Folding free energy function selects native-like protein sequences in the core but not on the surface.

ABSTRACT: An automatic protein design procedure is used to select amino acid sequences that optimize the folding free energy function for a given protein. The only information used in designing the sequences is a set of known backbone structures for each protein, a rotamer library, and a well established classical empirical force field, which relies on basic physical chemical principles that underlie molecular interactions and protein stability, and has not been adjusted to yield native-like sequences. Applying the procedure to 7 different known protein folds, representing a total of 45 different native protein structures, yields ensembles of designed sequences displaying remarkable similarity to their natural counterparts in the protein core, but which are distinctly non-native on the protein surfa

SUBMITTER: Jaramillo A 

PROVIDER: S-EPMC129712 | biostudies-literature | 2002 Oct

REPOSITORIES: biostudies-literature