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Chang C, Zhou G, Gao Y. Observing one-divalent-metal-ion dependent and histidine-promoted His-Me family I-PpoI nuclease catalysis in crystallo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.02.592236. [PMID: 38746211 PMCID: PMC11092635 DOI: 10.1101/2024.05.02.592236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Metal-ion-dependent nucleases play crucial roles in cellular defense and biotechnological applications. Time-resolved crystallography has resolved catalytic details of metal-ion-dependent DNA hydrolysis and synthesis, uncovering the essential roles of multiple metal ions during catalysis. The histidine-metal (His-Me) superfamily nucleases are renowned for binding one divalent metal ion and requiring a conserved histidine to promote catalysis. Many His-Me family nucleases, including homing endonucleases and Cas9 nuclease, have been adapted for biotechnological and biomedical applications. However, it remains unclear how the single metal ion in His-Me nucleases, together with the histidine, promotes water deprotonation, nucleophilic attack, and phosphodiester bond breakage. By observing DNA hydrolysis in crystallo with His-Me I-PpoI nuclease as a model system, we proved that only one divalent metal ion is required during its catalysis. Moreover, we uncovered several possible deprotonation pathways for the nucleophilic water. Interestingly, binding of the single metal ion and water deprotonation are concerted during catalysis. Our results reveal catalytic details of His-Me nucleases, which is distinct from multi-metal-ion-dependent DNA polymerases and nucleases.
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Affiliation(s)
- Caleb Chang
- Department of Biosciences, Rice University, Houston, Texas, 77005, USA
| | - Grace Zhou
- Department of Biosciences, Rice University, Houston, Texas, 77005, USA
| | - Yang Gao
- Department of Biosciences, Rice University, Houston, Texas, 77005, USA
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2
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Smith N, Dasgupta M, Wych DC, Dolamore C, Sierra RG, Lisova S, Marchany-Rivera D, Cohen AE, Boutet S, Hunter MS, Kupitz C, Poitevin F, Moss FR, Mittan-Moreau DW, Brewster AS, Sauter NK, Young ID, Wolff AM, Tiwari VK, Kumar N, Berkowitz DB, Hadt RG, Thompson MC, Follmer AH, Wall ME, Wilson MA. Changes in an enzyme ensemble during catalysis observed by high-resolution XFEL crystallography. SCIENCE ADVANCES 2024; 10:eadk7201. [PMID: 38536910 PMCID: PMC10971408 DOI: 10.1126/sciadv.adk7201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 02/21/2024] [Indexed: 04/01/2024]
Abstract
Enzymes populate ensembles of structures necessary for catalysis that are difficult to experimentally characterize. We use time-resolved mix-and-inject serial crystallography at an x-ray free electron laser to observe catalysis in a designed mutant isocyanide hydratase (ICH) enzyme that enhances sampling of important minor conformations. The active site exists in a mixture of conformations, and formation of the thioimidate intermediate selects for catalytically competent substates. The influence of cysteine ionization on the ICH ensemble is validated by determining structures of the enzyme at multiple pH values. Large molecular dynamics simulations in crystallo and time-resolved electron density maps show that Asp17 ionizes during catalysis and causes conformational changes that propagate across the dimer, permitting water to enter the active site for intermediate hydrolysis. ICH exhibits a tight coupling between ionization of active site residues and catalysis-activated protein motions, exemplifying a mechanism of electrostatic control of enzyme dynamics.
