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Zhao Z, Zhao L, Kong C, Zhou J, Zhou F. A review of biophysical strategies to investigate protein-ligand binding: What have we employed? Int J Biol Macromol 2024; 276:133973. [PMID: 39032877 DOI: 10.1016/j.ijbiomac.2024.133973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/15/2024] [Accepted: 07/16/2024] [Indexed: 07/23/2024]
Abstract
The protein-ligand binding frequently occurs in living organisms and plays a crucial role in the execution of the functions of proteins and drugs. It is also an indispensable part of drug discovery and screening. While the methods for investigating protein-ligand binding are diverse, each has its own objectives, strengths, and limitations, which all influence the choice of method. Many studies concentrate on one or a few specific methods, suggesting that comprehensive summaries are lacking. Therefore in this review, these methods are comprehensively summarized and are discussed in detail: prediction and simulation methods, thermal and thermodynamic methods, spectroscopic methods, methods of determining three-dimensional structures of the complex, mass spectrometry-based methods and others. It is also important to integrate these methods based on the specific objectives of the research. With the aim of advancing pharmaceutical research, this review seeks to deepen the understanding of the protein-ligand binding process.
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Affiliation(s)
- Zhen Zhao
- Beijing Key Laboratory of Functional Food from Plant Resources, College of Food Science and Nutritional Engineering, China Agricultural University, 17 Tsinghua East Road, Beijing 100083, China.
| | - Liang Zhao
- Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, 11 Fucheng Road, Beijing 100048, China.
| | - Chenxi Kong
- Beijing Key Laboratory of Functional Food from Plant Resources, College of Food Science and Nutritional Engineering, China Agricultural University, 17 Tsinghua East Road, Beijing 100083, China
| | - Jingxuan Zhou
- Beijing Key Laboratory of Functional Food from Plant Resources, College of Food Science and Nutritional Engineering, China Agricultural University, 17 Tsinghua East Road, Beijing 100083, China.
| | - Feng Zhou
- Beijing Key Laboratory of Functional Food from Plant Resources, College of Food Science and Nutritional Engineering, China Agricultural University, 17 Tsinghua East Road, Beijing 100083, China.
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2
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Wankowicz SA, Fraser JS. Comprehensive encoding of conformational and compositional protein structural ensembles through the mmCIF data structure. IUCRJ 2024; 11:494-501. [PMID: 38958015 PMCID: PMC11220883 DOI: 10.1107/s2052252524005098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 05/29/2024] [Indexed: 07/04/2024]
Abstract
In the folded state, biomolecules exchange between multiple conformational states crucial for their function. However, most structural models derived from experiments and computational predictions only encode a single state. To represent biomolecules accurately, we must move towards modeling and predicting structural ensembles. Information about structural ensembles exists within experimental data from X-ray crystallography and cryo-electron microscopy. Although new tools are available to detect conformational and compositional heterogeneity within these ensembles, the legacy PDB data structure does not robustly encapsulate this complexity. We propose modifications to the macromolecular crystallographic information file (mmCIF) to improve the representation and interrelation of conformational and compositional heterogeneity. These modifications will enable the capture of macromolecular ensembles in a human and machine-interpretable way, potentially catalyzing breakthroughs for ensemble-function predictions, analogous to the achievements of AlphaFold with single-structure prediction.
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Affiliation(s)
- Stephanie A. Wankowicz
- Department of Bioengineering and Therapeutic ScienceUniversity of CaliforniaSan FranciscoCA94117USA
| | - James S. Fraser
- Department of Bioengineering and Therapeutic ScienceUniversity of CaliforniaSan FranciscoCA94117USA
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3
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Behnam MAM, Klein CD. Alternate recognition by dengue protease: Proteolytic and binding assays provide functional evidence beyond an induced-fit. Biochimie 2024:S0300-9084(24)00138-X. [PMID: 38871044 DOI: 10.1016/j.biochi.2024.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/31/2024] [Accepted: 06/10/2024] [Indexed: 06/15/2024]
Abstract
Proteases are key enzymes in viral replication, and interfering with these targets is the basis for therapeutic interventions. We previously introduced a hypothesis about conformational selection in the protease of dengue virus and related flaviviruses, based on conformational plasticity noted in X-ray structures. The present work presents the first functional evidence for alternate recognition by the dengue protease, in a mechanism based primarily on conformational selection rather than induced-fit. Recognition of distinct substrates and inhibitors in proteolytic and binding assays varies to a different extent, depending on factors reported to influence the protease structure. The pH, salinity, buffer type, and temperature cause a change in binding, proteolysis, or inhibition behavior. Using representative inhibitors with distinct structural scaffolds, we identify two contrasting binding profiles to dengue protease. Noticeable effects are observed in the binding assay upon inclusion of a non-ionic detergent in comparison to the proteolytic assay. The findings highlight the impact of the selection of testing conditions on the observed ligand affinity or inhibitory potency. From a broader scope, the dengue protease presents an example, where the induced-fit paradigm appears insufficient to explain binding events with the biological target. Furthermore, this protein reveals the complexity of comparing or combining biochemical assay data obtained under different conditions. This can be particularly critical for artificial intelligence (AI) approaches in drug discovery that rely on large datasets of compounds activity, compiled from different sources using non-identical testing procedures. In such cases, mismatched results will compromise the model quality and its predictive power.
