; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; METABOLISM; REVIEW; SOLUBILITY;

COMPUTER SIMULATION; MODELS, CHEMICAL; MOLECULAR STRUCTURE; NUCLEIC ACIDS; PROTEINS; SOLUBILITY; WATER;

EID: 0036286851     PISSN: 00014842     EISSN: None     Source Type: Journal    
DOI: 10.1021/ar0100273     Document Type: Article

References (75)

1. Solvation of crystalline proteins
2. Modeling consistent with experiment
3. A connected-cluster of hydration around myoglobin
4. Statistical state solvation sites
5. Monte-Carlo computer simulation of the aqueous hydration of the glycine zwitterion at 25 °C
6. A global model of the protein-solvent interface
7. Modeling the DNA-solvent interface
8. Protein hydration density: Theory, simulations and crystallography
9. Direct observation of protein solvation and discrete disorder with experimental crystallographic phases
10. Ordered water in macromolecular structure
11. Structure and dynamics of the water around myoglobin
12. Recent advances in structure-based rational drug design
13. Determination of water structure around biomolecules using x-ray and neutron diffraction methods
14. Crystallographic refinement of the structure of bovine pancreatic trypsin inhibitor
15. Solvation of crystalline proteins
16. Conserved water molecules in a large family of microbial ribonucleases
17. Continuum electrostatic analysis of preferred solvation sites around proteins in solution
18. Modelling solvation effects in biomolecules
19. Protein hydration observed by x-ray diffraction
20. Distribution function implied dynamics versus residence times and correlations
21. Residence times of water molecules in the hydration sites of myoglobin
22. Liquid state computer simulations of biomolecular solvation problems
23. Reconstructing the protein-water interface
24. Accessibility and order of water sites in and around proteins
25. Structural chemistry of biomolecular hydration via computer simulation
26. Protein hydration
27. A statistical mechanical description of biomolecular hydration
28. Peptide conformations are restricted by solution stability
29. High apparent dielectric constants in the interior of a protein reflect water penetration
30. Dynamics of internal water in fatty acid bincling protein
31. A microscopic view of protein solvation
32. Dissection of the structural and functional role of a conserved hydration site in RNase T1
33. The pressure dependence of hydrophobic interactions is consistent with the observed pressure denaturation of proteins
34. Hydration of denatured and mollen globule proteins
35. Protein hydration in solution
36. Computer simulation and the design o new biological molecules
37. Diffusion of solvent around biomolecular solutes
38. Anomalous and anisotropic diffusion of plastocyanin hydration water
39. Molecular dynamics simulation of solvated azurin
40. Hydration of proteins
41. Protein hydration dynamics in aqueous solution
42. Water residence times around copper plastocyanin
43. Hydration structure of the a-chymotrypsin substrate binding pocket
44. The dynamics of protein hydration water
45. Discrimination of the native from misfolded protein models with an energy function including implicit solvation
46. Water: An integral part of nucleic acid structure
47. Structure and dynamics of water surrounding biomolecules
48. Molecular recognition mediated by bound water
49. Influence of drug binding on DNA hydration
50. Sodium and chlorine ions as part of the DNA solvation shell
51. The structure of sodium thymonucleate fibers
52. The structure of polydeoxyguanylic acid polydeoxycytidylic acid
53. Polymorphism of a synthetic DNA in solution
54. Hydration of DNA: Take 2
55. Ordered water structure around a B-DNA dodecamer
56. Ordered water structure in an A-DNA octamer at 1.7 A resolution
57. The B-DNA dodecamer at high resolution reveals a spine of water on sodium
58. A high-angle neutron fibre diffraction study of the hydration of B-DNA
59. NMR observation of individual molecules of hydration water bound to DNA duplexes
60. Structural equilibrium of DNA represented with different force fields
61. Crystallographic water sites from a theoretical perspective
62. Kinetics of DNA hydration
63. Determination of the residence time of water molecules hydration B′-DNA; B-DNA
64. Crystal studies of B-DNA: The answers and the questions, biopolymers
65. Influence of base composition, base sequence, and duplex structure on DNA hydration
66. Changes of hydration during conformational transitions of DNA
67. Solvent-accessible surfaces of nucleic acids
68. On the hydration of DNA. II
69. Sequence dependent hydration of DNA
70. On the hydration of DNA. I
71. The structure of a B-DNA decamer with a central T - A step
72. Influence of magnesium ions on duplex DNA