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Affiliation(s)
- Nathan Smith
- Department of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Medhanjali Dasgupta
- Department of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - David C. Wych
- Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, NM 875405, USA
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Cole Dolamore
- Department of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Raymond G. Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - Stella Lisova
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - Darya Marchany-Rivera
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - Aina E. Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - Mark S. Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - Christopher Kupitz
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - Frédéric Poitevin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - Frank R. Moss
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - David W. Mittan-Moreau
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Aaron S. Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Nicholas K. Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Iris D. Young
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Alexander M. Wolff
- Department of Chemistry and Biochemistry, University of California, Merced, CA 95340, USA
| | - Virendra K. Tiwari
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Nivesh Kumar
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - David B. Berkowitz
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Ryan G. Hadt
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michael C. Thompson
- Department of Chemistry and Biochemistry, University of California, Merced, CA 95340, USA
| | - Alec H. Follmer
- Department of Chemistry, University of California-Irvine, Irvine, CA 92697, USA
| | - Michael E. Wall
- Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, NM 875405, USA
| | - Mark A. Wilson
- Department of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
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3
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Banayan NE, Loughlin BJ, Singh S, Forouhar F, Lu G, Wong K, Neky M, Hunt HS, Bateman LB, Tamez A, Handelman SK, Price WN, Hunt JF. Systematic enhancement of protein crystallization efficiency by bulk lysine-to-arginine (KR) substitution. Protein Sci 2024; 33:e4898. [PMID: 38358135 PMCID: PMC10868448 DOI: 10.1002/pro.4898] [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: 06/18/2023] [Revised: 01/01/2024] [Accepted: 01/02/2024] [Indexed: 02/16/2024]
Abstract
Structural genomics consortia established that protein crystallization is the primary obstacle to structure determination using x-ray crystallography. We previously demonstrated that crystallization propensity is systematically related to primary sequence, and we subsequently performed computational analyses showing that arginine is the most overrepresented amino acid in crystal-packing interfaces in the Protein Data Bank. Given the similar physicochemical characteristics of arginine and lysine, we hypothesized that multiple lysine-to-arginine (KR) substitutions should improve crystallization. To test this hypothesis, we developed software that ranks lysine sites in a target protein based on the redundancy-corrected KR substitution frequency in homologs. This software can be run interactively on the worldwide web at https://www.pxengineering.org/. We demonstrate that three unrelated single-domain proteins can tolerate 5-11 KR substitutions with at most minor destabilization, and, for two of these three proteins, the construct with the largest number of KR substitutions exhibits significantly enhanced crystallization propensity. This approach rapidly produced a 1.9 Å crystal structure of a human protein domain refractory to crystallization with its native sequence. Structures from Bulk KR-substituted domains show the engineered arginine residues frequently make hydrogen-bonds across crystal-packing interfaces. We thus demonstrate that Bulk KR substitution represents a rational and efficient method for probabilistic engineering of protein surface properties to improve crystallization.
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Affiliation(s)
- Nooriel E. Banayan
- Department of Biological Sciences702A Sherman Fairchild Center, MC2434, Columbia UniversityNew YorkNew YorkUSA
| | - Blaine J. Loughlin
- Department of Biological Sciences702A Sherman Fairchild Center, MC2434, Columbia UniversityNew YorkNew YorkUSA
