Multi-constraint computational design suggests that native sequences of germline antibody H3 loops are nearly optimal for conformational flexibility.

ABSTRACT: The limited size of the germline antibody repertoire has to recognize a far larger number of potential antigens. The ability of a single antibody to bind multiple ligands due to conformational flexibility in the antigen-binding site can significantly enlarge the repertoire. Among the six complementarity determining regions (CDRs) that generally comprise the binding site, the CDR H3 loop is particularly variable. Computational protein design studies showed that predicted low energy sequences compatible with a given backbone structure often have considerable similarity to the corresponding native sequences of naturally occurring proteins, indicating that native protein sequences are close to optimal for their structures. Here, we take a step forward to determine whether conformational flexib

SUBMITTER: Babor M 

PROVIDER: S-EPMC3978785 | biostudies-literature | 2009 Jun

REPOSITORIES: biostudies-literature