DOI: 10.1073/pnas.101516298. Large vortex-like structure of dipole field in computer models of liquid water and dipole-bridge between biomolecules

Large vortex-like structure of dipole field in computer models of liquid water and dipole-bridge between biomolecules

10.1073/pnas.101516298

Crossref journal-article

Proceedings of the National Academy of Sciences

Proceedings of the National Academy of Sciences (341)

Abstract

We propose a framework to describe the cooperative orientational motions of water molecules in liquid water and around solute molecules in water solutions. From molecular dynamics (MD) simulation a new quantity “site-dipole field” is defined as the averaged orientation of water molecules that pass through each spatial position. In the site-dipole field of bulk water we found large vortex-like structures of more than 10 Å in size. Such coherent patterns persist more than 300 ps although the orientational memory of individual molecules is quickly lost. A 1-ns MD simulation of systems consisting of two amino acids shows that the fluctuations of site-dipole field of solvent are pinned around the amino acids, resulting in a stable dipole-bridge between side-chains of amino acids. The dipole-bridge is significantly formed even for the side-chain separation of 14 Å, which corresponds to five layers of water. The way that dipole-bridge forms sensitively depends on the side-chain orientations and thereby explains the specificity in the solvent-mediated interactions between biomolecules.

Bibliography

Higo, J., Sasai, M., Shirai, H., Nakamura, H., & Kugimiya, T. (2001). Large vortex-like structure of dipole field in computer models of liquid water and dipole-bridge between biomolecules. Proceedings of the National Academy of Sciences, 98(11), 5961â5964.

Authors 5

Junichi Higo (first)
Masaki Sasai (additional)
Hiroki Shirai (additional)
Haruki Nakamura (additional)
Takaki Kugimiya (additional)

References 15 Referenced 62

10.1142/2923
10.1021/cr00023a011
10.1103/PhysRevLett.82.3629
D Eisenberg, W Kauzman The Structures and Properties of Water (Oxford Univ. Press, London, 1969). / The Structures and Properties of Water by Eisenberg D (1969)
10.1021/j100308a038
10.1063/1.445869
10.1080/00268978200100281
10.1063/1.463935
10.1016/S0009-2614(99)00400-5
10.1002/(SICI)1097-0134(20000801)40:2<193::AID-PROT30>3.0.CO;2-0
10.1016/0097-8485(92)80010-W
P Kollman, R Dixson, W Cornell, T Fox, C Chipot, A Pohorille Computer Simulations of Biological Systems, eds W F Gunsteren, P K Weiner, A J Wilkinson (ESCOM, Dordrecht, The Netherlands) 3, 83–94 (1997). (10.1007/978-94-017-1120-3_2) / Computer Simulations of Biological Systems by Kollman P (1997)
10.1016/S0006-3495(99)77335-2
10.1038/33653
10.1017/S0033583500005746

Dates

Type	When
Created	23 years, 1 month ago (July 26, 2002, 10:44 a.m.)
Deposited	3 years, 4 months ago (April 12, 2022, 7:26 p.m.)
Indexed	1 year ago (Aug. 22, 2024, 3:30 p.m.)
Issued	24 years, 3 months ago (May 8, 2001)
Published	24 years, 3 months ago (May 8, 2001)
Published Online	24 years, 3 months ago (May 8, 2001)
Published Print	24 years, 3 months ago (May 22, 2001)

Funders 0

None

BibTeX

@article{Higo_2001, title={Large vortex-like structure of dipole field in computer models of liquid water and dipole-bridge between biomolecules}, volume={98}, ISSN={1091-6490}, url={http://dx.doi.org/10.1073/pnas.101516298}, DOI={10.1073/pnas.101516298}, number={11}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Higo, Junichi and Sasai, Masaki and Shirai, Hiroki and Nakamura, Haruki and Kugimiya, Takaki}, year={2001}, month=may, pages={5961–5964} }

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