| | - Shikha Singh
- Department of Biological Sciences702A Sherman Fairchild Center, MC2434, Columbia UniversityNew YorkNew YorkUSA
| | - Farhad Forouhar
- Department of Biological Sciences702A Sherman Fairchild Center, MC2434, Columbia UniversityNew YorkNew YorkUSA
| | - Guanqi Lu
- Department of Biological Sciences702A Sherman Fairchild Center, MC2434, Columbia UniversityNew YorkNew YorkUSA
| | - Kam‐Ho Wong
- Department of Biological Sciences702A Sherman Fairchild Center, MC2434, Columbia UniversityNew YorkNew YorkUSA
- Present address:
Vaccine Research and DevelopmentPfizer Inc.Pearl RiverNew YorkUSA
| | - Matthew Neky
- Department of Biological Sciences702A Sherman Fairchild Center, MC2434, Columbia UniversityNew YorkNew YorkUSA
- Present address:
Columbia UniversityNew YorkNew YorkUSA
| | - Henry S. Hunt
- Department of PhysicsStanford UniversityStanfordCaliforniaUSA
| | | | | | - Samuel K. Handelman
- Department of Biological Sciences702A Sherman Fairchild Center, MC2434, Columbia UniversityNew YorkNew YorkUSA
- Present address:
Department of Pain & Neuronal HealthEli Lily & Co.893 Delaware StIndianapolisIndianaUSA
| | - W. Nicholson Price
- Department of Biological Sciences702A Sherman Fairchild Center, MC2434, Columbia UniversityNew YorkNew YorkUSA
- Present address:
University of Michigan Law SchoolAnn ArborMichiganUSA
| | - John F. Hunt
- Department of Biological Sciences702A Sherman Fairchild Center, MC2434, Columbia UniversityNew YorkNew YorkUSA
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4
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Lee JHZ, Bruning JB, Bell SG. An In Crystallo Reaction with an Engineered Cytochrome P450 Peroxygenase. Chemistry 2024; 30:e202303335. [PMID: 37971151 DOI: 10.1002/chem.202303335] [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] [Received: 10/10/2023] [Revised: 11/10/2023] [Accepted: 11/16/2023] [Indexed: 11/19/2023]
Abstract
The cytochrome P450 monooxygenases (CYPs) are a class of heme-thiolate enzymes that insert oxygen into unactivated C-H bonds. These enzymes can be converted into peroxygenases via protein engineering, which enables their activity to occur using hydrogen peroxide (H2 O2 ) without the requirement for additional nicotinamide co-factors or partner proteins. Here, we demonstrate that soaking crystals of an engineered P450 peroxygenase with H2 O2 enables the enzymatic reaction to occur within the crystal. Crystals of the designed P450 peroxygenase, the T252E mutant of CYP199A4, in complex with 4-methoxybenzoic acid were soaked with different concentrations of H2 O2 for varying times to initiate the in crystallo O-demethylation reaction. Crystal structures of T252E-CYP199A4 showed a distinct loss of electron density that was consistent with the O-demethylated metabolite, 4-hydroxybenzoic acid. A new X-ray crystal structure of this enzyme with the 4-hydroxybenzoic acid product was obtained to enable comparison alongside the existing substrate-bound structure. The visualisation of enzymatic catalysis in action is challenging in structural biology and the ability to initiate the reactions of P450 enzymes, in crystallo by simply soaking crystals with H2 O2 will enable new structural biology methods and techniques to be applied to study their mechanism of action.
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Affiliation(s)
- Joel H Z Lee
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
| | - John B Bruning
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Stephen G Bell
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
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5
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Berkes A, Kleine-Doepke S, Leimkohl JP, Schikora H, Mehrabi P, Tellkamp F, Schulz EC. An electropneumatic cleaning device for piezo-actuator-driven picolitre-droplet dispensers. J Appl Crystallogr 2024; 57:209-214. [PMID: 38322725 PMCID: PMC10840313 DOI: 10.1107/s1600576723009573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 11/02/2023] [Indexed: 02/08/2024] Open
Abstract
Recently, we introduced the liquid application method for time-resolved analyses (LAMA). The time-consuming cleaning cycles required for the substrate solution exchange and storage of the sensitive droplet-dispenser nozzles present practical challenges. In this work, a dispenser cleaning system for the semi-automated cleaning of the piezo-actuator-driven picolitre-droplet dispensers required for LAMA is introduced to streamline typical workflows.
