Conformational Ensembles from Experimental Data and Computer Simulations

Conformational Ensembles from Experimental Data

and Computer Simulations

Poster Abstracts

151

114-POS

Board 34

Protein Evolution Under a Computational Microscope

Huafeng Xu

, David E. Shaw

D. E. Shaw Research, New York, NY, USA,

Columbia University, New York, NY, USA.

Protein evolution is often driven by changes in the amino acid sequence that alter the affinity and

specificity of the protein for its binding partners. Mutations that do not appear to affect the

specific interactions between the protein and its binding partner can have a surprisingly large

effect on the binding affinity. We have used long-timescale molecular dynamics (MD)

simulations to study how such mutations affect the binding affinities in two examples of protein

evolution: 1) the affinity maturation of a broadly neutralizing antibody lineage against influenza

hemagglutinin, in which two divergent maturation pathways have led to mature antibodies that

potently neutralize a broad range of H1 influenza viruses, and 2) the adaptation of influenza

hemagglutinin, in which hemagglutinins of avian strains have accrued mutations that favor

binding to human receptors over avian receptors (a requirement for human transmission). In the

affinity maturation study, our simulations contributed to the finding that the affinity increase in

the mature antibodies was primarily attributable to the stabilization of the CDR H3 loop in the

antigen-binding conformation. In the hemagglutinin adaptation study, our simulations suggested

that the human receptor adopts a dynamic ensemble of diverse conformations in binding to

hemagglutinin, including a novel conformation not yet seen in crystallography. We identified

mutations in an avian hemagglutinin that we predicted would favor the formation of new specific

interactions with the human receptor in the novel binding conformation, and then experimentally

verified increased affinity of the mutant hemagglutinin for the human receptor. Results from

these studies suggest that conformations generated by MD simulations, including some which

have not been previously identified by experimental structural determination, may help unravel

the structural mechanism underlying the evolution of proteins, and serve as starting points for

engineering biomolecular complexes with enhanced affinity and specificity.