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Skaist Mehlman T, Biel JT, Azeem SM, Nelson ER, Hossain S, Dunnett L, Paterson NG, Douangamath A, Talon R, Axford D, Orins H, von Delft F, Keedy DA. Room-temperature crystallography reveals altered binding of small-molecule fragments to PTP1B. eLife 2023; 12:84632. [PMID: 36881464 PMCID: PMC9991056 DOI: 10.7554/elife.84632] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 02/12/2023] [Indexed: 03/08/2023] Open
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.
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Affiliation(s)
- Tamar Skaist Mehlman
- Structural Biology Initiative, CUNY Advanced Science Research CenterNew YorkUnited States
- PhD Program in Biochemistry, CUNY Graduate CenterNew YorkUnited States
| | - Justin T Biel
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
| | - Syeda Maryam Azeem
- Structural Biology Initiative, CUNY Advanced Science Research CenterNew YorkUnited States
| | | | - Sakib Hossain
- Structural Biology Initiative, CUNY Advanced Science Research CenterNew YorkUnited States
| | - Louise Dunnett
- Diamond Light SourceDidcotUnited Kingdom
- Research Complex at Harwell, Harwell Science and Innovation CampusDidcotUnited Kingdom
| | | | - Alice Douangamath
- Diamond Light SourceDidcotUnited Kingdom
- Research Complex at Harwell, Harwell Science and Innovation CampusDidcotUnited Kingdom
| | | | | | - Helen Orins
- Structural Biology Initiative, CUNY Advanced Science Research CenterNew YorkUnited States
| | - Frank von Delft
- Diamond Light SourceDidcotUnited Kingdom
- Research Complex at Harwell, Harwell Science and Innovation CampusDidcotUnited Kingdom
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- Department of Biochemistry, University of JohannesburgJohannesburgSouth Africa
| | - Daniel A Keedy
- Structural Biology Initiative, CUNY Advanced Science Research CenterNew YorkUnited States
- Department of Chemistry and Biochemistry, City College of New YorkNew YorkUnited States
- PhD Programs in Biochemistry, Biology, and Chemistry, CUNY Graduate CenterNew YorkUnited States
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Chatterjee A, Pratakshya P, Kwansa AL, Kaimal N, Cannon AH, Sartori B, Marmiroli B, Orins H, Feng Z, Drake S, Couvrette J, Le L, Bernstorff S, Yingling YG, Gorodetsky AA. Squid Skin Cell-Inspired Refractive Index Mapping of Cells, Vesicles, and Nanostructures. ACS Biomater Sci Eng 2023; 9:978-990. [PMID: 36692450 DOI: 10.1021/acsbiomaterials.2c00088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The fascination with the optical properties of naturally occurring systems has been driven in part by nature's ability to produce a diverse palette of vibrant colors from a relatively small number of common structural motifs. Within this context, some cephalopod species have evolved skin cells called iridophores and leucophores whose constituent ultrastructures reflect light in different ways but are composed of the same high refractive index material─a protein called reflectin. Although such natural optical systems have attracted much research interest, measuring the refractive indices of biomaterial-based structures across multiple different environments and establishing theoretical frameworks for accurately describing the obtained refractive index values has proven challenging. Herein, we employ a synergistic combination of experimental and computational methodologies to systematically map the three-dimensional refractive index distributions of model self-assembled reflectin-based structures both in vivo and in vitro. When considered together, our findings may improve understanding of squid skin cell functionality, augment existing methods for characterizing protein-based optical materials, and expand the utility of emerging holotomographic microscopy techniques.
