Abstract
The local density of water molecules around a biomolecule is constructed from calculated two- and three-points correlation functions of polar solvents in water using a Potential-of-Mean-Force (PMF) expansion. As a simple approximation, the hydration of all polar (including charged) groups in a biomolecule is represented by the hydration of water oxygen in bulk water, and the effect of non-polar groups on hydration are neglected, except for excluded volume effects. Pair and triplet correlation functions are calculated by molecular dynamics simulations. We present calculations of the structural hydration for ideal A-DNA molecules with sequences [d(CG)5]2 and [d(C5G5)]2. We find that this method can accurately reproduce the hydration patterns of A-DNA observed in neutron diffraction experiments on oriented DNA fibers (P. Langan et al. J. Biomol. Struct. Dyn., 10, 489(1992)).
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Arnott, S., & Hukins, D.W.L., (1972). Optimized parameters for A-DNA and B-DNA. Biochem. Biophys. Res. Commun., 47:1504–1510.
Austin, R.H., Robertson, M.W., & Mansky, P., (1989). Far-infrared perturbation of reaction rates in myoglobin at low temperatures. Phys. Rev. Lett., 62:1912–1915.
Berman, H., (1991). Hydration of DNA. Curr. Opin. Struct. Biol., 1:423–427.
Brooks, C.L., Karplus, M., & Montgomery-Pettitt, B., (1988). Proteins: A theoretical perspective of dynamics, structure and thermodynamics. Adv. Chem. Phys., 71:259pp.
Clementi, E., (1976). Lecture Notes in Chemistry, Vol. 2. Determination of Liquid Water Structure. Coordination Numbers for Ions and Solvation of Biological Molecules. Springer Verlag, Berlin.
Doster, W., Cusack, S., & Petry, W., (1989). Dynamical transition of myoglobin revealed by inelastic neutron scattering. Nature, 337:754–756.
Forsyth, V.T., Langan, P., Mahendrasingam, A., Fuller, W., & Mason, S.A., (1992). High angle neutron fiber diffraction studies of DNA. Neutron News, 3(4):21–24.
Grimm, H., Stiller, H., Majkrzak, C.F., Rupprecht, A., & Dahlborg, U., (1987). Observation of acoustic umklapp phonons in water-stabilized DNA by neutron scattering. Phys. Rev. Lett., 59:1780–1783.
Hummer, G., & Soumpasis, D.M., (1994a). Computation of the water density distribution at the ice-water interface using the potentials-of-mean-force expansion. Phys Rev. E., 49:591–596.
Hummer, G., & Soumpasis, D.M., (1994b). In Structural Biology: The State of the Art, R.H. Sarma and M.H. Sarma, editors. Adenine Press, Schenectady, NY, Vol 2, p273.
Hummer, G., & Soumpasis, D.M., (1994c). Statistical mechanical treatment of the structural hydration of biological macromolecules: results for B-DNA. Phys. Rev. E., 50:5085–5095.
Hummer, G., Garcia, A.E., & Soumpasis, D.M., (1995a). Hydration of nucleic acid fragments: Comparison of theory and experiment for high resolution crystal structures of RNA, DNA and DNA-drug complexes. Biophys. J., 68(5): 1639–1652.
Hummer, G., Soumpasis, D.M., & Garcia, A.E., (1995b). Potential-of-mean-force description of ionic interactions and structural hydration in biomolecular systems. In Nonlinear Excitations in Biomolecules, M. Peyrard, editor. Springer, Paris. pp83–99.
Jorgensen, W.L., (1981). Transferable intermolecular potential functions for water, alcohols and ethers. Application to liquid water. J. Am. Chem. Soc., 103:335–340. See also
Jorgensen, W.L., Chandrasekhar, J., & Madura, J.D., (1983). Comparison of simple potential functions for simulating liquid water. J. Chem. Phys., 79:926–935.
Langan, P., Forsyth, V.T., Mahendrasingam, A., Pigram, W.J., Mason, S.A., & Fuller, W., (1992). A high angle neutron fibre diffraction study of the hydration of the A conformation of the DNA double helix. J. Biomol. Struct. Dyn., 10:489–503.
Levitt, M., (1989). Molecular dynamics of macromolecules in water. Chemica Scripta, 29A: 197–203.
Lindsay, S.M., Powell, J.W., & Rupprecht, A., (1984). Observation of low-lying Raman bands in DNA by tandem interferometry. Phys. Rev. Lett., 53:1853–1855. For a review see,
S.M. Lindsay, (1987). In Structure and Dynamics of Nucleic Acids, Proteins and Membranes, E. Clementi and S. Chin, editors. Plenum, New York.
Marky, L.A., & Kupke, D.W., (1989). Probing the hydration of the minor groove of AT synthetic DNA polymers by volume and heat changers. Biochem., 28:9982–9988.
Nemethy, G., & Scheraga, H.A., (1962). The structure of water and hydrophobic bonding in proteins III: The thermodynamic properties of hydrophobic bonds in proteins. J. Phys. Chem., 66:1773–1789.
Otting, G., & Wüthrich, K., (1989). Studies of protein hydration in aqueous solution by direct NMR observation of individual protein-bound water molecules. J. Am. Chem. Soc., 111:1871–1875.
Otting, G., Liepinsh, E., & Wüthrich, K., (1991). Protein hydration in aqueous solution. Science, 254:974–980.
Schoenborn, B.P., (1988). The solvent effects in protein crystals. A neutron diffraction analysis of solvent and ion density. J. Mol. Biol., 201:741–749.
Soumpasis, D.M., (1993). In Computation of Biomolecular Structures. Achievements, Problems and Perspectives. D.M. Soumpasis and T.M. Jovin, editors. p223. Springer, Berlin.
Soumpasis, D.M., Garcia, A.E., Klement, R., & Jovin, T.M., (1990). The potential-of-mean-force (PMF) approach for treating ionic effects on biomolecular structures in solution. In Theoretical Biochemistry and Molecular Biophysics, D.L. Beveridge and R. Lavery, editors. Adenine Press, Schenectady, NY, Vol. 1, pp343–360.
Tao, N.J., (1988) Ph.D. Thesis, Arizona State University, Tempe, Arizona (USA).
Tao, N.J., Lindsay, S.M., & Rupprecht, A., (1987). The dynamics of the DNA hydration shell at gigahetz frequencies. Biopolymers, 26:171–188.
Teeter, M.M., (1991). Water-protein interactions: theory and experiment. Ann. Rev. Biophys. Biophys. Chem., 20:577–600.
Tominaga, Y., Shida, M., Kubota, K., Urabe, H., Nishimura, Y., & Tsuboi, M., (1985). Coupled dynamics between DNA double helix and hydrated water by low frequency Raman spectroscopy. J. Chem. Phys., 83:5972–5975.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 1996 Springer Science+Business Media New York
About this chapter
Cite this chapter
García, A.E., Hummer, G., Soumpasis, D.M. (1996). Theoretical Description of Biomolecular Hydration. In: Schoenborn, B.P., Knott, R.B. (eds) Neutrons in Biology. Basic Life Sciences, vol 64. Springer, Boston, MA. https://doi.org/10.1007/978-1-4615-5847-7_26
Download citation
DOI: https://doi.org/10.1007/978-1-4615-5847-7_26
Publisher Name: Springer, Boston, MA
Print ISBN: 978-1-4613-7680-4
Online ISBN: 978-1-4615-5847-7
eBook Packages: Springer Book Archive