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Affiliation(s)
- Mira A M Behnam
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
| | - Christian D Klein
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany.
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4
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Mehlman T, Ginn HM, Keedy DA. An expanded trove of fragment-bound structures for the allosteric enzyme PTP1B from computational reanalysis of large-scale crystallographic data. Structure 2024:S0969-2126(24)00187-4. [PMID: 38861991 DOI: 10.1016/j.str.2024.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 04/15/2024] [Accepted: 05/15/2024] [Indexed: 06/13/2024]
Abstract
Due to their low binding affinities, detecting small-molecule fragments bound to protein structures from crystallographic datasets has been a challenge. Here, we report a trove of 65 new fragment hits for PTP1B, an "undruggable" therapeutic target enzyme for diabetes and cancer. These structures were obtained from computational analysis of data from a large crystallographic screen, demonstrating the power of this approach to elucidate many (∼50% more) "hidden" ligand-bound states of proteins. Our new structures include a fragment hit found in a novel binding site in PTP1B with a unique location relative to the active site, one that links adjacent allosteric sites, and, perhaps most strikingly, a fragment that induces long-range allosteric protein conformational responses. Altogether, our research highlights the utility of computational analysis of crystallographic data, makes publicly available dozens of new ligand-bound structures of a high-value drug target, and identifies novel aspects of ligandability and allostery in PTP1B.
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Affiliation(s)
- Tamar Mehlman
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031, USA; PhD Program in Biochemistry, CUNY Graduate Center, New York, NY 10016, USA
| | - Helen M Ginn
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany; Institute for Nanostructure and Solid State Physics, Universität Hamburg, Hamburg, Germany; Division of Life Sciences, Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, UK
| | - Daniel A Keedy
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031, USA; Department of Chemistry and Biochemistry, City College of New York, New York, NY 10031, USA; PhD Programs in Biochemistry, Biology, & Chemistry, CUNY Graduate Center, New York, NY 10016, USA.
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5
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Day JEH, Berdini V, Castro J, Chessari G, Davies TG, Day PJ, St Denis JD, Fujiwara H, Fukaya S, Hamlett CCF, Hearn K, Hiscock SD, Holvey RS, Ito S, Kandola N, Kodama Y, Liebeschuetz JW, Martins V, Matsuo K, Mortenson PN, Muench S, Nakatsuru Y, Ochiiwa H, Palmer N, Peakman T, Price A, Reader M, Rees DC, Rich SJ, Shah A, Shibata Y, Smyth T, Twigg DG, Wallis NG, Williams G, Wilsher NE, Woodhead A, Shimamura T, Johnson CN. Fragment-Based Discovery of Allosteric Inhibitors of SH2 Domain-Containing Protein Tyrosine Phosphatase-2 (SHP2). J Med Chem 2024. [PMID: 38462716 DOI: 10.1021/acs.jmedchem.3c02118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
The ubiquitously expressed protein tyrosine phosphatase SHP2 is required for signaling downstream of receptor tyrosine kinases (RTKs) and plays a role in regulating many cellular processes. Genetic knockdown and pharmacological inhibition of SHP2 suppresses RAS/MAPK signaling and inhibit the proliferation of RTK-driven cancer cell lines. Here, we describe the first reported fragment-to-lead campaign against SHP2, where X-ray crystallography and biophysical techniques were used to identify fragments binding to multiple sites on SHP2. Structure-guided optimization, including several computational methods, led to the discovery of two structurally distinct series of SHP2 inhibitors binding to the previously reported allosteric tunnel binding site (Tunnel Site). One of these series was advanced to a low-nanomolar lead that inhibited tumor growth when dosed orally to mice bearing HCC827 xenografts. Furthermore, a third series of SHP2 inhibitors was discovered binding to a previously unreported site, lying at the interface of the C-terminal SH2 and catalytic domains.
