Molecular Strategy for Designing Robust Proteins:
Looking Deeper at the Surface
George Makhatadze,
Rensselaer Polytechnic Institute
The progress in understanding the forces responsible for the protein stability has been enormous, largely through the combination of experimental and theoretical approaches. It has been shown that the hydrophobic effect, hydrogen bonding and packing interactions between residues buried in the protein interior are dominant factors that define protein stability. The role of surface residues for protein stability received much less attention. It was believed that surface residues are not important for protein stability particularly because their interactions with the solvent should be similar in the native and unfolded states. However, our experimental data using different model proteins shows that the surface residues contribute to protein stability through a variety of factors. These factors can be operationally divided into long-range interactions (charge-charge interactions between ionizable groups) and short-range local interactions (salt-bridges, hydrophobicity and packing, peptide bond hydration, a-helical propensity, helix capping). Quantitative analyses of the contribution of these different factors to the protein stability will be presented and their applicability to the design of thermostable enzymes will be discussed. In addition, several examples providing experimental validation for these computational protein design approaches will be given.