Computational protein design with explicit consideration of surface hydrophobic patches.

ABSTRACT: De novo protein design requires the identification of amino-acid sequences that favor the target-folded conformation and are soluble in water. One strategy for promoting solubility is to disallow hydrophobic residues on the protein surface during design. However, naturally occurring proteins often have hydrophobic amino acids on their surface that contribute to protein stability via the partial burial of hydrophobic surface area or play a key role in the formation of protein-protein interactions. A less restrictive approach for surface design that is used by the modeling program Rosetta is to parameterize the energy function so that the number of hydrophobic amino acids designed on the protein surface is similar to what is observed in naturally occurring monomeric proteins. Previous studie

SUBMITTER: Jacak R 

PROVIDER: S-EPMC3277657 | biostudies-literature | 2012 Mar

REPOSITORIES: biostudies-literature