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Meisburger SP, Ando N. Scaling and merging macromolecular diffuse scattering with mdx2. Acta Crystallogr D Struct Biol 2024; 80:299-313. [PMID: 38606664 PMCID: PMC11066883 DOI: 10.1107/s2059798324002705] [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: 01/22/2024] [Accepted: 03/25/2024] [Indexed: 04/13/2024] Open
Abstract
Diffuse scattering is a promising method to gain additional insight into protein dynamics from macromolecular crystallography experiments. Bragg intensities yield the average electron density, while the diffuse scattering can be processed to obtain a three-dimensional reciprocal-space map that is further analyzed to determine correlated motion. To make diffuse scattering techniques more accessible, software for data processing called mdx2 has been created that is both convenient to use and simple to extend and modify. mdx2 is written in Python, and it interfaces with DIALS to implement self-contained data-reduction workflows. Data are stored in NeXus format for software interchange and convenient visualization. mdx2 can be run on the command line or imported as a package, for instance to encapsulate a complete workflow in a Jupyter notebook for reproducible computing and education. Here, mdx2 version 1.0 is described, a new release incorporating state-of-the-art techniques for data reduction. The implementation of a complete multi-crystal scaling and merging workflow is described, and the methods are tested using a high-redundancy data set from cubic insulin. It is shown that redundancy can be leveraged during scaling to correct systematic errors and obtain accurate and reproducible measurements of weak diffuse signals.
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Affiliation(s)
- Steve P. Meisburger
- Cornell High Energy Synchrotron Source, Cornell University, Ithaca, NY 14850, USA
| | - Nozomi Ando
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14850, 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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Meisburger SP, Ando N. Scaling and merging macromolecular diffuse scattering with mdx2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.16.575887. [PMID: 38293202 PMCID: PMC10827198 DOI: 10.1101/2024.01.16.575887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Diffuse scattering is a promising method to gain additional insight into protein dynamics from macromolecular crystallography (MX) experiments. Bragg intensities yield the average electron density, while the diffuse scattering can be processed to obtain a three-dimensional reciprocal space map, that is further analyzed to determine correlated motion. To make diffuse scattering techniques more accessible, we have created software for data processing called mdx2 that is both convenient to use and simple to extend and modify. Mdx2 is written in Python, and it interfaces with DIALS to implement self-contained data reduction workflows. Data are stored in NeXus format for software interchange and convenient visualization. Mdx2 can be run on the command line or imported as a package, for instance to encapsulate a complete workflow in a Jupyter notebook for reproducible computing and education. Here, we describe mdx2 version 1.0, a new release incorporating state-of-the-art techniques for data reduction. We describe the implementation of a complete multi-crystal scaling and merging workflow, and test the methods using a high-redundancy dataset from cubic insulin. We show that redundancy can be leveraged during scaling to correct systematic errors, and obtain accurate and reproducible measurements of weak diffuse signals.
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Affiliation(s)
- Steve P. Meisburger
- Cornell High Energy Synchrotron Source, Cornell University, Ithaca, New York 14850, USA
| | - Nozomi Ando
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14850, USA
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Abstract
Diffuse scattering is a powerful technique to study disorder and dynamics of macromolecules at atomic resolution. Although diffuse scattering is always present in diffraction images from macromolecular crystals, the signal is weak compared with Bragg peaks and background, making it a challenge to visualize and measure accurately. Recently, this challenge has been addressed using the reciprocal space mapping technique, which leverages ideal properties of modern X-ray detectors to reconstruct the complete three-dimensional volume of continuous diffraction from diffraction images of a crystal (or crystals) in many different orientations. This chapter will review recent progress in reciprocal space mapping with a particular focus on the strategy implemented in the mdx-lib and mdx2 software packages. The chapter concludes with an introductory data processing tutorial using Python packages DIALS, NeXpy, and mdx2.
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Affiliation(s)
- Steve P Meisburger
- Cornell High Energy Synchrotron Source, Cornell University, Ithaca, NY, United States.
| | - Nozomi Ando
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, United States.