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Affiliation(s)
- James E H Day
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Valerio Berdini
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Joan Castro
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Gianni Chessari
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Thomas G Davies
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Philip J Day
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Jeffrey D St Denis
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Hideto Fujiwara
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Satoshi Fukaya
- Taiho Pharmaceutical Co., Ltd., 3 Okubo, Tsukuba, Ibaraki 300-2611, Japan
| | | | - Keisha Hearn
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Steven D Hiscock
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Rhian S Holvey
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Satoru Ito
- Taiho Pharmaceutical Co., Ltd., 3 Okubo, Tsukuba, Ibaraki 300-2611, Japan
| | - Navrohit Kandola
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Yasuo Kodama
- Taiho Pharmaceutical Co., Ltd., 3 Okubo, Tsukuba, Ibaraki 300-2611, Japan
| | - John W Liebeschuetz
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Vanessa Martins
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Kenichi Matsuo
- Taiho Pharmaceutical Co., Ltd., 3 Okubo, Tsukuba, Ibaraki 300-2611, Japan
| | - Paul N Mortenson
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Sandra Muench
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Yoko Nakatsuru
- Taiho Pharmaceutical Co., Ltd., 3 Okubo, Tsukuba, Ibaraki 300-2611, Japan
| | - Hiroaki Ochiiwa
- Taiho Pharmaceutical Co., Ltd., 3 Okubo, Tsukuba, Ibaraki 300-2611, Japan
| | - Nicholas Palmer
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Torren Peakman
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Amanda Price
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Michael Reader
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - David C Rees
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Sharna J Rich
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Alpesh Shah
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Yoshihiro Shibata
- Taiho Pharmaceutical Co., Ltd., 3 Okubo, Tsukuba, Ibaraki 300-2611, Japan
| | - Tomoko Smyth
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - David G Twigg
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Nicola G Wallis
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Glyn Williams
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Nicola E Wilsher
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Andrew Woodhead
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Tadashi Shimamura
- Taiho Pharmaceutical Co., Ltd., 3 Okubo, Tsukuba, Ibaraki 300-2611, Japan
| | - Christopher N Johnson
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
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6
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Guerrero L, Ebrahim A, Riley BT, Kim M, Huang Q, Finke AD, Keedy DA. Pushed to extremes: distinct effects of high temperature versus pressure on the structure of STEP. Commun Biol 2024; 7:59. [PMID: 38216663 PMCID: PMC10786866 DOI: 10.1038/s42003-023-05609-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 11/20/2023] [Indexed: 01/14/2024] Open
Abstract
Protein function hinges on small shifts of three-dimensional structure. Elevating temperature or pressure may provide experimentally accessible insights into such shifts, but the effects of these distinct perturbations on protein structures have not been compared in atomic detail. To quantitatively explore these two axes, we report the first pair of structures at physiological temperature versus. high pressure for the same protein, STEP (PTPN5). We show that these perturbations have distinct and surprising effects on protein volume, patterns of ordered solvent, and local backbone and side-chain conformations. This includes interactions between key catalytic loops only at physiological temperature, and a distinct conformational ensemble for another active-site loop only at high pressure. Strikingly, in torsional space, physiological temperature shifts STEP toward previously reported active-like states, while high pressure shifts it toward a previously uncharted region. Altogether, our work indicates that temperature and pressure are complementary, powerful, fundamental macromolecular perturbations.
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Affiliation(s)
- Liliana Guerrero
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, 10031, USA
- PhD Program in Biochemistry, CUNY Graduate Center, New York, NY, 10016, USA
| | - Ali Ebrahim
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, 10031, USA
| | - Blake T Riley
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, 10031, USA
| | - Minyoung Kim
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, 10031, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Qingqiu Huang
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY, 14853, USA
| | - Aaron D Finke
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY, 14853, USA
| | - Daniel A Keedy
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, 10031, USA.
- Department of Chemistry and Biochemistry, City College of New York, New York, NY, 10031, USA.
- PhD Programs in Biochemistry, Biology, & Chemistry, CUNY Graduate Center, New York, NY, 10016, USA.
