Room-temperature serial synchrotron crystallography of apo PTP1B

Sharma, Shivani; Ebrahim, Ali; Keedy, D.A.

doi:10.1101/2022.07.28.501725

Cited by 2 publications

(2 citation statements)

References 60 publications

(77 reference statements)

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“…Notably, these changes involve essentially complete closing of the allosteric L16 site, but only partial closing (~50%) of the active-site WPD loop -- in contrast to the previous paradigm in which the WPD loop and allosteric sites are precisely conformationally coupled (Keedy et al, 2018). Similar (de)coupling was also seen recently with serial synchrotron crystallography of apo PTP1B (Sharma et al, 2022). Thus, RT crystallography can add important nuance to our understanding of allosteric mechanisms in PTPs (Choy et al, 2017; Cui et al, 2017; Hjortness et al, 2018) and likely other proteins.…”

Section: Discussionsupporting

confidence: 84%

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

Mehlman

Biel

Azeem

et al. 2022

Preprint

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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*, Hill*, 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 cryogenic-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.

show abstract

Section: Discussionsupporting

confidence: 84%

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

Mehlman

Biel

Azeem

et al. 2022

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…Notably, these changes involve essentially complete closing of the allosteric L16 site, but only partial closing (~50%) of the active-site WPD loop --in contrast to the previous paradigm in which the WPD loop and allosteric sites are precisely conformationally coupled (Keedy et al, 2018). Similar (de)coupling was also seen recently with serial synchrotron crystallography of apo PTP1B (Sharma et al, 2022). Thus, RT crystallography can add important nuance to our understanding of allosteric mechanisms in PTPs (Choy et al, 2017;Cui et al, 2017;Hjortness et al, 2018) and likely other proteins.…”

Section: Discussionsupporting

confidence: 71%

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

Mehlman

Biel

Azeem

et al. 2023

eLife

View full text Add to dashboard Cite

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.

show abstract

Room-temperature serial synchrotron crystallography of apo PTP1B

Cited by 2 publications

References 60 publications

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

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

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

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