Daniel Keedy, Ph.D.

  • Associate Professor, Structural Biology Initiative
  • Associate Professor of Chemistry & Biochemistry, The City College of New York

Prior to his appointment, Daniel Keedy, Ph.D. 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 working with Jane and David Richardson, 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.

Professor Keedy was appointed to the ASRC in January 2018.

About the Keedy Lab

The Keedy Lab combines computation and experiments to reveal alternative protein conformations and explore how they underlie dynamic functions such as catalysis, ligand binding, and allosteric regulation.

Research Interests

Professor Keedy develops experimental and computational methods to control proteins by biasing toward specific conformations that underlie functions such as allostery, ligand binding, and catalysis. 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.

Publications

Wu J, Baranowski MR, Aleshin AE, Isiorho EA, Lambert LJ, De Backer LJS, Han YN, Das R, Sheffler DJ, Bobkov AA, Lemberikman AM, Keedy DA, Cosford NDP, Tautz L. Fragment Screening Identifies Novel Allosteric Binders and Binding Sites in the VHR (DUSP3) Phosphatase. ACS Omega. 2025.

Guerrero L, Ebrahim A, Riley BT, Kim SH, Bishop AC, Wu J, Han YN, Tautz L, Keedy DA. Three STEPs Forward: A Trio of Unexpected Structures of PTPN5. Proteins: Structure, Function, and Bioinformatics. 2025

Woods VA*, Sharma S*, Lemberikman AM, Keedy DA. Orchestrating function: concerted dynamics, allostery, and catalysis in protein tyrosine phosphatases. Current Opinion in Structural Biology. 2025.

Sharma S, Mehlman (Skaist) T, Sagabala RS, Boivin B, Keedy DA. High-resolution double vision of the allosteric phosphatase PTP1B. Acta Cryst F. 2024. 80(Pt 1):1-12.

Atomwise AIMS Program: Wallach I, …, Keedy DA, …, Smith KS, …, Singh N, …, Hossain S, …, Dzhumaev S, …, Azeem SM, …, Mehlman T, …, Woods VA…, Heifets A (688 total authors). AI is a viable alternative to high throughput screening: a 318-target study. Scientific Reports. 2024. 2;14(1):7526.

Mehlman (Skaist) T, Ginn HM, Keedy DA. An expanded trove of fragment-bound structures for the allosteric enzyme PTP1B from computational reanalysis of large-scale crystallographic data. Structure. 2024. 8;32(8):1231-1238.e4.

Wankowicz SA, Ravikumar A, Sharma S, Riley BT, Raju A, Hogan D, van den Bedem H, Keedy DA, Fraser JS. Automated multiconformer model building for X-ray crystallography and cryo-EM. eLife. 2024. 

Woods VA, Abzalimov RR, Keedy DA. Native dynamics and allosteric responses in PTP1B probed by high-resolution HDX-MS. Protein Science. 2024. 33(6):e5024.

Guerrero L*, Ebrahim A*, Riley BT, Kim M, Huang Q, Finke AD, Keedy DA (*contributed equally). Pushed to extremes: distinct effects of high temperature versus pressure on the structure of STEP. Communications Biology. 2024. 7(1):59.

Mehlman T. S., Biel J. T., Azeem S. M., Nelson E. R., Hossain S., Dunnett L., Paterson N. G., Douangamath A., Talon R., Axford D., Orins H., von Delft F., Keedy D. A. Room-temperature crystallography reveals altered binding of small-molecule fragments to PTP1B. eLife 2023 12:e84632

Headshot: Daniel Keedy

Phone Number

212.413.3246