Room-temperature crystallography reveals altered binding of small-molecule fragments to PTP1B
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*, 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..
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Preprint| Erscheinungsjahr: |
2024 |
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| Erschienen: |
2024 |
| Enthalten in: |
bioRxiv.org - (2024) vom: 23. Apr. Zur Gesamtaufnahme - year:2024 |
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| Sprache: |
Englisch |
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| Beteiligte Personen: |
Mehlman, Tamar (Skaist) [VerfasserIn] |
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| doi: |
10.1101/2022.11.02.514751 |
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XBI037783491 |
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| 520 | |a 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*, 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. | ||
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| 700 | 1 | |a Azeem, Syeda Maryam |e verfasserin |0 (orcid)0000-0002-7712-527X |4 aut | |
| 700 | 1 | |a Nelson, Elliot R. |e verfasserin |0 (orcid)0000-0002-5460-8076 |4 aut | |
| 700 | 1 | |a Hossain, Sakib |e verfasserin |0 (orcid)0000-0002-2602-9245 |4 aut | |
| 700 | 1 | |a Dunnett, Louise E. |e verfasserin |0 (orcid)0000-0001-6710-6959 |4 aut | |
| 700 | 1 | |a Paterson, Neil G. |e verfasserin |0 (orcid)0000-0003-4292-6971 |4 aut | |
| 700 | 1 | |a Douangamath, Alice |e verfasserin |0 (orcid)0000-0002-9196-8644 |4 aut | |
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| 700 | 1 | |a Keedy, Daniel A. |e verfasserin |0 (orcid)0000-0002-9184-7586 |4 aut | |
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