Room-temperature crystallography reveals altered binding of small-molecule fragments to PTP1B

DOI: 10.7554/eLife.84632

Authors: Tamar Skaist Mehlmam (CUNY Advanced Science Research Center) , Justin T. Biel (University of California, San Francisco) , Syeda Maryam Azeem (CUNY Advanced Science Research Center) , Elliot R. Nelson (Diamond Light Source) , Sakib Hossain (CUNY Advanced Science Research Center) , Louise Dunnett (Diamond Light Source; Research Complex at Harwell) , Neil G. Paterson (Diamond Light Source) , Alice Douangamath (Diamond Light Source; Research Complex at Harwell) , Romain Talon (Diamond Light Source) , Danny Axford (Diamond Light Source) , Helen Orins (CUNY Advanced Science Research Center) , Frank Von Delft (Diamond Light Source; Research Complex at Harwell; University of Oxford; University of Johannesburg) , Daniel A. Keedy (CUNY Advanced Science; City College of New York Research Center)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Elife , VOL 12

State: Published (Approved)
Published: March 2023
Diamond Proposal Number(s): 15751 , 18340 , 23570

Abstract: Much of our current understanding of how small-molecule ligands interact with proteins stems from X-ray crystal structures determined at cryogenic (cryo) temperature. For proteins alone, room-temperature (RT) crystallography can reveal previously hidden, biologically relevant alternate conformations. However, less is understood about how RT crystallography may impact the conformational landscapes of protein-ligand complexes. Previously, we showed that small-molecule fragments cluster in putative allosteric sites using a cryo crystallographic screen of the therapeutic target PTP1B (Keedy et al., 2018). Here, we have performed two RT crystallographic screens of PTP1B using many of the same fragments, representing the largest RT crystallographic screens of a diverse library of ligands to date, and enabling a direct interrogation of the effect of data collection temperature on protein-ligand interactions. We show that at RT, fewer ligands bind, and often more weakly – but with a variety of temperature-dependent differences, including unique binding poses, changes in solvation, new binding sites, and distinct protein allosteric conformational responses. Overall, this work suggests that the vast body of existing cryo-temperature protein-ligand structures may provide an incomplete picture, and highlights the potential of RT crystallography to help complete this picture by revealing distinct conformational modes of protein-ligand systems. Our results may inspire future use of RT crystallography to interrogate the roles of protein-ligand conformational ensembles in biological function.

Subject Areas: Biology and Bio-materials

Diamond Offline Facilities: XChem
Instruments: I03-Macromolecular Crystallography , I24-Microfocus Macromolecular Crystallography

Added On: 13/03/2023 08:41

Discipline Tags:

Structural biology Life Sciences & Biotech

Technical Tags:

Diffraction Macromolecular Crystallography (MX) Fragment Screening