Abstract
Conformational motions of proteins are necessary for their functions. To date, experimental studies measuring conformational fluctuations of a whole protein structure have revealed that water molecules hydrating proteins are necessary to induce protein functional motions. However, the underlying microscopic mechanism behind such regulation remains unsolved. To clarify the mechanism, multi-domain proteins are good targets because it is obvious that water molecules between domains play an important role in domain motions. Here, we show how changes in hydration structure microscopically correlate with large-amplitude motions of a multi-domain protein, through molecular dynamics simulation supported by structural analyses and biochemical experiments. We first identified collective domain motions of the protein, which open/close an active-site cleft between domains. The analyses on changes in hydration structure revealed that changes in local hydration in the depth of the cleft are necessary for the domain motion and vice versa. In particular, ‘wetting’/‘drying’ at a hydrophobic pocket and ‘adsorption’/‘dissociation’ of a few water molecules at a hydrophilic crevice in the cleft were induced by dynamic rearrangements of hydrogen-bond networks, and worked as a switch for the domain motions. Our results microscopically demonstrated the importance of hydrogen-bond networks of water molecules in understanding energy landscapes of protein motions.
Highlights
To understand the role of water molecules in functional motions of a multi-domain protein, here we study the spontaneous domain motions of unliganded GDH in solution through a 200-ns molecular dynamics (MD) simulation in explicit aqueous solvent
The domain motion observed in the MD simulation agreed well with the conformational variety observed in the crystal structures
The amplitude of the domain motion in the simulation agreed with the conformational variety of domains observed in the surface topography of GDH crystals measured by atomic force microscopy (AFM)
Summary
The present analyses on the MD trajectory revealed that the number of water molecules in HS2 restricts the minimum size of the hydrophilic crevice and correlated with the open/close motion of N-domain (Fig. 6c,e). As well as HS1, the amino-acid residues forming HS2 are well conserved among GDH from various organisms (Supplementary Fig. 12b) Considering these results of the structural and hydration dynamics in HS1 and HS2 along with the N-domain motion, the local conformational changes in these two sites accompanying ‘wetting’/‘drying’ and ‘adsorption’/‘dissociation’ of water molecules, respectively, are one of essential factors inducing the stochastic N-domain motion necessary to clamp the substrates to be catalysed (Fig. 8b). Our results show the importance of water molecules in understanding energy landscapes of protein functional motions, and should be important for design and engineering of protein functions
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