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Affiliation(s)
- Alexander Berkes
- Institute for Nanostructure and Solid State Physics, University of Hamburg, Hamburg, Germany
| | - Stephan Kleine-Doepke
- Institute for Nanostructure and Solid State Physics, University of Hamburg, Hamburg, Germany
| | | | - Hendrik Schikora
- Max-Planck-Institute for the Structure and Dynamics of Matter, Hamburg, Germany
| | - Pedram Mehrabi
- Institute for Nanostructure and Solid State Physics, University of Hamburg, Hamburg, Germany
- Max-Planck-Institute for the Structure and Dynamics of Matter, Hamburg, Germany
| | - Friedjof Tellkamp
- Max-Planck-Institute for the Structure and Dynamics of Matter, Hamburg, Germany
| | - Eike C. Schulz
- Institute for Nanostructure and Solid State Physics, University of Hamburg, Hamburg, Germany
- Max-Planck-Institute for the Structure and Dynamics of Matter, Hamburg, Germany
- University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
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6
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Henning RW, Kosheleva I, Šrajer V, Kim IS, Zoellner E, Ranganathan R. BioCARS: Synchrotron facility for probing structural dynamics of biological macromolecules. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2024; 11:014301. [PMID: 38304444 PMCID: PMC10834067 DOI: 10.1063/4.0000238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 01/10/2024] [Indexed: 02/03/2024]
Abstract
A major goal in biomedical science is to move beyond static images of proteins and other biological macromolecules to the internal dynamics underlying their function. This level of study is necessary to understand how these molecules work and to engineer new functions and modulators of function. Stemming from a visionary commitment to this problem by Keith Moffat decades ago, a community of structural biologists has now enabled a set of x-ray scattering technologies for observing intramolecular dynamics in biological macromolecules at atomic resolution and over the broad range of timescales over which motions are functionally relevant. Many of these techniques are provided by BioCARS, a cutting-edge synchrotron radiation facility built under Moffat leadership and located at the Advanced Photon Source at Argonne National Laboratory. BioCARS enables experimental studies of molecular dynamics with time resolutions spanning from 100 ps to seconds and provides both time-resolved x-ray crystallography and small- and wide-angle x-ray scattering. Structural changes can be initiated by several methods-UV/Vis pumping with tunable picosecond and nanosecond laser pulses, substrate diffusion, and global perturbations, such as electric field and temperature jumps. Studies of dynamics typically involve subtle perturbations to molecular structures, requiring specialized computational techniques for data processing and interpretation. In this review, we present the challenges in experimental macromolecular dynamics and describe the current state of experimental capabilities at this facility. As Moffat imagined years ago, BioCARS is now positioned to catalyze the scientific community to make fundamental advances in understanding proteins and other complex biological macromolecules.
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Affiliation(s)
- Robert W. Henning
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
| | - Irina Kosheleva
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
| | - Vukica Šrajer
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
| | - In-Sik Kim
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
| | - Eric Zoellner
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
| | - Rama Ranganathan
- BioCARS, Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
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7
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Botha S, Fromme P. Review of serial femtosecond crystallography including the COVID-19 pandemic impact and future outlook. Structure 2023; 31:1306-1319. [PMID: 37898125 PMCID: PMC10842180 DOI: 10.1016/j.str.2023.10.005] [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: 07/18/2023] [Revised: 09/28/2023] [Accepted: 10/04/2023] [Indexed: 10/30/2023]
Abstract
Serial femtosecond crystallography (SFX) revolutionized macromolecular crystallography over the past decade by enabling the collection of X-ray diffraction data from nano- or micrometer sized crystals while outrunning structure-altering radiation damage effects at room temperature. The serial manner of data collection from millions of individual crystals coupled with the femtosecond duration of the ultrabright X-ray pulses enables time-resolved studies of macromolecules under near-physiological conditions to unprecedented temporal resolution. In 2020 the rapid spread of the coronavirus SARS-CoV-2 resulted in a global pandemic of coronavirus disease-2019. This led to a shift in how serial femtosecond experiments were performed, along with rapid funding and free electron laser beamtime availability dedicated to SARS-CoV-2-related studies. This review outlines the current state of SFX research, the milestones that were achieved, the impact of the global pandemic on this field as well as an outlook into exciting future directions.
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Affiliation(s)
- Sabine Botha
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; Department of Physics, Arizona State University, Tempe, AZ 85287-1504, USA.
| | - Petra Fromme
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA.