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7
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Mehlman T(S, Ginn HM, Keedy DA. An expanded view of ligandability in the allosteric enzyme PTP1B from computational reanalysis of large-scale crystallographic data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.05.574428. [PMID: 38260327 PMCID: PMC10802458 DOI: 10.1101/2024.01.05.574428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The recent advent of crystallographic small-molecule fragment screening presents the opportunity to obtain unprecedented numbers of ligand-bound protein crystal structures from a single high-throughput experiment, mapping ligandability across protein surfaces and identifying useful chemical footholds for structure-based drug design. However, due to the low binding affinities of most fragments, detecting bound fragments from crystallographic datasets has been a challenge. Here we report a trove of 65 new fragment hits across 59 new liganded crystal structures for PTP1B, an "undruggable" therapeutic target enzyme for diabetes and cancer. These structures were obtained from computational analysis of data from a large crystallographic screen, demonstrating the power of this approach to elucidate many (~50% more) "hidden" ligand-bound states of proteins. Our new structures include a fragment hit found in a novel binding site in PTP1B with a unique location relative to the active site, one that validates another new binding site recently identified by simulations, one that links adjacent allosteric sites, and, perhaps most strikingly, a fragment that induces long-range allosteric protein conformational responses via a previously unreported intramolecular conduit. Altogether, our research highlights the utility of computational analysis of crystallographic data, makes publicly available dozens of new ligand-bound structures of a high-value drug target, and identifies novel aspects of ligandability and allostery in PTP1B.
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Affiliation(s)
- Tamar (Skaist) Mehlman
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
- PhD Program in Biochemistry, CUNY Graduate Center, New York, NY 10016
| | - Helen M. Ginn
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
- Institute for Nanostructure and Solid State Physics, Universität Hamburg, Hamburg, Germany
- Division of Life Sciences, Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, UK
| | - Daniel A. Keedy
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
- Department of Chemistry and Biochemistry, City College of New York, New York, NY 10031
- PhD Programs in Biochemistry, Biology, & Chemistry, CUNY Graduate Center, New York, NY 10016
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8
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Paulson L, Narayanasamy SR, Shelby ML, Frank M, Trebbin M. Advanced manufacturing provides tailor-made solutions for crystallography with x-ray free-electron lasers. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2024; 11:011101. [PMID: 38389979 PMCID: PMC10883715 DOI: 10.1063/4.0000229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/15/2024] [Indexed: 02/24/2024]
Abstract
Serial crystallography at large facilities, such as x-ray free-electron lasers and synchrotrons, evolved as a powerful method for the high-resolution structural investigation of proteins that are critical for human health, thus advancing drug discovery and novel therapies. However, a critical barrier to successful serial crystallography experiments lies in the efficient handling of the protein microcrystals and solutions at microscales. Microfluidics are the obvious approach for any high-throughput, nano-to-microliter sample handling, that also requires design flexibility and rapid prototyping to deal with the variable shapes, sizes, and density of crystals. Here, we discuss recent advances in polymer 3D printing for microfluidics-based serial crystallography research and present a demonstration of emerging, large-scale, nano-3D printing approaches leading into the future of 3D sample environment and delivery device fabrication from liquid jet gas-dynamic virtual nozzles devices to fixed-target sample environment technology.
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Affiliation(s)
- Lars Paulson
- Department of Chemistry & Research and Education in Energy, Environment and Water (RENEW), The State University of New York at Buffalo, Buffalo, New York 14260, USA
| | - Sankar Raju Narayanasamy
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - Megan L. Shelby
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
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9
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Sharma S, Skaist Mehlman T, Sagabala RS, Boivin B, Keedy DA. High-resolution double vision of the allosteric phosphatase PTP1B. Acta Crystallogr F Struct Biol Commun 2024; 80:1-12. [PMID: 38133579 PMCID: PMC10833341 DOI: 10.1107/s2053230x23010749] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 12/14/2023] [Indexed: 12/23/2023] Open
Abstract
Protein tyrosine phosphatase 1B (PTP1B) plays important roles in cellular homeostasis and is a highly validated therapeutic target for multiple human ailments, including diabetes, obesity and breast cancer. However, much remains to be learned about how conformational changes may convey information through the structure of PTP1B to enable allosteric regulation by ligands or functional responses to mutations. High-resolution X-ray crystallography can offer unique windows into protein conformational ensembles, but comparison of even high-resolution structures is often complicated by differences between data sets, including non-isomorphism. Here, the highest resolution crystal structure of apo wild-type (WT) PTP1B to date is presented out of a total of ∼350 PTP1B structures in the PDB. This structure is in a crystal form that is rare for PTP1B, with two unique copies of the protein that exhibit distinct patterns of conformational heterogeneity, allowing a controlled comparison of local disorder across the two chains within the same asymmetric unit. The conformational differences between these chains are interrogated in the apo structure and between several recently reported high-resolution ligand-bound structures. Electron-density maps in a high-resolution structure of a recently reported activating double mutant are also examined, and unmodeled alternate conformations in the mutant structure are discovered that coincide with regions of enhanced conformational heterogeneity in the new WT structure. These results validate the notion that these mutations operate by enhancing local dynamics, and suggest a latent susceptibility to such changes in the WT enzyme. Together, these new data and analysis provide a detailed view of the conformational ensemble of PTP1B and highlight the utility of high-resolution crystallography for elucidating conformational heterogeneity with potential relevance for function.
