Research Expertise & Professional Interests
John Straub explores protein dynamics and thermodynamics using theoretical and computational methods, with a particular focus on elucidating pathways for conformational change associated with protein energy transfer, signaling, folding, and aggregation.
The Straub Group investigates fundamental aspects of protein dynamics and thermodynamics underlying the formation of protein structure, through folding and aggregation, and enabling protein function, through pathways of energy flow and signaling. Student and postdoctoral research scientists in the Straub Group work to develop and employ state-of-the-art computational methods while working in collaboration with leading experimental research groups.
Kinetic and thermodynamic properties defining protein aggregation are elucidated through pioneering computational studies of the earliest stages of amyloid protein aggregation, including the formation of small oligomers (dimers through hexamers) from monomeric protein, and the production of monomeric protein from amyloid precursor proteins.
Novel computational algorithms for enhanced sampling of conformational ensembles in complex biomolecular systems include effective approaches for global optimization and enhanced conformational sampling, in complex molecular systems, and novel coarse-grained models of proteins, for use in protein structure prediction.
Novel computational approaches for the exploration of reaction dynamics allow for direct simulation of both ultrafast (quantum) and long-time (classical) dynamical events that translate how protein structure supports dynamical energy flow associated with protein function.
Pathways and mechanism for energy and signal flow in proteins are explored using classical and quantum dynamical simulations. This includes fundamental aspects of energy transfer associated with ligand binding and redox events in a variety of heme protein systems, with the ultimate goal of relating protein dynamics to function. Professor Straub’s book, “Proteins: Energy, Heat and Signal Flow,” co-edited with David Leitner, captures the state-of-the-art in theoretical studies of protein dynamics and signaling.