John E. Straub
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.
Degrees and Positions
- BS, University of Maryland, 1982
- MA, Columbia University, 1984
- MPhil, Columbia University, 1986
- PhD, Columbia University, 1987
- NIH Postdoctoral Fellow, Harvard University, 1987-1990
- Alfred P. Sloan Research Fellow 1995-1997
- Metcalf Award for Excellence in Teaching, Boston University 2005
- Fellow, Institute for Advanced Studies, Hebrew University, Jerusalem, Israel, 1998
- Visiting Professor, Montana State University, Bozeman, Montana, 2006
Prof. Straub’s new 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.
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.
- Pathways and mechanism for energy and signal flow in proteins are explored using classical and quantum dynamical simulations. Our research has made contributions to fundamental aspects of energy transfer associated with ligand binding and redox events in a variety of heme protein systems.
- 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.
Techniques & Resources
- Scientific Computing and Visualization (SCV) and the Center for Computational Science (CCS) at Boston University provide outstanding hardware, software, and personnel resources to support research in a wide range of computational sciences.
- Computational Tools regularly employed included GAUSSIAN, for quantum chemical calculations, CHARMM and NAMD, for classical molecular dynamics simulations, and VMD, for protein visualization, in addition to a variety of “home grown” computational programs for molecular dynamics and Monte Carlo simulation and analysis.
- Theoretical and Computational Science is a rapidly evolving field that can be explored through a variety of courses offered in the fundamentals of Computational Physics, Quantum Mechanics, and Statistical Mechanics, as well as regular colloquia, symposia, and workshops.
The Straub Group’s doctoral students benefit from a rich environment for interdisciplinary computational science research at BU that is complemented by participation in active collaborations with leading experimental biophysical research laboratories.
What’s Next for Graduates of the Straub Group?
The Straub Group has a distinguished history of mentoring exceptionally talented graduate students who now occupy faculty positions at leading research institutions.
- Jianpeng Ma, Baylor College of Medicine & Rice University
- Patricia Amara, Institute for Structural Biology, Grenoble, France
- Ioan Andricioaei, University of California at Irvine
- Shuanghong “Sharon” Huo, Clark University
- Francesca Massi, University of Massachusetts Medical Center
- Nicolae-Viorel “Vio” Buchete, University College Dublin, Ireland
Office Hours: by Appointment
Explore Professor Straub’s relation to Gay-Lussac in his chemical genealogy.
Examine a list of publications.