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Affiliation(s)
- Shivani Sharma
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031, USA
- PhD Program in Biology, CUNY Graduate Center, New York, NY 10016, USA
| | - Tamar Skaist Mehlman
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031, USA
| | - Reddy Sudheer Sagabala
- Department of Nanobioscience, College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, NY 12203, USA
| | - Benoit Boivin
- Department of Nanobioscience, College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, NY 12203, USA
| | - Daniel A. Keedy
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031, USA
- Department of Chemistry and Biochemistry, City College of New York, New York, NY 10031, USA
- PhD Programs in Biochemistry, Biology and Chemistry, CUNY Graduate Center, New York, NY 10016, USA
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10
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Csorba N, Ábrányi-Balogh P, Keserű GM. Covalent fragment approaches targeting non-cysteine residues. Trends Pharmacol Sci 2023; 44:802-816. [PMID: 37770315 DOI: 10.1016/j.tips.2023.08.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 08/28/2023] [Accepted: 08/30/2023] [Indexed: 09/30/2023]
Abstract
Covalent fragment approaches combine advantages of covalent binders and fragment-based drug discovery (FBDD) for target identification and validation. Although early applications focused mostly on cysteine labeling, the chemistries of available warheads that target other orthosteric and allosteric protein nucleophiles has recently been extended. The range of different warheads and labeling chemistries provide unique opportunities for screening and optimizing warheads necessary for targeting non-cysteine residues. In this review, we discuss these recently developed amino-acid-specific and promiscuous warheads, as well as emerging labeling chemistries, which includes novel transition metal catalyzed, photoactive, electroactive, and noncatalytic methodologies. We also highlight recent applications of covalent fragments for the development of molecular glues and proteolysis-targeting chimeras (PROTACs), and their utility in chemical proteomics-based target identification and validation.
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Affiliation(s)
- Noémi Csorba
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary; National Laboratory for Drug Research and Development, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary; Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Szent Gellért tér 4, 1111 Budapest, Hungary
| | - Péter Ábrányi-Balogh
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary; National Laboratory for Drug Research and Development, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary; Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Szent Gellért tér 4, 1111 Budapest, Hungary
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary; National Laboratory for Drug Research and Development, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary; Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Szent Gellért tér 4, 1111 Budapest, Hungary.
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11
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Thompson MC. Combining temperature perturbations with X-ray crystallography to study dynamic macromolecules: A thorough discussion of experimental methods. Methods Enzymol 2023; 688:255-305. [PMID: 37748829 DOI: 10.1016/bs.mie.2023.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Temperature is an important state variable that governs the behavior of microscopic systems, yet crystallographers rarely exploit temperature changes to study the structure and dynamics of biological macromolecules. In fact, approximately 90% of crystal structures in the Protein Data Bank were determined under cryogenic conditions, because sample cryocooling makes crystals robust to X-ray radiation damage and facilitates data collection. On the other hand, cryocooling can introduce artifacts into macromolecular structures, and can suppress conformational dynamics that are critical for function. Fortunately, recent advances in X-ray detector technology, X-ray sources, and computational data processing algorithms make non-cryogenic X-ray crystallography easier and more broadly applicable than ever before. Without the reliance on cryocooling, high-resolution crystallography can be combined with various temperature perturbations to gain deep insight into the conformational landscapes of macromolecules. This Chapter reviews the historical reasons for the prevalence of cryocooling in macromolecular crystallography, and discusses its potential drawbacks. Next, the Chapter summarizes technological developments and methodologies that facilitate non-cryogenic crystallography experiments. Finally, the chapter discusses the theoretical underpinnings and practical aspects of multi-temperature and temperature-jump crystallography experiments, which are powerful tools for understanding the relationship between the structure, dynamics, and function of proteins and other biological macromolecules.
