Model for the peptide-free conformation of class II MHC proteins.

ABSTRACT:

Background

Major histocompatibility complex proteins are believed to undergo significant conformational changes concomitant with peptide binding, but structural characterization of these changes has remained elusive.

Methodology/principal findings

Here we use molecular dynamics simulations and experimental probes of protein conformation to investigate the peptide-free state of class II MHC proteins. Upon computational removal of the bound peptide from HLA-DR1-peptide complex, the alpha50-59 region folded into the P1-P4 region of the peptide binding site, adopting the same conformation as a bound peptide. Strikingly, the structure of the hydrophobic P1 pocket is maintained by engagement of the side chain of Phe alpha54. In addition, conserved hydrogen bonds observed in crysta

SUBMITTER: Painter CA 

PROVIDER: S-EPMC2408972 | biostudies-literature | 2008 Jun

REPOSITORIES: biostudies-literature