1
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Liang Z, Yu Y, Zou B, Fu M, Hu T, Yin X, Wang J, Xu Y, Cheng L. The effect of structural changes on the activity of peroxidase with different initial state under high-pressure freezing. Food Chem 2024; 459:140314. [PMID: 39024881 DOI: 10.1016/j.foodchem.2024.140314] [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: 02/03/2024] [Revised: 06/27/2024] [Accepted: 07/01/2024] [Indexed: 07/20/2024]
Abstract
The combined impact of initial state, pressure, and freezing on peroxidase denaturation during high-pressure freezing (HPF) processing of enzyme-containing foods remains unclear. This study investigated solid-liquid (initial low/high concentration) biphasic peroxidase using spectroscopic and computer simulation techniques to analyze structural changes affecting peroxidase (POD) activity under HPF. The results indicate that the primary factors determining POD activity during HPF treatment can be ranked as follows: concentration > physical state > pressure > freezing. Higher initial concentrations strengthen protein interactions, leading to a 1% increase in the molecular diameter and a 34% increase in molecular height of HL-POD, thereby increasing aggregation likelihood during crystallization and facilitating structural changes that activate enzymes by 6-17%. The amide I peak proves to be a reliable indicator for monitoring both POD activity and structural alterations. This study offers valuable insights for optimizing HPF technology in food processing.
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Affiliation(s)
- Zhanhong Liang
- Sericultural & Argi-Food Research Institute, Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Agricultural Products Processing, No. 133 Yiheng street, Dongguanzhuang road, Tianhe District, Guangzhou 510610, China; School of Food Science, Guangdong Pharmaceutical University, Zhongshan 528400, China
| | - Yuanshan Yu
- Sericultural & Argi-Food Research Institute, Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Agricultural Products Processing, No. 133 Yiheng street, Dongguanzhuang road, Tianhe District, Guangzhou 510610, China
| | - Bo Zou
- Sericultural & Argi-Food Research Institute, Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Agricultural Products Processing, No. 133 Yiheng street, Dongguanzhuang road, Tianhe District, Guangzhou 510610, China
| | - Manqin Fu
- Sericultural & Argi-Food Research Institute, Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Agricultural Products Processing, No. 133 Yiheng street, Dongguanzhuang road, Tianhe District, Guangzhou 510610, China
| | - Tenggen Hu
- Sericultural & Argi-Food Research Institute, Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Agricultural Products Processing, No. 133 Yiheng street, Dongguanzhuang road, Tianhe District, Guangzhou 510610, China
| | - Xiaomeng Yin
- Guangzhou Conghua District Agriculture and rural Bureau, Guangzhou 510610, China
| | - Jin Wang
- Guangzhou Conghua District Agriculture and rural Bureau, Guangzhou 510610, China
| | - Yujuan Xu
- Sericultural & Argi-Food Research Institute, Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Agricultural Products Processing, No. 133 Yiheng street, Dongguanzhuang road, Tianhe District, Guangzhou 510610, China.
| | - Lina Cheng
- Sericultural & Argi-Food Research Institute, Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Agricultural Products Processing, No. 133 Yiheng street, Dongguanzhuang road, Tianhe District, Guangzhou 510610, China.
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2
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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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3
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Knight AL, Widjaja V, Lisi GP. Temperature as a modulator of allosteric motions and crosstalk in mesophilic and thermophilic enzymes. Front Mol Biosci 2023; 10:1281062. [PMID: 37877120 PMCID: PMC10591084 DOI: 10.3389/fmolb.2023.1281062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 09/27/2023] [Indexed: 10/26/2023] Open
Abstract
Mesophilic and thermophilic enzyme counterparts are often studied to understand how proteins function under harsh conditions. To function well outside of standard temperature ranges, thermophiles often tightly regulate their structural ensemble through intra-protein communication (via allostery) and altered interactions with ligands. It has also become apparent in recent years that the enhancement or diminution of allosteric crosstalk can be temperature-dependent and distinguish thermophilic enzymes from their mesophilic paralogs. Since most studies of allostery utilize chemical modifications from pH, mutations, or ligands, the impact of temperature on allosteric function is comparatively understudied. Here, we discuss the biophysical methods, as well as critical case studies, that dissect temperature-dependent function of mesophilic-thermophilic enzyme pairs and their allosteric regulation across a range of temperatures.