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8
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Smith N, Dasgupta M, Wych DC, Dolamore C, Sierra RG, Lisova S, Marchany-Rivera D, Cohen AE, Boutet S, Hunter MS, Kupitz C, Poitevin F, Moss FR, Brewster AS, Sauter NK, Young ID, Wolff AM, Tiwari VK, Kumar N, Berkowitz DB, Hadt RG, Thompson MC, Follmer AH, Wall ME, Wilson MA. Changes in an Enzyme Ensemble During Catalysis Observed by High Resolution XFEL Crystallography. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.15.553460. [PMID: 37645800 PMCID: PMC10462001 DOI: 10.1101/2023.08.15.553460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Enzymes populate ensembles of structures with intrinsically different catalytic proficiencies that are difficult to experimentally characterize. We use time-resolved mix-and-inject serial crystallography (MISC) at an X-ray free electron laser (XFEL) to observe catalysis in a designed mutant (G150T) isocyanide hydratase (ICH) enzyme that enhances sampling of important minor conformations. The active site exists in a mixture of conformations and formation of the thioimidate catalytic intermediate selects for catalytically competent substates. A prior proposal for active site cysteine charge-coupled conformational changes in ICH is validated by determining structures of the enzyme over a range of pH values. A combination of large molecular dynamics simulations of the enzyme in crystallo and time-resolved electron density maps shows that ionization of the general acid Asp17 during catalysis causes additional conformational changes that propagate across the dimer interface, connecting the two active sites. These ionization-linked changes in the ICH conformational ensemble permit water to enter the active site in a location that is poised for intermediate hydrolysis. ICH exhibits a tight coupling between ionization of active site residues and catalysis-activated protein motions, exemplifying a mechanism of electrostatic control of enzyme dynamics.
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Affiliation(s)
- Nathan Smith
- Department of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE, 68588
| | - Medhanjali Dasgupta
- Department of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE, 68588
| | - David C. Wych
- Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, NM 875405
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Cole Dolamore
- Department of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE, 68588
| | - Raymond G. Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025
| | - Stella Lisova
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025
| | - Darya Marchany-Rivera
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025
| | - Aina E. Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025
| | - Mark S. Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025
| | - Christopher Kupitz
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025
| | - Frédéric Poitevin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025
| | - Frank R. Moss
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025
| | - Aaron S. Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Nicholas K. Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Iris D. Young
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Alexander M. Wolff
- Department of Chemistry and Biochemistry, University of California, Merced, CA, 93540
| | - Virendra K. Tiwari
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588
| | - Nivesh Kumar
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588
| | - David B. Berkowitz
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588
| | - Ryan G. Hadt
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA USA
| | - Michael C. Thompson
- Department of Chemistry and Biochemistry, University of California, Merced, CA, 93540
| | - Alec H. Follmer
- Department of Chemistry, University of California-Irvine, Irvine, CA 92697
| | - Michael E. Wall
- Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, NM 875405
| | - Mark A. Wilson
- Department of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE, 68588
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9
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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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10
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Wang N, Peng H, Yang C, Guo W, Wang M, Li G, Liu D. Metabolic Engineering of Model Microorganisms for the Production of Xanthophyll. Microorganisms 2023; 11:1252. [PMID: 37317226 DOI: 10.3390/microorganisms11051252] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/19/2023] [Accepted: 05/06/2023] [Indexed: 06/16/2023] Open
Abstract
Xanthophyll is an oxidated version of carotenoid. It presents significant value to the pharmaceutical, food, and cosmetic industries due to its specific antioxidant activity and variety of colors. Chemical processing and conventional extraction from natural organisms are still the main sources of xanthophyll. However, the current industrial production model can no longer meet the demand for human health care, reducing petrochemical energy consumption and green sustainable development. With the swift development of genetic metabolic engineering, xanthophyll synthesis by the metabolic engineering of model microorganisms shows great application potential. At present, compared to carotenes such as lycopene and β-carotene, xanthophyll has a relatively low production in engineering microorganisms due to its stronger inherent antioxidation, relatively high polarity, and longer metabolic pathway. This review comprehensively summarized the progress in xanthophyll synthesis by the metabolic engineering of model microorganisms, described strategies to improve xanthophyll production in detail, and proposed the current challenges and future efforts needed to build commercialized xanthophyll-producing microorganisms.