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Affiliation(s)
- Michael C Thompson
- Department of Chemistry and Biochemistry, University of California, Merced, Merced, CA, United States.
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Martin MP, Endicott JA, Noble MEM, Tatum NJ. Crystallographic fragment screening in academic cancer drug discovery. Methods Enzymol 2023; 690:211-234. [PMID: 37858530 DOI: 10.1016/bs.mie.2023.06.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Fragment-based drug discovery (FBDD) has brought several drugs to the clinic, notably to target proteins once considered to be challenging, or even undruggable. Screening in FBDD relies upon observing and/or measuring weak (millimolar-scale) binding events using biophysical techniques or crystallographic fragment screening. This latter structural approach provides no information about binding affinity but can reveal binding mode and atomic detail on protein-fragment interactions to accelerate hit-to-lead development. In recent years, high-throughput platforms have been developed at synchrotron facilities to screen thousands of fragment-soaked crystals. However, using accessible manual techniques it is possible to run informative, smaller-scale screens within an academic lab setting. This chapter describes general protocols for home laboratory-scale fragment screening, from fragment soaking through to structure solution and, where appropriate, signposts to background, protocols or alternatives elsewhere.
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Affiliation(s)
- Mathew P Martin
- Cancer Research Horizons Therapeutic Innovation, Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Translation and Clinical Research Institute, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne, United Kingdom
| | - Jane A Endicott
- Cancer Research Horizons Therapeutic Innovation, Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Translation and Clinical Research Institute, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne, United Kingdom
| | - Martin E M Noble
- Cancer Research Horizons Therapeutic Innovation, Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Translation and Clinical Research Institute, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne, United Kingdom
| | - Natalie J Tatum
- Cancer Research Horizons Therapeutic Innovation, Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Translation and Clinical Research Institute, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne, United Kingdom.
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13
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Doppler D, Sonker M, Egatz-Gomez A, Grieco A, Zaare S, Jernigan R, Meza-Aguilar JD, Rabbani MT, Manna A, Alvarez RC, Karpos K, Cruz Villarreal J, Nelson G, Yang JH, Carrion J, Morin K, Ketawala GK, Pey AL, Ruiz-Fresneda MA, Pacheco-Garcia JL, Hermoso JA, Nazari R, Sierra R, Hunter MS, Batyuk A, Kupitz CJ, Sublett RE, Lisova S, Mariani V, Boutet S, Fromme R, Grant TD, Botha S, Fromme P, Kirian RA, Martin-Garcia JM, Ros A. Modular droplet injector for sample conservation providing new structural insight for the conformational heterogeneity in the disease-associated NQO1 enzyme. LAB ON A CHIP 2023; 23:3016-3033. [PMID: 37294576 PMCID: PMC10503405 DOI: 10.1039/d3lc00176h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Droplet injection strategies are a promising tool to reduce the large amount of sample consumed in serial femtosecond crystallography (SFX) measurements at X-ray free electron lasers (XFELs) with continuous injection approaches. Here, we demonstrate a new modular microfluidic droplet injector (MDI) design that was successfully applied to deliver microcrystals of the human NAD(P)H:quinone oxidoreductase 1 (NQO1) and phycocyanin. We investigated droplet generation conditions through electrical stimulation for both protein samples and implemented hardware and software components for optimized crystal injection at the Macromolecular Femtosecond Crystallography (MFX) instrument at the Stanford Linac Coherent Light Source (LCLS). Under optimized droplet injection conditions, we demonstrate that up to 4-fold sample consumption savings can be achieved with the droplet injector. In addition, we collected a full data set with droplet injection for NQO1 protein crystals with a resolution up to 2.7 Å, leading to the first room-temperature structure of NQO1 at an XFEL. NQO1 is a flavoenzyme associated with cancer, Alzheimer's and Parkinson's disease, making it an attractive target for drug discovery. Our results reveal for the first time that residues Tyr128 and Phe232, which play key roles in the function of the protein, show an unexpected conformational heterogeneity at room temperature within the crystals. These results suggest that different substates exist in the conformational ensemble of NQO1 with functional and mechanistic implications for the enzyme's negative cooperativity through a conformational selection mechanism. Our study thus demonstrates that microfluidic droplet injection constitutes a robust sample-conserving injection method for SFX studies on protein crystals that are difficult to obtain in amounts necessary for continuous injection, including the large sample quantities required for time-resolved mix-and-inject studies.