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Affiliation(s)
| | | | - George P. Lisi
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, United States
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4
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Du S, Wankowicz SA, Yabukarski F, Doukov T, Herschlag D, Fraser JS. Refinement of multiconformer ensemble models from multi-temperature X-ray diffraction data. Methods Enzymol 2023; 688:223-254. [PMID: 37748828 PMCID: PMC10637719 DOI: 10.1016/bs.mie.2023.06.009] [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: 09/27/2023]
Abstract
Conformational ensembles underlie all protein functions. Thus, acquiring atomic-level ensemble models that accurately represent conformational heterogeneity is vital to deepen our understanding of how proteins work. Modeling ensemble information from X-ray diffraction data has been challenging, as traditional cryo-crystallography restricts conformational variability while minimizing radiation damage. Recent advances have enabled the collection of high quality diffraction data at ambient temperatures, revealing innate conformational heterogeneity and temperature-driven changes. Here, we used diffraction datasets for Proteinase K collected at temperatures ranging from 313 to 363 K to provide a tutorial for the refinement of multiconformer ensemble models. Integrating automated sampling and refinement tools with manual adjustments, we obtained multiconformer models that describe alternative backbone and sidechain conformations, their relative occupancies, and interconnections between conformers. Our models revealed extensive and diverse conformational changes across temperature, including increased bound peptide ligand occupancies, different Ca2+ binding site configurations and altered rotameric distributions. These insights emphasize the value and need for multiconformer model refinement to extract ensemble information from diffraction data and to understand ensemble-function relationships.
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Affiliation(s)
- Siyuan Du
- Department of Biochemistry, Stanford University, Stanford, CA, United States; Department of Chemistry, Stanford University, Stanford, CA, United States
| | - Stephanie A Wankowicz
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States
| | - Filip Yabukarski
- Department of Biochemistry, Stanford University, Stanford, CA, United States; Bristol-Myers Squibb, San Diego, CA, United States
| | - Tzanko Doukov
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, United States
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, CA, United States; Department of Chemical Engineering, Stanford University, Stanford, CA, United States; Stanford ChEM-H, Stanford University, Stanford, CA, United States
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States; Quantitative Biosciences Institute, University of California, San Francisco, CA, United States.
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5
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Colloc'h N, Dhaussy AC, Girard E. Exploring the structural dynamics of proteins by pressure perturbation using macromolecular crystallography. Methods Enzymol 2023; 688:349-381. [PMID: 37748831 DOI: 10.1016/bs.mie.2023.06.007] [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
High pressure is a convenient thermodynamic parameter to probe the dynamics of proteins as it is intimately related to volume which is essential for protein function. To be biologically active, a protein fluctuates between different substates. Pressure perturbation can promote some hidden substates by modifying the population between them. High pressure macromolecular crystallography (HPMX) is a perfect tool to capture and to characterize such substates at a molecular level providing new insights on protein dynamics. The present chapter describes the use of the diamond anvil cell to perform HPMX experiments. It also provides tips on sample preparation and optimal data collection as well as on efficient analysis of the resulting high-pressure structures.
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Affiliation(s)
- Nathalie Colloc'h
- Imagerie et stratégies thérapeutiques pour les cancers et tissus cérébraux (ISTCT), CNRS Université de Caen Normandie, Centre Cyceron, Caen, France
| | | | - Eric Girard
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France.
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6
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Du S, Wankowicz SA, Yabukarski F, Doukov T, Herschlag D, Fraser JS. Refinement of Multiconformer Ensemble Models from Multi-temperature X-ray Diffraction Data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.05.539620. [PMID: 37205593 PMCID: PMC10187334 DOI: 10.1101/2023.05.05.539620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Conformational ensembles underlie all protein functions. Thus, acquiring atomic-level ensemble models that accurately represent conformational heterogeneity is vital to deepen our understanding of how proteins work. Modeling ensemble information from X-ray diffraction data has been challenging, as traditional cryo-crystallography restricts conformational variability while minimizing radiation damage. Recent advances have enabled the collection of high quality diffraction data at ambient temperatures, revealing innate conformational heterogeneity and temperature-driven changes. Here, we used diffraction datasets for Proteinase K collected at temperatures ranging from 313 to 363K to provide a tutorial for the refinement of multiconformer ensemble models. Integrating automated sampling and refinement tools with manual adjustments, we obtained multiconformer models that describe alternative backbone and sidechain conformations, their relative occupancies, and interconnections between conformers. Our models revealed extensive and diverse conformational changes across temperature, including increased bound peptide ligand occupancies, different Ca2+ binding site configurations and altered rotameric distributions. These insights emphasize the value and need for multiconformer model refinement to extract ensemble information from diffraction data and to understand ensemble-function relationships.
