Contribution of the hydrophobic effect to protein stability : molecular dynamics simulations of the lie → Ala mutation in Barnase

Unité de Conformation de Macromolécules Biologiques, CP160, P2, Université Libre de Bruxelles, Av P Héger, 1050 Bruxelles, Belgium, France.

Abstract

Hydrophobic interactions are believed to make a major contribution to the stability of native protein structures in an aqueous solution. Although the general role of these interactions in protein folding is understood, mainly in terms of the classical picture of Kauzmann, it is essential to obtain a more detailed quantitative description of the underlying factors. Site directed mutagenesis experiments combined with thermal and spectroscopic stability measurements, are now being used to dissect the contributions of individual amino-acids (1). But there are basic questions concerning, for example, the effect of hydrophobic solvation of individual non-polar residues and its relationships to their bulk properties in the protein interior (2) which are difficult to approach experimentally. Theoretical analyses based on a detailed microscopic description are needed to provide fuller understanding of the physical phenomena involved. Methods for computing free energy changes by use of molecular dynamics (3) and Monte Carlo (4) simulation techniques are particularly well suited for this purpose. Such calculations are potentially very useful because they evaluate thermodynamic quantities that can be directly compared with experiment. Here we describe the application of such methods to the Ile → Ala substitution at position 96 in barnase, an extra-cellular ribonuclease from B. Amyloliquefaciens. This 110-residue enzyme is of particular interest because it is being used as a paradigm for studying protein stability and folding (5). It contains significant amount of secondary structure and its crystal structure is known to high resolution (6). We report the results and analysis of simulations of the "alchemical" transformations Ile96 → Ala in the native and solvated proteins, and Ala96 → Ile in an extended conformation used as a model for the denatured state in water. The computations are shown to yield a free energy change for protein stability (-3.42/-5.21 kcal/mol) in satisfactory agreement with experimental values (-3.3/4.0 kcal/ mol) (5,7). The major contributions to the free energy difference are shown to arise from covalent terms involving degrees of freedom of the mutated side-chain, and from non-bonded interactions made by that side chain with its environment in the folded proteins. Using simulations of the Ala96 → He transformation in the extended gas phase as reference, it is furthermore shown that hydration effects play a minor role in the overall free energy balance for the Ile ↔ Ala exchange. The implications of these results for our understanding of the hydrophobic effect and its role in protein stability are discussed.