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Affiliation(s)
- Diandra Doppler
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Mukul Sonker
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Ana Egatz-Gomez
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Alice Grieco
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Blas Cabrera, Spanish National Research Council (CSIC), Serrano 119, 28006, Madrid, Spain.
| | - Sahba Zaare
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
- Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Rebecca Jernigan
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Jose Domingo Meza-Aguilar
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Mohammad T Rabbani
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Abhik Manna
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Roberto C Alvarez
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
- Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Konstantinos Karpos
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
- Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Jorvani Cruz Villarreal
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Garrett Nelson
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
- Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Jay-How Yang
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Jackson Carrion
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Katherine Morin
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Gihan K Ketawala
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Angel L Pey
- Departamento de Química Física, Unidad de Excelencia en Química Aplicada a Biomedicina y Medioambiente e Instituto de Biotecnología, Universidad de Granada, Av. Fuentenueva s/n, 18071, Granada, Spain
| | - Miguel Angel Ruiz-Fresneda
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Blas Cabrera, Spanish National Research Council (CSIC), Serrano 119, 28006, Madrid, Spain.
| | - Juan Luis Pacheco-Garcia
- Departamento de Química Física, Universidad de Granada, Av. Fuentenueva s/n, 18071 Granada, Spain
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Blas Cabrera, Spanish National Research Council (CSIC), Serrano 119, 28006, Madrid, Spain.
| | - Reza Nazari
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
- Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Raymond Sierra
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, 94025 CA, USA
| | - Mark S Hunter
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, 94025 CA, USA
| | - Alexander Batyuk
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, 94025 CA, USA
| | - Christopher J Kupitz
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, 94025 CA, USA
| | - Robert E Sublett
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, 94025 CA, USA
| | - Stella Lisova
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, 94025 CA, USA
| | - Valerio Mariani
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, 94025 CA, USA
| | - Sébastien Boutet
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, 94025 CA, USA
| | - Raimund Fromme
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Thomas D Grant
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, 955 Main St, Buffalo, NY, 14203, USA
| | - Sabine Botha
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
- Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Petra Fromme
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Richard A Kirian
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
- Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Jose Manuel Martin-Garcia
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Blas Cabrera, Spanish National Research Council (CSIC), Serrano 119, 28006, Madrid, Spain.
| | - Alexandra Ros
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
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Guerrero L, Ebrahim A, Riley BT, Kim M, Huang Q, Finke AD, Keedy DA. Pushed to extremes: distinct effects of high temperature vs. pressure on the structure of an atypical phosphatase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.02.538097. [PMID: 37205580 PMCID: PMC10187168 DOI: 10.1101/2023.05.02.538097] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Protein function hinges on small shifts of three-dimensional structure. Elevating temperature or pressure may provide experimentally accessible insights into such shifts, but the effects of these distinct perturbations on protein structures have not been compared in atomic detail. To quantitatively explore these two axes, we report the first pair of structures at physiological temperature vs. high pressure for the same protein, STEP (PTPN5). We show that these perturbations have distinct and surprising effects on protein volume, patterns of ordered solvent, and local backbone and side-chain conformations. This includes novel interactions between key catalytic loops only at physiological temperature, and a distinct conformational ensemble for another active-site loop only at high pressure. Strikingly, in torsional space, physiological temperature shifts STEP toward previously reported active-like states, while high pressure shifts it toward a previously uncharted region. Together, our work argues that temperature and pressure are complementary, powerful, fundamental macromolecular perturbations.
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Affiliation(s)
- Liliana Guerrero
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
- PhD Program in Biochemistry, CUNY Graduate Center, New York, NY 10016
| | - Ali Ebrahim
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
| | - Blake T Riley
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
| | - Minyoung Kim
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Qingqiu Huang
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853
| | - Aaron D Finke
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853
| | - Daniel A Keedy
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
- Department of Chemistry and Biochemistry, City College of New York, New York, NY 10031
- PhD Programs in Biochemistry, Biology, & Chemistry, CUNY Graduate Center, New York, NY 10016
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