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Affiliation(s)
- Siyuan Du
- Department of Biochemistry, Stanford University, Stanford, California 94305, United States
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Stephanie A. Wankowicz
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94143, United States
| | - Filip Yabukarski
- Department of Biochemistry, Stanford University, Stanford, California 94305, United States
- Bristol-Myers Squibb, San Diego, California 92121, United States
| | - Tzanko Doukov
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, California 94305, United States
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
- Stanford ChEM-H, Stanford University, Stanford, California 94305, United States
| | - James S. Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94143, United States
- Quantitative Biosciences Institute, University of California, San Francisco, California 94143, United States
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7
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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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8
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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] [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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9
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Doukov T, Herschlag D, Yabukarski F. Obtaining anomalous and ensemble information from protein crystals from 220 K up to physiological temperatures. Acta Crystallogr D Struct Biol 2023; 79:212-223. [PMID: 36876431 PMCID: PMC9986799 DOI: 10.1107/s205979832300089x] [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: 11/03/2022] [Accepted: 01/31/2023] [Indexed: 03/01/2023] Open
Abstract
X-ray crystallography has been invaluable in delivering structural information about proteins. Previously, an approach has been developed that allows high-quality X-ray diffraction data to be obtained from protein crystals at and above room temperature. Here, this previous work is built on and extended by showing that high-quality anomalous signal can be obtained from single protein crystals using diffraction data collected at 220 K up to physiological temperatures. The anomalous signal can be used to directly determine the structure of a protein, i.e. to phase the data, as is routinely performed under cryoconditions. This ability is demonstrated by obtaining diffraction data from model lysozyme, thaumatin and proteinase K crystals, the anomalous signal from which allowed their structures to be solved experimentally at 7.1 keV X-ray energy and at room temperature with relatively low data redundancy. It is also demonstrated that the anomalous signal from diffraction data obtained at 310 K (37°C) can be used to solve the structure of proteinase K and to identify ordered ions. The method provides useful anomalous signal at temperatures down to 220 K, resulting in an extended crystal lifetime and increased data redundancy. Finally, we show that useful anomalous signal can be obtained at room temperature using X-rays of 12 keV energy as typically used for routine data collection, allowing this type of experiment to be carried out at widely accessible synchrotron beamline energies and enabling the simultaneous extraction of high-resolution data and anomalous signal. With the recent emphasis on obtaining conformational ensemble information for proteins, the high resolution of the data allows such ensembles to be built, while the anomalous signal allows the structure to be experimentally solved, ions to be identified, and water molecules and ions to be differentiated. Because bound metal-, phosphorus- and sulfur-containing ions all have anomalous signal, obtaining anomalous signal across temperatures and up to physiological temperatures will provide a more complete description of protein conformational ensembles, function and energetics.
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Affiliation(s)
- Tzanko Doukov
- SMB, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Daniel Herschlag
- Deparment of Biochemistry, Stanford University, Stanford, CA 94305, USA
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Filip Yabukarski
- Deparment of Biochemistry, Stanford University, Stanford, CA 94305, USA
- Bristol-Myers Squibb, San Diego, CA 92121, USA
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10
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Thorne RE. Determining biomolecular structures near room temperature using X-ray crystallography: concepts, methods and future optimization. Acta Crystallogr D Struct Biol 2023; 79:78-94. [PMID: 36601809 PMCID: PMC9815097 DOI: 10.1107/s2059798322011652] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 12/04/2022] [Indexed: 01/05/2023] Open
Abstract
For roughly two decades, cryocrystallography has been the overwhelmingly dominant method for determining high-resolution biomolecular structures. Competition from single-particle cryo-electron microscopy and micro-electron diffraction, increased interest in functionally relevant information that may be missing or corrupted in structures determined at cryogenic temperature, and interest in time-resolved studies of the biomolecular response to chemical and optical stimuli have driven renewed interest in data collection at room temperature and, more generally, at temperatures from the protein-solvent glass transition near 200 K to ∼350 K. Fischer has recently reviewed practical methods for room-temperature data collection and analysis [Fischer (2021), Q. Rev. Biophys. 54, e1]. Here, the key advantages and physical principles of, and methods for, crystallographic data collection at noncryogenic temperatures and some factors relevant to interpreting the resulting data are discussed. For room-temperature data collection to realize its potential within the structural biology toolkit, streamlined and standardized methods for delivering crystals prepared in the home laboratory to the synchrotron and for automated handling and data collection, similar to those for cryocrystallography, should be implemented.
