Trade-off between positive and negative design of protein stability: from lattice models to real proteins.

ABSTRACT: Two different strategies for stabilizing proteins are (i) positive design in which the native state is stabilized and (ii) negative design in which competing non-native conformations are destabilized. Here, the circumstances under which one strategy might be favored over the other are explored in the case of lattice models of proteins and then generalized and discussed with regard to real proteins. The balance between positive and negative design of proteins is found to be determined by their average "contact-frequency", a property that corresponds to the fraction of states in the conformational ensemble of the sequence in which a pair of residues is in contact. Lattice model proteins with a high average contact-frequency are found to use negative design more than model proteins with a low

SUBMITTER: Noivirt-Brik O 

PROVIDER: S-EPMC2781108 | biostudies-literature | 2009 Dec

REPOSITORIES: biostudies-literature