Conformational Ensembles from Experimental Data and Computer Simulations

Conformational Ensembles from Experimental Data and Computer Simulations

Poster Abstracts

114-POS Board 34 Protein Evolution Under a Computational Microscope Huafeng Xu 1 , David E. Shaw 1 ,

1 D. E. Shaw Research, New York, NY, USA, 2 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.

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