Statistical mechanical treatment of the structural hydration of biological macromolecules: Results for [ital B]-DNA

Journal Article · Thu Dec 01 04:00:00 EST 1994 · Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics; (United States)

DOI:https://doi.org/10.1103/PhysRevE.50.5085· OSTI ID:6822998

Hummer, G ^[1]; Soumpasis, D M ^[2]

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1. Theoretical Biology and Biophysics Group T-10, MS K710, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)
2. Biocomputation Group, Max Planck Institute for Biophysical Chemistry, P.O. Box 2841, D-37018 Goettingen (Germany)

We constructed an efficient and accurate computational tool based on the potentials-of-mean-force approach for computing the detailed hydrophilic hydration of complex molecular structures in aqueous environments. Using the pair and triplet correlation functions database previously obtained from computer simulations of the simple point charge model of water, we computed the detailed structural organization of water around two [ital B]-DNA molecules with sequences d(AATT)[sub 3][center dot]d(AATT)[sub 3] and d(CCGG)[sub 3][center dot]d(CCGG)[sub 3], and canonical structure. [[ital A], T, C, and G denote adenine, thymine, cytosine, and guanine, respectively, and d(...) denotes the deoxyribose in the sugar-phosphate backbone.] The results obtained are in agreement with the experimental observations. A[center dot]T base-pair stretches are found to support the marked minor-groove spines of hydration'' observed in x-ray crystal structures. The hydrophilic hydration of the minor groove of the molecule d(CCGG)[sub 3][center dot]d(CCGG)[sub 3] exhibits a double ribbon of high water density, which is also in agreement with x-ray crystallography observations of C[center dot]G base-pair regions. The major grooves, on the other hand, do not show a comparably strong localization of water molecules. The quantitative results are compared with a computer simulation study of Forester [ital et] [ital al]. [Mol. Phys. 72, 643 (1991)]. We find good agreement for the hydration of the -NH[sub 2] groups, the cylindrically averaged water density distributions, and the overall hydration number. The agreement is less satisfactory for the phosphate groups. However, by refining the treatment of the anionic oxygens on the phosphate groups, almost full quantitative agreement is achieved.

• OSTI ID: 6822998
• Journal Information: Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics; (United States), Journal Name: Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics; (United States) Vol. 50:6; ISSN 1063-651X; ISSN PLEEE8
• Country of Publication: United States
• Language: English

Related Subjects

550200* -- Biochemistry
59 BASIC BIOLOGICAL SCIENCES
CORRELATION FUNCTIONS
DNA
FUNCTIONS
HYDRATION
HYDROGEN COMPOUNDS
INTERMOLECULAR FORCES
MECHANICS
NUCLEIC ACIDS
ORGANIC COMPOUNDS
OXYGEN COMPOUNDS
PHOSPHATES
PHOSPHORUS COMPOUNDS
SOLVATION
STATISTICAL MECHANICS
WATER