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Affiliation(s)
- Robert E. Thorne
- Physics Department, Cornell University, Ithaca, NY 14853, USA
- MiTeGen LLC, PO Box 3867, Ithaca, NY 14850, USA
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11
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Aumonier S, Engilberge S, Caramello N, von Stetten D, Gotthard G, Leonard GA, Mueller-Dieckmann C, Royant A. Slow protein dynamics probed by time-resolved oscillation crystallography at room temperature. IUCRJ 2022; 9:756-767. [PMID: 36381146 PMCID: PMC9634615 DOI: 10.1107/s2052252522009150] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/14/2022] [Indexed: 05/23/2023]
Abstract
The development of serial crystallography over the last decade at XFELs and synchrotrons has produced a renaissance in room-temperature macromolecular crystallography (RT-MX), and fostered many technical and methodological breakthroughs designed to study phenomena occurring in proteins on the picosecond-to-second timescale. However, there are components of protein dynamics that occur in much slower regimes, of which the study could readily benefit from state-of-the-art RT-MX. Here, the room-temperature structural study of the relaxation of a reaction intermediate at a synchrotron, exploiting a handful of single crystals, is described. The intermediate in question is formed in microseconds during the photoreaction of the LOV2 domain of phototropin 2 from Arabidopsis thaliana, which then decays in minutes. This work monitored its relaxation in the dark using a fast-readout EIGER X 4M detector to record several complete oscillation X-ray diffraction datasets, each of 1.2 s total exposure time, at different time points in the relaxation process. Coupled with in crystallo UV-Vis absorption spectroscopy, this RT-MX approach allowed the authors to follow the relaxation of the photoadduct, a thio-ether covalent bond between the chromophore and a cysteine residue. Unexpectedly, the return of the chromophore to its spectroscopic ground state is followed by medium-scale protein rearrangements that trigger a crystal phase transition and hinder the full recovery of the structural ground state of the protein. In addition to suggesting a hitherto unexpected role of a conserved tryptophan residue in the regulation of the photocycle of LOV2, this work provides a basis for performing routine time-resolved protein crystallography experiments at synchrotrons for phenomena occurring on the second-to-hour timescale.
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Affiliation(s)
- Sylvain Aumonier
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs CS 40220, Grenoble 38043, France
| | - Sylvain Engilberge
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs CS 40220, Grenoble 38043, France
| | - Nicolas Caramello
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs CS 40220, Grenoble 38043, France
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, HARBOR, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - David von Stetten
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs CS 40220, Grenoble 38043, France
| | - Guillaume Gotthard
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs CS 40220, Grenoble 38043, France
| | - Gordon A. Leonard
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs CS 40220, Grenoble 38043, France
| | - Christoph Mueller-Dieckmann
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs CS 40220, Grenoble 38043, France
| | - Antoine Royant
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs CS 40220, Grenoble 38043, France
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71 avenue des Martyrs, Grenoble 38044, France
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12
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Greisman JB, Dalton KM, Sheehan CJ, Klureza MA, Kurinov I, Hekstra DR. Native SAD phasing at room temperature. Acta Crystallogr D Struct Biol 2022; 78:986-996. [PMID: 35916223 PMCID: PMC9344477 DOI: 10.1107/s2059798322006799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 07/01/2022] [Indexed: 11/10/2022] Open
Abstract
Single-wavelength anomalous diffraction (SAD) is a routine method for overcoming the phase problem when solving macromolecular structures. This technique requires the accurate measurement of intensities to determine differences between Bijvoet pairs. Although SAD experiments are commonly conducted at cryogenic temperatures to mitigate the effects of radiation damage, such temperatures can alter the conformational ensemble of the protein and may impede the merging of data from multiple crystals due to non-uniform freezing. Here, a strategy is presented to obtain high-quality data from room-temperature, single-crystal experiments. To illustrate the strengths of this approach, native SAD phasing at 6.55 keV was used to solve four structures of three model systems at 295 K. The resulting data sets allow automatic phasing and model building, and reveal alternate conformations that reflect the structure of proteins at room temperature.