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Affiliation(s)
- Atrouli Chatterjee
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697, United States
| | - Preeta Pratakshya
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Albert L Kwansa
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Nikhil Kaimal
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697, United States
| | - Andrew H Cannon
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Barbara Sartori
- Institute of Inorganic Chemistry, Graz University of Technology, Graz 8010, Austria
| | - Benedetta Marmiroli
- Institute of Inorganic Chemistry, Graz University of Technology, Graz 8010, Austria
| | - Helen Orins
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697, United States
| | - Zhijing Feng
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697, United States
| | - Samantha Drake
- Department of Materials Science and Engineering, University of California, Irvine, Irvine, California 92697, United States
| | - Justin Couvrette
- Department of Materials Science and Engineering, University of California, Irvine, Irvine, California 92697, United States
| | - LeAnn Le
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697, United States
| | | | - Yaroslava G Yingling
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Alon A Gorodetsky
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697, United States.,Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States.,Department of Materials Science and Engineering, University of California, Irvine, Irvine, California 92697, United States
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Umerani MJ, Pratakshya P, Chatterjee A, Cerna Sanchez JA, Kim HS, Ilc G, Kovačič M, Magnan C, Marmiroli B, Sartori B, Kwansa AL, Orins H, Bartlett AW, Leung EM, Feng Z, Naughton KL, Norton-Baker B, Phan L, Long J, Allevato A, Leal-Cruz JE, Lin Q, Baldi P, Bernstorff S, Plavec J, Yingling YG, Gorodetsky AA. Structure, self-assembly, and properties of a truncated reflectin variant. Proc Natl Acad Sci U S A 2020; 117:32891-32901. [PMID: 33323484 PMCID: PMC7780002 DOI: 10.1073/pnas.2009044117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Naturally occurring and recombinant protein-based materials are frequently employed for the study of fundamental biological processes and are often leveraged for applications in areas as diverse as electronics, optics, bioengineering, medicine, and even fashion. Within this context, unique structural proteins known as reflectins have recently attracted substantial attention due to their key roles in the fascinating color-changing capabilities of cephalopods and their technological potential as biophotonic and bioelectronic materials. However, progress toward understanding reflectins has been hindered by their atypical aromatic and charged residue-enriched sequences, extreme sensitivities to subtle changes in environmental conditions, and well-known propensities for aggregation. Herein, we elucidate the structure of a reflectin variant at the molecular level, demonstrate a straightforward mechanical agitation-based methodology for controlling this variant's hierarchical assembly, and establish a direct correlation between the protein's structural characteristics and intrinsic optical properties. Altogether, our findings address multiple challenges associated with the development of reflectins as materials, furnish molecular-level insight into the mechanistic underpinnings of cephalopod skin cells' color-changing functionalities, and may inform new research directions across biochemistry, cellular biology, bioengineering, and optics.
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Affiliation(s)
- Mehran J. Umerani
- Department of Materials Science and Engineering, University of California, Irvine, CA 92697
| | | | - Atrouli Chatterjee
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA 92697
| | - Juana A. Cerna Sanchez
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697
| | - Ho Shin Kim
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, NC 27695
| | - Gregor Ilc
- Slovenian NMR Centre, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Matic Kovačič
- Slovenian NMR Centre, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Christophe Magnan
- Department of Computer Science, University of California, Irvine, CA 92697
| | - Benedetta Marmiroli
- Institute of Inorganic Chemistry, Graz University of Technology, 8010 Graz, Austria
| | - Barbara Sartori
- Institute of Inorganic Chemistry, Graz University of Technology, 8010 Graz, Austria
| | - Albert L. Kwansa
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, NC 27695
| | - Helen Orins
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA 92697
| | - Andrew W. Bartlett
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA 92697
| | - Erica M. Leung
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA 92697
| | - Zhijing Feng
- Department of Materials Science and Engineering, University of California, Irvine, CA 92697
| | - Kyle L. Naughton
- Department of Physics and Astronomy, University of California, Irvine, CA 92697
| | | | - Long Phan
- Department of Materials Science and Engineering, University of California, Irvine, CA 92697
| | - James Long
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA 92697
| | - Alex Allevato
- Department of Materials Science and Engineering, University of California, Irvine, CA 92697
| | - Jessica E. Leal-Cruz
- Department of Materials Science and Engineering, University of California, Irvine, CA 92697
| | - Qiyin Lin
- Irvine Materials Research Institute, University of California, Irvine, CA 92697
| | - Pierre Baldi
- Department of Computer Science, University of California, Irvine, CA 92697
| | | | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Yaroslava G. Yingling
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, NC 27695
| | - Alon A. Gorodetsky
- Department of Materials Science and Engineering, University of California, Irvine, CA 92697
- Department of Chemistry, University of California, Irvine, CA 92697
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA 92697
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