Research progress of molecular structure and dynamics of biological water

Ye Shu-Ji; Li Chuan-Zhao; Zhang Jia-Hui; Tan Jun-Jun; Luo Yi

doi:10.7498/aps.68.20181273

Abstract

The specific water molecules that are confined within the solvation shell adjacent to the surface of biological macromolecules (including protein, enzyme, DNA, RNA, cell membrane, etc.) are called biological water molecules. Such water around the biomolecule surface plays a very important role in the structure, stability, dynamics, and function of biological macromolecules. A molecular-level understanding of the structure and dynamics of biological water, as well as the nature of its influence on biological structure and function is the key to revealing the mechanism of the biological functions. However, the researches in this field are still in the initial stage. Here in this paper, we review the relevant researches and recent progress of hydration water from three aspects. The first aspect is about the influence of hydration water on biological structure and function. It is evident that water actively participates in many biological processes such as protein folding, proton donation and migration, ligand binding and drug design, and allosteric effects. For example, water mediates the collapse of the chain and the search for the native topology through a funneled energy landscape. The second aspect is about the structure of water molecules around the biomolecules investigated by nuclear magnetic resonance (NMR), dielectric relaxation, neutron scattering, X-ray diffraction and ultrafast optical spectroscopy. The third aspect is about the dynamic behaviors of biological water, including the relaxation time scale, dynamic property, dynamic coupling between biomolecules and water molecules, and sub-diffusive motion of the water molecules along the protein surfaces. Different techniques measure different timescales for the motion of proteins and their hydration environment. While NMR and dielectric relaxation methods reveal the motion of biological water on a time scale from several tens of picoseconds to nanoseconds, ultrafast optical spectroscopy such as fluorescence and vibrational spectroscopy probes the hydrogen-bonding fluctuations of water on a time scale from the femtosecond to picosecond. It is therefore highly necessary to acquire a real and complete picture of the structure and dynamics of biological water by combining several different techniques. Finally, some unsolved scientific problems are also summarized in this review.

Keywords:

Authors and contacts

Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China

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Cited By

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[2]	Pal S K, Zewail A H 2004 Chem. Rev. 104 2099
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[4]	Bagchi B 2005 Chem. Rev. 105 3197
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[8]	Kamal J K A, Zhao L, Zewail A H 2004 Proc. Natl. Acad. Sci. U.S.A. 101 13411
[9]	Pal S K, Peon J, Zewail A H 2002 Proc. Natl. Acad. Sci. U.S.A 99 15297
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[16]	Fecko C J, Eaves J D, Loparo J J, Tokmakoff A, Geissler P L 2003 Science 301 1698
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