Dynamics of hydration in hen egg white lysozyme

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• 作者：Sterpone ; Fabio ; Ceccarelli ; Matteo ; Marchi ; Massimo
• 关键词：molecular dynamics ; residence time ; hydration ; lysozyme ; simulation ; NMRD ; nuclear magnetic relaxation dispersion ; MD ; molecular dynamics ; r-RESPA ; reversible reference system propagation algorithm ; SPME ; smooth particle mesh Ewald ; lysoA ; molecular dynam
• 刊名：Journal of Molecular Biology
• 出版年：2001
• 出版时间：August 10, 2001
• 年：2001
• 卷：311
• 期：2
• 页码：409-419
• 全文大小：235 K

文摘

We investigate the hydration dynamics of a small globular protein, hen egg-white lysozyme. Extensive simulations (two trajectories of 9 ns each) were carried out to identify the time-scales and mechanism of water attachment to this protein. The location of the surface and integral water molecules in lysozyme was also investigated. Three peculiar temporal scales of the hydration dynamics can be discerned: two among these, with sub-nanosecond mean residence time, τ_w, are characteristic of surface hydration water; the slower time-scale (τ_wlign=center border=0 SRC=/images/glyphs/BQ1.GIF>2/3 ns) is associated with buried water molecules in hydrophilic pores and in superficial clefts. The computed τ_w values in the two independent runs fall in a similar range and are consistent with each other, thus adding extra weight to our result. The τ_w of surface water obtained from the two independent trajectories is 20 and 24 ps. In both simulations only three water molecules are bound to lysozyme for the entire length of the trajectories, in agreement with nuclear magnetic relaxation dispersion estimates. Locations other than those identified in the protein crystal are found to be possible for these long-residing water molecules. The dynamics of the hydration water molecules observed in our simulations implies that each water molecule visits a multitude of residues during the lifetime of its bound with the protein. The number of residues seen by a single water molecule increases with the time-scale of its residence time and, on average, is equal to one only for the water molecules with shorter residence time. Thus, τ_w values obtained from inelastic neutron scattering and based on jump-diffusion models are likely not to account for the contribution of water molecules with longer residence time.