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PreprintCited by 84Enzyme Structure and FunctionProtein Tyrosine PhosphatasesProtein Structure and Dynamics

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

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Mehlman, Tamar (Skaist), Biel, Justin T., Azeem, Syeda Maryam, Nelson, Elliot R., Hossain, Sakib, Dunnett, Louise E., Paterson, Neil G., Douangamath, Alice, Talon, Romain, Axford, Danny, Orins, Helen, von Delft, Frank, Keedy, Daniel A.·2022·eLife
DOI 10.1101/2022.11.02.514751PMC PMC9991056

Preprint — published as 10.7554/elife.84632 · Paper page

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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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Research works printed but not linked: 71

  1. 10.1126/science.abj8754 · DOI · Paper page
  2. 10.1073/pnas.1703287114 · DOI
  3. 10.1093/nar/28.1.235 · DOI · Paper page
  4. Bradford, S. Y. C. , El Khoury, L. , Ge, Y. , Osato, M. , Mobley, D. L. , & Fischer, M. (2021). Temperature artifacts in protein structures bias ligand-binding predictions. Chemical Science. https://doi.org/10.1039/D1SC02751D · DOI
  5. 2018, Estimate your dose:RADDOSE-3D, Protein Science: A Publication of the Protein Society, 27, 217, 10.1002/pro.3302 · DOI
  6. 10.1038/nature18621 · DOI · Paper page
  7. 10.1016/j.molcel.2017.01.014 · DOI
  8. 2017, Gentle, fast and effective crystal soaking by acoustic dispensing, Acta Crystallographica. Section D, Structural Biology, 73, 246
  9. Corso, G. , Stärk, H. , Jing, B. , Barzilay, R. , & Jaakkola, T. (2022). DiffDock: Diffusion Steps, Twists,and Turns for Molecular Docking. In arXiv [q-bio.BM]. arXiv. http://arxiv.org/abs/2210.01776 · arXiv
  10. 2016, A poised fragment library enables rapid synthetic expansion yielding the first reported inhibitors of PHIP (2), an atypical bromodomain, Chemical Science, 7, 2322, 10.1039/C5SC03115J · DOI
  11. 10.1016/j.jmb.2017.06.009 · DOI
  12. 2017, SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules, Scientific Reports, 7, 42717, 10.1038/srep42717 · DOI · Paper page
  13. 2019, Water Networks Can Determine the Affinity of Ligand Binding to Proteins, Journal of the American Chemical Society, 141, 15818, 10.1021/jacs.9b06275 · DOI
  14. 2020, Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease, Nature Communications, 11, 5047, 10.1038/s41467-020-18709-w · DOI
  15. 2020, Instrumentation and experimental procedures for robust collection of X-ray diffraction data from protein crystals across physiological temperatures, Journal of Applied Crystallography, 53, 1493
  16. Ebrahim, A. , Riley, B. T. , Kumaran, D. , Andi, B. , Fuchs, M. R. , McSweeney, S. , & Keedy, D. A. (2022). The temperature-dependent conformational ensemble of SARS-CoV-2 main protease (Mpro). IUCrJ, 9(5). https://doi.org/10.1107/S2052252522007497 · DOI
  17. 10.1126/science.283.5407.1544 · DOI · Paper page
  18. 10.1107/S0907444905036693 · DOI
  19. 10.1073/pnas.1323440111 · DOI
  20. 2021, Macromolecular room temperature crystallography, Quarterly Reviews of Biophysics, 54, e1, 10.1017/S0033583520000128 · DOI
  21. 2015, One Crystal, Two Temperatures: Cryocooling Penalties Alter Ligand Binding to Transient Protein Sites, Chembiochem: A European Journal of Chemical Biology, 16, 1560, 10.1002/cbic.201500196 · DOI
  22. 10.1038/nature08615 · DOI
  23. 10.1073/pnas.1111325108 · DOI
  24. 10.1107/S1399004715010342. · DOI
  25. IUCr, 2021, xia2.multiplex: a multi-crystal data analysis pipeline, Acta Crystallographica Section A: Foundations and Advances, 77, C149, 10.1107/S0108767321095325 · DOI
  26. 2020, Pre-clustering data sets using cluster4x improves the signal-to-noise ratio of high-throughput crystallography drug-screening analysis, Acta Crystallographica. Section D, Structural Biology, 76, 1134
  27. 10.1126/science.abf7945 · DOI
  28. 10.3390/cryst11121579 · DOI
  29. 10.1073/pnas.0308315101 · DOI
  30. 10.1021/acs.biochem.8b00656 · DOI
  31. 2020, Minimally disruptive optical control of protein tyrosine phosphatase 1B, Nature Communications, 11, 788, 10.1038/s41467-020-14567-8 · DOI
  32. 10.1107/S0907444909047337 · DOI · Paper page
  33. 2019, Journey to the center of the protein: allostery from multitemperature multiconformer X-ray crystallography, Acta Crystallographica. Section D, Structural Biology, 75, 123
  34. Keedy, D. A. , Hill, Z. B. , Biel, J. T. , Kang, E. , & Rettenmaier, T. J. (2018). An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering. eLife. https://elifesciences.org/articles/36307 · DOI
  35. Keedy, D. A. , Kenner, L. R. , Warkentin, M. , Woldeyes, R. A. , Hopkins, J. B. , Thompson, M. C. , Brewster, A. S. , Van Benschoten, A. H. , Baxter, E. L. , Uervirojnangkoorn, M. , McPhillips, S. E. , Song, J. , Alonso-Mori, R. , Holton, J. M. , Weis, W. I. , Brunger, A. T. , Soltis, S. M. , Lemke, H. , Gonzalez, A. ,… Fraser, J. S. (2015). Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography. eLife, 4. https://doi.org/10.7554/eLife.07574 · DOI
