The role of continuous and discrete water structures in protein function
Theoretical Biology and Biophysics Group MS K710, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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Received: 20 June 2012
Revised: 12 March 2014
Published online: 27 March 2014
Proteins have evolved to perform numerous roles as specific catalysts and nano-machines. Some of the mechanisms exploited by evolution are clear. Hydrophobicity drives the stabilization energy of folding, charges mediate long-range interactions and facilitate catalysis, and specific geometries and hydrogen bonding patterns facilitate molecular recognition and catalysis. In this work, we examine the energy landscape of protein dynamics in terms of the continuous and discrete water structures that control protein dynamics. We observe that the internal structures at the active site of proteins are constantly shaped by strong interactions with hydration shell and bulk water motions. By describing the energy landscape of proteins in terms of its three component motions; conformational, hydration and protonation, and electronic structure, it is possible to systematically understand protein function.
© EDP Sciences, Springer-Verlag, 2014