Protein engineering aims at modifying the sequence of a protein to get a better understanding of its structure/activity relationship, or to obtain a desired change in its activity.
Computational molecular modeling provides a rational method to obtain a detailed knowledge of the structure and function of the protein, as well as on the structural and energetic effect of mutations on protein-protein association and on protein structural stability, which can eventually be used to make desired changes. Several methods are available that can be provided by the PMF, depending on the required accuracy and number of residues involved in the studied process.
Free energy simulations are the most accurate methods for studying these effects, and are the technique of choice for the study of a limited number of mutations. However, despite increased computational power, these methods are still quite time consuming and cannot be applied to study the role of a large number of residues. Among the simplified approaches that have been developed to address this issue, the molecular mechanics - Generalized Born surface area (MM-GBSA) approach is one of the most promising and widely used to estimate the importance of each residue on protein-protein association, opening the way to the rational design of engineered proteins. We have implemented this approach using the CHARMM package and the efficient GB-MV2 solvation model. Also, we have developed a new intuitive approach to decompose approximately the vibrational entropy term into atomic contributions, increasing significantly the correlation between the calculated and experimentally determined free energy changes upon mutations (Proteins 2007, 67, 1026).
Also, we continue the improvement of the relative CMEPS approach (J. Comput. Chem. 2006) to study the impact of mutations on protein structural stability and determine the most important residues for the protein fold. This technique has been applied successfully to the study of insulin p53 (Hum. Mutat. 2006, 27, 926) and PPAR (J. Biol. Chem. 2007, 282, 9666) structural stability. In several cases, mutations potentially increasing protein activities were suggested rationally using these approaches, and successfully tested experimentally (paper in preparation). Also, these techniques have been used to design new experiments providing detailed information about the structure/activity relationship of proteins (J. Biol. Chem. 2007, 282, 9666).