  36. Keedy, D. A. , Van Den Bedem, H. , Sivak, D. A. , & Petsko, G. A. (2014). Crystal cryocooling distorts conformational heterogeneity in a model Michaelis complex of DHFR. Structure. https://www.sciencedirect.com/science/article/pii/S0969212614001403 · DOI
  37. 2014, Targeting the disordered C terminus of PTP1B with an allosteric inhibitor, Nature Chemical Biology, 10, 558, 10.1038/nchembio.1528 · DOI
  38. 10.1172/JCI80323 · DOI · Paper page
  39. 2020, Discovery of allosteric binding sites by crystallographic fragment screening, Current Opinion in Structural Biology, 65, 209, 10.1016/j.sbi.2020.08.004 · DOI
  40. 2018, Structural reorganization of SHP2 by oncogenic mutations and implications for oncoprotein resistance to allosteric inhibition, Nature Communications, 9, 4508, 10.1038/s41467-018-06823-9 · DOI · Paper page
  41. 2019, On-chip crystallization for serial crystallography experiments and on-chip ligand-binding studies, IUCrJ, 6, 714
  42. 2020, Room-temperature crystallography using a microfluidic protein crystal array device and its application to protein-ligand complex structure analysis, Chemical Science, 11, 9072, 10.1039/D0SC02117B · DOI
  43. 2022, New insights into the molecular mechanisms of glutaminase C inhibitors in cancer cells using serial room temperature crystallography, The Journal of Biological Chemistry, 298, 101535, 10.1016/j.jbc.2021.101535 · DOI
  44. 10.1021/ja401221b · DOI
  45. 2019, High-throughput structures of protein–ligand complexes at room temperature using serial femtosecond crystallography, IUCrJ, 6, 1074, 10.1107/S2052252519011655 · DOI
  46. 10.1107/S0907444909029436 · DOI
  47. 2018, Phosphatases start shedding their stigma of undruggability. Nature Reviews, Drug Discovery, 17, 847, 10.1038/nrd.2018.201 · DOI
  48. 10.1107/S0907444911001314 · DOI
  49. 10.1126/science.abd3623 · DOI
  50. 10.1073/pnas.0600973103 · DOI
  51. 2017, A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density, Nature Communications, 8, 15123, 10.1038/ncomms15123 · DOI
  52. 2017, Proper modelling of ligand binding requires an ensemble of bound and unbound states, Acta Crystallographica. Section D, Structural Biology, 73, 256
  53. 10.1002/jcc.24417 · DOI
  54. 10.1021/jacs.9b02822 · DOI · Paper page
  55. 2019, VMXi: a fully automated, fully remote, high-flux in situ macromolecular crystallography beamline, Journal of Synchrotron Radiation, 26, 291
  56. Sharma, S. , Ebrahim, A. , & Keedy, D. A. (2022). Room-temperature serial synchrotron crystallography of apo PTP1B. In bioRxiv (p. 2022.07.28.501725). https://doi.org/10.1101/2022.07.28.501725 · DOI
  57. 2021, A capillary-based microfluidic device enables primary high-throughput room-temperature crystallographic screening, Journal of Applied Crystallography, 54, 1034
  58. 10.1016/j.jsb.2015.05.006 · DOI
  59. The COVID Moonshot Consortium, Achdout, H. , Aimon, A. , Bar-David, E. , Barr, H. , Ben-Shmuel, A. , Bennett, J. , Bilenko, V. A. , Boby, M. L. , Borden, B. , Bowman, G. R. , Brun, J. , Bvnbs, S. , Calmiano, M. , Carbery, A. , Carney, D. , Cattermole, E. , Chang, E. , Chernyshenko, E. ,… Zitzmann, N. (2022). Open Science Discovery of Oral Non-Covalent SARS-CoV-2 Main Protease Inhibitor Therapeutics. In bioRxiv (p. 2020.10.29.339317).https://doi.org/10.1101/2020.10.29.339317 · DOI
  60. 10.1073/pnas.1705624114 · DOI
  61. 2022, Conserved conformational dynamics determine enzyme activity, Science Advances, 8, eabo5546, 10.1126/sciadv.abo5546 · DOI
  62. 10.1038/nature01681 · DOI
  63. 2018, qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps, Journal of Medicinal Chemistry, 61, 11183, 10.1021/acs.jmedchem.8b01292 · DOI
  64. Wallach, I. , Dzamba, M. , & Heifets, A. (2015). AtomNet: A Deep Convolutional Neural Network for Bioactivity Prediction in Structure-based Drug Discovery. In arXiv [cs.LG]. arXiv. http://arxiv.org/abs/1510.02855 · arXiv
  65. 2006, Hyperquenching for protein cryocrystallography, Journal of Applied Crystallography, 39, 805, 10.1107/S0021889806037484 · DOI
  66. 2017, Serial millisecond crystallography for routine room-temperature structure determination at synchrotrons, Nature Communications, 8, 542, 10.1038/s41467-017-00630-4 · DOI
  67. 2004, Allosteric inhibition of protein tyrosine phosphatase 1B, Nature Structural & Molecular Biology, 11, 730, 10.1038/nsmb803 · DOI
  68. 2011, Overview of the CCP4 suite and current developments. Acta Crystallographica, Section D, Biological Crystallography, 67, 235
  69. 2018, DIALS: implementation and evaluation of a new integration package. Acta Crystallographica, Section D, Structural Biology, 74, 85
  70. 10.1006/jmbi.1998.2400 · DOI
  71. 10.1021/acs.accounts.6b00537 · DOI