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Huang CY, Aumonier S, Engilberge S, Eris D, Smith KML, Leonarski F, Wojdyla JA, Beale JH, Buntschu D, Pauluhn A, Sharpe ME, Metz A, Olieric V, Wang M. Probing ligand binding of endothiapepsin by `temperature-resolved' macromolecular crystallography. Acta Crystallogr D Struct Biol 2022; 78:964-974. [PMID: 35916221 PMCID: PMC9344481 DOI: 10.1107/s205979832200612x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 06/09/2022] [Indexed: 12/03/2022] Open
Abstract
A room-temperature X-ray crystallographic method using temperature as a trigger to record movie-like structural snapshots has been developed and applied to study ligand binding and protein plasticity. Continuous developments in cryogenic X-ray crystallography have provided most of our knowledge of 3D protein structures, which has recently been further augmented by revolutionary advances in cryoEM. However, a single structural conformation identified at cryogenic temperatures may introduce a fictitious structure as a result of cryogenic cooling artefacts, limiting the overview of inherent protein physiological dynamics, which play a critical role in the biological functions of proteins. Here, a room-temperature X-ray crystallographic method using temperature as a trigger to record movie-like structural snapshots has been developed. The method has been used to show how TL00150, a 175.15 Da fragment, undergoes binding-mode changes in endothiapepsin. A surprising fragment-binding discrepancy was observed between the cryo-cooled and physiological temperature structures, and multiple binding poses and their interplay with DMSO were captured. The observations here open up new promising prospects for structure determination and interpretation at physiological temperatures with implications for structure-based drug discovery.
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Yabukarski F, Doukov T, Mokhtari DA, Du S, Herschlag D. Evaluating the impact of X-ray damage on conformational heterogeneity in room-temperature (277 K) and cryo-cooled protein crystals. Acta Crystallogr D Struct Biol 2022; 78:945-963. [PMID: 35916220 PMCID: PMC9344472 DOI: 10.1107/s2059798322005939] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 06/02/2022] [Indexed: 11/10/2022] Open
Abstract
Cryo-cooling has been nearly universally adopted to mitigate X-ray damage and facilitate crystal handling in protein X-ray crystallography. However, cryo X-ray crystallographic data provide an incomplete window into the ensemble of conformations that is at the heart of protein function and energetics. Room-temperature (RT) X-ray crystallography provides accurate ensemble information, and recent developments allow conformational heterogeneity (the experimental manifestation of ensembles) to be extracted from single-crystal data. Nevertheless, high sensitivity to X-ray damage at RT raises concerns about data reliability. To systematically address this critical issue, increasingly X-ray-damaged high-resolution data sets (1.02–1.52 Å resolution) were obtained from single proteinase K, thaumatin and lysozyme crystals at RT (277 K). In each case a modest increase in conformational heterogeneity with X-ray damage was observed. Merging data with different extents of damage (as is typically carried out) had negligible effects on conformational heterogeneity until the overall diffraction intensity decayed to ∼70% of its initial value. These effects were compared with X-ray damage effects in cryo-cooled crystals by carrying out an analogous analysis of increasingly damaged proteinase K cryo data sets (0.9–1.16 Å resolution). X-ray damage-associated heterogeneity changes were found that were not observed at RT. This property renders it difficult to distinguish real from artefactual conformations and to determine the conformational response to changes in temperature. The ability to acquire reliable heterogeneity information from single crystals at RT, together with recent advances in RT data collection at accessible synchrotron beamlines, provides a strong motivation for the widespread adoption of RT X-ray crystallography to obtain conformational ensemble information.
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Mokhtari DA, Appel MJ, Fordyce PM, Herschlag D. High throughput and quantitative enzymology in the genomic era. Curr Opin Struct Biol 2021; 71:259-273. [PMID: 34592682 PMCID: PMC8648990 DOI: 10.1016/j.sbi.2021.07.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/23/2021] [Indexed: 12/28/2022]
Abstract
Accurate predictions from models based on physical principles are the ultimate metric of our biophysical understanding. Although there has been stunning progress toward structure prediction, quantitative prediction of enzyme function has remained challenging. Realizing this goal will require large numbers of quantitative measurements of rate and binding constants and the use of these ground-truth data sets to guide the development and testing of these quantitative models. Ground truth data more closely linked to the underlying physical forces are also desired. Here, we describe technological advances that enable both types of ground truth measurements. These advances allow classic models to be tested, provide novel mechanistic insights, and place us on the path toward a predictive understanding of enzyme structure and function.
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Affiliation(s)
- D A Mokhtari
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA
| | - M J Appel
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA
| | - P M Fordyce
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA; ChEM-H Institute, Stanford University, Stanford, CA, 94305, USA; Department of Genetics, Stanford University, Stanford, CA, 94305, USA; Chan Zuckerberg Biohub San Francisco, CA, 94110, USA.
| | - D Herschlag
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA; Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA; ChEM-H Institute, Stanford University, Stanford, CA, 94305, USA.
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