High-resolution design of a protein loop.

ABSTRACT: Despite having irregular structure, protein loops often adopt specific conformations that are critical to protein function. Most studies in de novo protein design have focused on creating proteins with regular elements of secondary structure connected by very short loops or turns. To design longer protein loops that adopt specific conformations, we have developed a protocol within the Rosetta molecular modeling program that iterates between optimizing the sequence and conformation of a loop in search of low-energy sequence-structure pairs. We have tested the procedure by designing 10-residue loops for the connection between the second and third strand in the beta-sandwich protein tenascin. Three low-energy designs from 7,200 flexible backbone trajectories were selected for experimental cha

SUBMITTER: Hu X 

PROVIDER: S-EPMC2077077 | biostudies-literature | 2007 Nov

REPOSITORIES: biostudies-literature