生物分子结合水的结构与动力学研究进展
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摘要
生物结合水在维护生物大分子的结构、稳定性以及调控动力学性质和生理功能等方面起着决定性的作用.从分子水平上理解生物结合水分子的结构与性质及其影响生物结构和功能的本质与规律,是揭示生物大分子生理功能机理的关键.目前生物结合水的结构与动力学相关研究尚处于初步阶段.本文从三个方面介绍当前生物结合水的相关研究及其进展:首先介绍结合水对蛋白质折叠、质子给予与迁移、配体结合与药物设计以及变构效应等生物结构和功能的影响;然后介绍生物分子周围的水分子结构研究情况;最后从时间尺度、动力学属性、生物分子与水分子之间的动力学耦合作用、蛋白质表面结合水次扩散运动等角度介绍生物分子水合动力学的研究进展,并归纳出一些目前尚待进一步解决的科学问题.
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.
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.
引文
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