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Pei X, Bhatt N, Wang H, Ando N, Meisburger SP. Introduction to diffuse scattering and data collection. Methods Enzymol 2023; 688:1-42. [PMID: 37748823 DOI: 10.1016/bs.mie.2023.07.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
A long-standing goal in X-ray crystallography has been to extract information about the collective motions of proteins from diffuse scattering: the weak, textured signal that is found in the background of diffraction images. In the past few years, the field of macromolecular diffuse scattering has seen dramatic progress, and many of the past challenges in measurement and interpretation are now considered tractable. However, the concept of diffuse scattering is still new to many researchers, and a general set of procedures needed to collect a high-quality dataset has never been described in detail. Here, we provide the first guidelines for performing diffuse scattering experiments, which can be performed at any macromolecular crystallography beamline that supports room-temperature studies with a direct detector. We begin with a brief introduction to the theory of diffuse scattering and then walk the reader through the decision-making processes involved in preparing for and conducting a successful diffuse scattering experiment. Finally, we define quality metrics and describe ways to assess data quality both at the beamline and at home. Data obtained in this way can be processed independently by crystallographic software and diffuse scattering software to produce both a crystal structure, which represents the average atomic coordinates, and a three-dimensional diffuse scattering map that can then be interpreted in terms of models for protein motions.
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Affiliation(s)
- Xiaokun Pei
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, United States
| | - Neti Bhatt
- Department of Physics, Cornell University, Ithaca, NY, United States
| | - Haoyue Wang
- Graduate Field of Biophysics, Cornell University, Ithaca, NY, United States
| | - Nozomi Ando
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, United States; Department of Physics, Cornell University, Ithaca, NY, United States; Graduate Field of Biophysics, Cornell University, Ithaca, NY, United States.
| | - Steve P Meisburger
- Cornell High Energy Synchrotron Source, Cornell University, Ithaca, NY, United States.
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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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Meisburger SP, Ando N. Processing macromolecular diffuse scattering data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.04.543637. [PMID: 37333125 PMCID: PMC10274731 DOI: 10.1101/2023.06.04.543637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Diffuse scattering is a powerful technique to study disorder and dynamics of macromolecules at atomic resolution. Although diffuse scattering is always present in diffraction images from macromolecular crystals, the signal is weak compared with Bragg peaks and background, making it a challenge to visualize and measure accurately. Recently, this challenge has been addressed using the reciprocal space mapping technique, which leverages ideal properties of modern X-ray detectors to reconstruct the complete three-dimensional volume of continuous diffraction from diffraction images of a crystal (or crystals) in many different orientations. This chapter will review recent progress in reciprocal space mapping with a particular focus on the strategy implemented in the mdx-lib and mdx2 software packages. The chapter concludes with an introductory data processing tutorial using Python packages DIALS, NeXpy , and mdx2 .
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Affiliation(s)
- Steve P. Meisburger
- Cornell High Energy Synchrotron Source, Cornell University, Ithaca, New York 14850, USA
| | - Nozomi Ando
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14850, USA
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Su Z, Dasgupta M, Poitevin F, Mathews II, van den Bedem H, Wall ME, Yoon CH, Wilson MA. Reproducibility of protein x-ray diffuse scattering and potential utility for modeling atomic displacement parameters. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2021; 8:044701. [PMID: 34258328 PMCID: PMC8270650 DOI: 10.1063/4.0000087] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 06/07/2021] [Indexed: 06/13/2023]
Abstract
Protein structure and dynamics can be probed using x-ray crystallography. Whereas the Bragg peaks are only sensitive to the average unit-cell electron density, the signal between the Bragg peaks-diffuse scattering-is sensitive to spatial correlations in electron-density variations. Although diffuse scattering contains valuable information about protein dynamics, the diffuse signal is more difficult to isolate from the background compared to the Bragg signal, and the reproducibility of diffuse signal is not yet well understood. We present a systematic study of the reproducibility of diffuse scattering from isocyanide hydratase in three different protein forms. Both replicate diffuse datasets and datasets obtained from different mutants were similar in pairwise comparisons (Pearson correlation coefficient ≥0.8). The data were processed in a manner inspired by previously published methods using custom software with modular design, enabling us to perform an analysis of various data processing choices to determine how to obtain the highest quality data as assessed using unbiased measures of symmetry and reproducibility. The diffuse data were then used to characterize atomic mobility using a liquid-like motions (LLM) model. This characterization was able to discriminate between distinct anisotropic atomic displacement parameter (ADP) models arising from different anisotropic scaling choices that agreed comparably with the Bragg data. Our results emphasize the importance of data reproducibility as a model-free measure of diffuse data quality, illustrate the ability of LLM analysis of diffuse scattering to select among alternative ADP models, and offer insights into the design of successful diffuse scattering experiments.
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Affiliation(s)
| | - Medhanjali Dasgupta
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Frédéric Poitevin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Irimpan I. Mathews
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | | | - Michael E. Wall
- Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Chun Hong Yoon
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Mark A. Wilson
- Department of Biochemistry and the Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588, USA
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