Jeffrey Peng

Functional Dynamics of Proteins and Ligands

The life of the cell depends on protein molecules - nanometer-sized "molecular machines" - that serve the vast array of functions supporting cell maintenance and growth. Historically, explanations of protein function emphasized specific 3-d structures, thereby fostering a static view of proteins. Yet, many proteins have substantial regions of flexibility involved in their functional mechanisms, and their number continues to increase. It is now clear that a static view is too limiting. To explain protein function and evolution, we need to acknowledge their intrinsic flexibility and understand the atomic-level determinants of their functional dynamics. From a physics standpoint, proteins give an opportunity to understand the behavior of complex, dynamical systems.

The over-arching goal of our lab is a predictive understanding of how conformational dynamics affects the evolution of protein function. Our main methods are multi-dimensional liquid-state NMR spectroscopy and computation. Specific research areas include: i) exploring the role of conformational dynamics in allosteric signaling; ii) defining flexibility-function correlations for proteins conferring antibiotic resistance; and iii) development of improved NMR methods for establishing flexibility-activity relationships in iterative inhibitor design. These research areas are relevant to deepening our understanding of the physics of proteins and how they evolve, particularly in the context of drug resistance.

Publications

1. "NMR Relaxation Dispersion Reveals Macrocycle Breathing Dynamics in a Cyclodextrin-based Rotaxane" Stoffel S.; Zhang Q.W.; Li D.H.; Smith B.D.; Peng, J.W. J. Am. Chem. Soc. 2020, 142(16), 7413-7424.
2. "Extended Impact of Pin1 Catalytic Loop Phosphorylation Revealed by S71E Phosphomimetic" Mahoney B.J.; Zhang M.; Zintsmaster J.S.; Peng, J.W. J. Mol. Biol. 2018, 430(5), 710-721.
3. "Enhanced Sampling of Interdomain Motion Using Map-Restrained Langevin Dynamics and NMR: Application to Pin1" Bouchard J.J.; Xia J.; Case D.A.; Peng, J.W. J. Mol. Biol. 2018, 430(14), 2164-2180.
4. "A gratuitous β-Lactamase inducer uncovers hidden active site dynamics of the Staphylococcus aureus BlaR1 sensor domain" Frederick, T.E.; Peng, J.W. PLoS One 2018, 13(5), e0197241.