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Affiliation(s)
- Nan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huakang Peng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Caifeng Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wenfang Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Mengqi Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Gangqiang Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Dehu Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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11
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Schmidt M. Biological function investigated by time-resolved structure determination. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2023; 10:010901. [PMID: 36846099 PMCID: PMC9946696 DOI: 10.1063/4.0000177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
Inspired by recent progress in time-resolved x-ray crystallography and the adoption of time-resolution by cryo-electronmicroscopy, this article enumerates several approaches developed to become bigger/smaller, faster, and better to gain new insight into the molecular mechanisms of life. This is illustrated by examples where chemical and physical stimuli spawn biological responses on various length and time-scales, from fractions of Ångströms to micro-meters and from femtoseconds to hours.
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Affiliation(s)
- Marius Schmidt
- Physics Department, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, Wisconsin 53211, USA
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Worrall JAR, Hough MA. Serial femtosecond crystallography approaches to understanding catalysis in iron enzymes. Curr Opin Struct Biol 2022; 77:102486. [PMID: 36274419 DOI: 10.1016/j.sbi.2022.102486] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 09/11/2022] [Accepted: 09/16/2022] [Indexed: 12/14/2022]
Abstract
Enzymes with iron-containing active sites play crucial roles in catalysing a myriad of oxidative reactions essential to aerobic life. Defining the three-dimensional structures of iron enzymes in resting, oxy-bound intermediate and substrate-bound states is particularly challenging, not least because of the extreme susceptibility of the Fe(III) and Fe(IV) redox states to radiation-induced chemistry caused by intense X-ray or electron beams. The availability of novel sources such as X-ray free electron lasers has enabled structures that are effectively free of the effects of radiation-induced chemistry and allows time-resolved structures to be determined. Important to both applications is the ability to obtain in crystallo spectroscopic data to identify the redox state of the iron in any particular structure or timepoint.
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Affiliation(s)
- Jonathan A R Worrall
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK
| | - Michael A Hough
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK; Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK.
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Smith N, Wilson MA. Understanding Cysteine Chemistry Using Conventional and Serial X-Ray Protein Crystallography. CRYSTALS 2022; 12:1671. [PMID: 36685087 PMCID: PMC9850494 DOI: 10.3390/cryst12111671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Proteins that use cysteine residues for catalysis or regulation are widely distributed and intensively studied, with many biomedically important examples. Enzymes where cysteine is a catalytic nucleophile typically generate covalent catalytic intermediates whose structures are important for understanding mechanism and for designing targeted inhibitors. The formation of catalytic intermediates can change enzyme conformational dynamics, sometimes activating protein motions that are important for catalytic turnover. However, these transiently populated intermediate species have been challenging to structurally characterize using traditional crystallographic approaches. This review describes the use and promise of new time-resolved serial crystallographic methods to study cysteine-dependent enzymes, with a focus on the main (Mpro) and papain-like (PLpro) cysteine proteases of SARS-CoV-2 as well as other examples. We review features of cysteine chemistry that are relevant for the design and execution of time-resolved serial crystallography experiments. In addition, we discuss emerging X-ray techniques such as time-resolved sulfur X-ray spectroscopy that may be able to detect changes in sulfur charge state and covalency during catalysis or regulatory modification. In summary, cysteine-dependent enzymes have features that make them especially attractive targets for new time-resolved serial crystallography approaches, which can reveal both changes to enzyme structure and dynamics during catalysis in crystalline samples.
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Potential of Time-Resolved Serial Femtosecond Crystallography Using High Repetition Rate XFEL Sources. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12052551] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This perspective review describes emerging techniques and future opportunities for time-resolved serial femtosecond crystallography (TR-SFX) experiments using high repetition rate XFEL sources. High repetition rate sources are becoming more available with the European XFEL in operation and the recently upgraded LCLS-II will be available in the near future. One efficient use of these facilities for TR-SFX relies on pump–probe experiments using a laser to trigger a reaction of light-responsive proteins or mix-and-inject experiments for light-unresponsive proteins. With the view to widen the application of TR-SFX, the promising field of photocaged compounds is under development, which allows the very fast laser triggering of reactions that is no longer limited to naturally light-responsive samples. In addition to reaction triggering, a key concern when performing an SFX experiment is efficient sample usage, which is a main focus of new high repetition rate-compatible sample delivery methods.
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