Metadata

Authors
Mehlman, T. (., Biel, J. T., Azeem, S. M., Nelson, E. R., Hossain, S., Dunnett, L. E., Paterson, N. G., Douangamath, A., Talon, R., Axford, D., Orins, H., von Delft, F., & Keedy, D. A.
Affiliations
  • The Graduate Center, CUNY (US)
  • University of California, San Francisco (US)
  • Diamond Light Source (GB)
  • CUNY Advanced Science Research Center (US)
  • University of Johannesburg (ZA)
Corresponding author
Keedy, Daniel A.
ORCID
Venue
eLife
Publisher
openRxiv
Published
2022-11-03
Volume
12
ISSN
2050-084X (ISSN-L)
DOI
10.1101/2022.11.02.514751
PMC
PMC9991056
OpenAlex
W4323312158
Cited by
84
References
1
Citations by year
2026: 14 · 2025: 33 · 2024: 22 · 2023: 15
FWCI
6.19
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • eLife (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • CUNY Academic Works (City University of New York) (submittedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • National Science Foundation
  • U.S. Department of Education (GAANN PA200A150068, PA200A150068)
  • City University of New York
  • Diamond Light Source
  • National Institutes of Health
  • Graduate Center
  • City College of New York
  • National Science Foundation of Sri Lanka
  • National Institute of General Medical Sciences (R35GM133769)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Tyrosine Phosphatases
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Keywords
room-temperature crystallography, PTP1B, small-molecule fragments, protein-ligand binding, protein conformational ensembles, allosteric site, binding poses, fragment screening
MeSH terms
Allosteric Site, Binding Sites, Crystallography, Ligands, Temperature, Protein Tyrosine Phosphatase, Non-Receptor Type 1

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