Protein Dynamics in Organic Media at Varying Water Activity Studied by Molecular Dynamics Simulation

Abstract

In nonaqueous enzymology, control of enzyme hydration is commonly approached by fixing the thermodynamic water activity of the medium. In this work, we present a strategy for evaluating the water activity in molecular dynamics simulations of proteins in water/organic solvent mixtures. The method relies on determining the water content of the bulk phase and uses a combination of Kirkwood-Buff theory and free energy calculations to determine corresponding activity coefficients. We apply the method in a molecular dynamics study of Candida antarctica lipase B in pure water and the organic solvents methanol, tert-butyl alcohol, methyl tert-butyl ether, and hexane, each mixture at five different water activities. It is shown that similar water activity yields similar enzyme hydration in the different solvents. However, both solvent and water activity are shown to have profound effects on enzyme structure and flexibility.

The fate of proteins in outer space

“…The same question may be asked in the cases where water is replaced by organic solvents (Soares et al, 2003;Chen et al, 2008;Wedberg et al, 2012;Klibanov, 2010). Van der Waals interactions still operate, and dipolar interactions will increase in strength as water is removed.…”

“…An important family of experimental tools for studying proteins and protein-protein interactions consists of matrix-assisted laser desorption/ionization (MALDI), time-of-flight mass spectrometry (TOF) and electrospray (Smith et al, 1990;Robinson et al, 2007;Wyttenbach and Bowers, 2007;Breuker and McLafferty, 2008;Benesch and Robinson, 2009;Liu et al, 2009;Liu and Schey, 2008;Barrera et al, 2008). Many proteins, and many protein-protein complexes, retain their structural integrity in vacuo, at least for a sufficiently long time, for many of their essential structural features to be retained and be capable of study in intimate detail (Patriksson et al, 2007;Meyer et al, 2009).…”

“…For this work, our guiding principles were to provide insights into protein hydration and dehydration in the light of an abundance of excellent published work (Smith et al, 1990;Robinson et al, 2007;Wyttenbach and Bowers, 2007;Breuker and McLafferty, 2008;Benesch and Robinson, 2009;Liu et al, 2009;Liu and Schey, 2008;Barrera et al, 2008) but in particular by the large-scale systematic experimental study of protein hydration (Chen et al, 2008). In that seminal work, distinction was made between three categories of water molecules: individual water molecules hydrogen-bonded to donor/acceptor atoms on the surface or in crevices, bound waters immediately surrounding these, and remaining crystal waters (meaning water molecules located in the crystal structure) surrounding the former which have the normal attributes of bulk water.…”

- Global and Local Properties of Mixtures: An Expanded Paradigm for the Study of Mixtures

“…Recently, we have explored different approaches to this property via MD simulation (Wedberg, Abildskov, and Peters 2012). Two main strategies to study how protein properties depend on water activity are termed "real-time" control and "a posteriori" analysis.…”

New insights into the molecular mechanism of methanol-induced inactivation ofThermomyces lanuginosuslipase: a molecular dynamics simulation study

“…It has been reported that motions of surface residues are linked to the stability of lipase in polar solvents (methanol, acetonitrile, DMSO and dimethylformamide) [17], [42] and [43]. It is also known that polar solvents, as dehydrating agents, are able to bind to the surface residues of enzyme (lipase, protease and -12 -other enzymes), perturbing the essential layer of water that provides enzyme with conformational flexibility needed for catalysis and thus decreasing the enzymatic activity [40], [44], [45], [46], [47], [48], and [49]. Therefore, the capacity of lipases to tolerate polar solvents could be improved by introducing more intra-protein interactions on the flexible surface region or reducing the interactions between polar solvent molecules and enzyme surface residues.…”