However, despite the fact that previous studies have shown that values calculated from MD simulationswhen run for tens of nanosecondsare generally in good agreement with experiment (21,42C45), simulation occasions in this range turned out to be insufficient to quantify local preferential interactions coefficients (47)

However, despite the fact that previous studies have shown that values calculated from MD simulationswhen run for tens of nanosecondsare generally in good agreement with experiment (21,42C45), simulation occasions in this range turned out to be insufficient to quantify local preferential interactions coefficients (47). Convergence of local preferential conversation coefficients from MD simulations is perceived as a formidable challenge because is intrinsically a fluctuation difference and is Nec-4 prone to large levels of noise (48) and because dissection of the influence of different protein group contributions is not?straightforward (49). side-chain motions that are slower than the longest intrinsic solvation timescale of 10?ns. Differences of local solvent preferences Nec-4 between distinct protein side-chain conformations predict solvent effects on Nec-4 local protein structure in good agreement with experiment. This study extends the application scope of preferential conversation theory and enables molecular understanding of solvent effects on protein structure through comprehensive characterization of local protein solvation. Introduction Cosolvents such as denaturants, salts, amino acids, polyols, and sugars play an important role in many protein processes involving protein folding, stabilization, and association (1C3). This is because the addition of cosolvents to aqueous protein solutions commonly alters the equilibrium between protein conformations (4C6). Over the past decades, a rigorous thermodynamic framework has been developed that relates cosolvent effects on protein conformations with solvent preferences of the protein surface (4,7C19). This frameworkwhich is usually often referred to as preferential conversation theorystipulates that adding cosolvent to a protein solution will shift the protein toward conformations with a greater degree of preferential solvation by the cosolvent. Preferential solvation of a protein is quantified by the preferential conversation coefficient (4,20). Because every solvent molecule at the protein surface contributes to (7,11,21), detailed characterization of protein solvation is required for molecular understanding of solvent effects on protein conformations. Preferential interactions reflect relative preferences of the protein surface for either cosolvent or water, and are manifested in local concentration ratios of cosolvent and water that are either greater (preferential solvation), smaller (preferential hydration), or equal (neutral solvation) with respect to the bulk solvent (4). Because protein surfaces comprise actually and chemically distinct surface loci, protein solvation in a mixed solvent can be conceived of as an ensemble of preferentially hydrated, solvated, and neutral solvent regions near the protein surface (4,22). Just like a protein displays a mosaic of heterogeneous surface loci to the solvent, the solvent surrounding a protein is expected to form a mosaic of solvent regions with varying degrees of preferential interactions. Unfortunately, characterization of the protein solvation mosaic has remained elusive to this day. Although various spectroscopy- and NMR-based techniques have revealed many aspects of protein solvation, these techniques do not allow quantifying local solvation preferences (23C25). On the other hand, equilibrium techniques such as vapor pressure osmometry and dialysis-densitometry allow the measurement of the preferential conversation coefficient of the ensemble-average of all protein conformations in a solvent mixture (4,26,27). However, equilibrium techniques cannot quantify differences of between distinct protein conformations and are unable to handle local preferential interactions at distinct protein surface loci. One approach to understand solvent effects on Nec-4 protein conformations was pioneered by Tanford (22), who quantified thermodynamic solvent effects on smaller constituent groups of a protein molecule and hypothesized the additivity of individual contributions of the constituent groups. Group additivity has proven to be a useful assumption for quantifying the effects of a number of cosolvents on protein folding (28C30); however, other studies reported solvent effects on proteins for which group additivity is not valid (31C33). Rabbit Polyclonal to MED27 Hence, more research is needed to determine the range of cosolvents and the extent of conformational changes for which group additivity holds. Solvent effects on protein (un)folding events have been directly observed from extended molecular-dynamics (MD) simulations (34C38), and solvent effects around the free energy scenery of peptides and mini-proteins have been quantified through advanced sampling techniques (39C41). These techniques have provided a wealth of information around the folding mechanisms of proteins, but they have also generated widely differing views around the molecular mechanisms by which cosolvents alter protein conformations. Perhaps the most prevalent reason for this disagreement is the difficulty to differentiate cause and effect between.