Proteins inherently fluctuate between conformations to perform functions in the cell. For example, they sample product‐binding, transition‐state‐ stabilizing, and product‐release states during catalysis, and they integrate signals from remote regions of the structure for allosteric regulation. However, there is a lack of understanding of how these dynamic processes occur at the basic atomic level. To address this gap, Dr. Daniel A. Keedy and his colleagues have combined multitemperature (instead of traditional cryogenic‐ temperature) X‐ray crystallography with algorithms for modeling alternative conformations based on electron density. The results reveal previously unrecognized tendrils of an allosteric network in a therapeutic target, protein tyrosine phosphatase 1B (PTP1B), validated with small molecules that bind to the new allosteric sites and modulate enzyme activity. Temperature is a scientifically informative and easily manipulated experimental parameter at synchrotron beamlines, so their approach is widely applicable to other proteins that yield well-diffracting crystals. Moreover, the general principles are extensible to other perturbations such as pH, pressure, ligand concentration, etc. Future work will explore strategies for leveraging X‐ray data across such perturbation series to more quantitatively measure how different parts of a protein structure are coupled to each other, and the functional consequences for regulation of cellular networks.
Dr. Keedy is an Assistant Professor with the Structural Biology Initiative at the ASRC and the Department of Chemistry and Biochemistry at the City College of New York beginning January 8, 2018. Prior to his appointment, he was an AP Giannini Postdoctoral Fellow in Bioengineering and Therapeutic Sciences at the University of California, San Francisco working with Professor James Fraser. He earned his PhD in Biochemistry and Structural Biology & Biophysics from Duke University after receiving his BA in Biochemistry & Molecular Biology from Rhodes College. His research on protein structural flexibility, temperature‐dependent X‐ray crystallography, and allosteric regulation has led to over 15 publications in leading scientific journals and over ten presentations at a variety of scientific meetings. His research interests include experimental and computational methods to control proteins by biasing toward specific confromations that underlie functions such as allostery, ligand binding, and catalyis. His work reveals new opportunities to modulate the activities of therapeutic targets such as tyrosine phosphatases with small molecules and protein engineering, and also offers insights into more general evolutionary processes that led to functional diversity in the human genome.
Daniel A. Keedy, Ph.D
Assistant Professor, Structural Biology Initiative,
CUNY Advanced Science Research Center,
Department of Chemistry and Biochemistry,
City College of New York Biochemistry and Chemistry Ph.D. Programs
Tuesday, February 27, 2018 12‐1:15PM
Steinman Hall Room 402