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  1. AU=Meisburger Steve P.
  2. AU="Silveira, Fernando A. O."
  3. AU="Toru Nabika"
  4. AU="Vojkovic, Marina"
  5. AU="Gaier, Eric D"
  6. AU="Chandler Crews"
  7. AU="Comte, Marie-Hélène"
  8. AU="Cohen, Or"
  9. AU="Abdellatifi, Mohamed"
  10. AU="Luebbe, Elizabeth"
  11. AU="Emidio, Adriana"
  12. AU=Masmejan Sophie
  13. AU="Samantha Ridley"
  14. AU="Moghaddam-Alvandi, Arash"
  15. AU="Khanolkar, Amey R."
  16. AU="Vasquez Martinez, Rodolfo"
  17. AU="Morgan, E"

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  1. Artikel: Scaling and merging macromolecular diffuse scattering with

    Meisburger, Steve P / Ando, Nozomi

    bioRxiv : the preprint server for biology

    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 ... ...

    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
    Sprache Englisch
    Erscheinungsdatum 2024-01-16
    Erscheinungsland United States
    Dokumenttyp Preprint
    DOI 10.1101/2024.01.16.575887
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Artikel ; Online: Scaling and merging macromolecular diffuse scattering with mdx2.

    Meisburger, Steve P / Ando, Nozomi

    Acta crystallographica. Section D, Structural biology

    2024  Band 80, Heft Pt 5, Seite(n) 299–313

    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 ... ...

    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.
    Mesh-Begriff(e) Software ; Macromolecular Substances/chemistry ; Crystallography, X-Ray/methods ; Proteins/chemistry ; Insulin/chemistry
    Chemische Substanzen Macromolecular Substances ; Proteins ; Insulin
    Sprache Englisch
    Erscheinungsdatum 2024-04-12
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ZDB-ID 2968623-4
    ISSN 2059-7983 ; 0907-4449
    ISSN (online) 2059-7983
    ISSN 0907-4449
    DOI 10.1107/S2059798324002705
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  3. Artikel: Processing macromolecular diffuse scattering data.

    Meisburger, Steve P / Ando, Nozomi

    bioRxiv : the preprint server for biology

    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 ... ...

    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
    Sprache Englisch
    Erscheinungsdatum 2023-06-06
    Erscheinungsland United States
    Dokumenttyp Preprint
    DOI 10.1101/2023.06.04.543637
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  4. Artikel ; Online: Processing macromolecular diffuse scattering data.

    Meisburger, Steve P / Ando, Nozomi

    Methods in enzymology

    2023  Band 688, Seite(n) 43–86

    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 ... ...

    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.
    Mesh-Begriff(e) Macromolecular Substances
    Chemische Substanzen Macromolecular Substances
    Sprache Englisch
    Erscheinungsdatum 2023-08-25
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 1557-7988
    ISSN (online) 1557-7988
    DOI 10.1016/bs.mie.2023.06.010
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  5. Artikel ; Online: Robust total X-ray scattering workflow to study correlated motion of proteins in crystals.

    Meisburger, Steve P / Case, David A / Ando, Nozomi

    Nature communications

    2023  Band 14, Heft 1, Seite(n) 1228

    Abstract: The breathing motions of proteins are thought to play a critical role in function. However, current techniques to study key collective motions are limited to spectroscopy and computation. We present a high-resolution experimental approach based on the ... ...

    Abstract The breathing motions of proteins are thought to play a critical role in function. However, current techniques to study key collective motions are limited to spectroscopy and computation. We present a high-resolution experimental approach based on the total scattering from protein crystals at room temperature (TS/RT-MX) that captures both structure and collective motions. To reveal the scattering signal from protein motions, we present a general workflow that enables robust subtraction of lattice disorder. The workflow introduces two methods: GOODVIBES, a detailed and refinable lattice disorder model based on the rigid-body vibrations of a crystalline elastic network; and DISCOBALL, an independent method of validation that estimates the displacement covariance between proteins in the lattice in real space. Here, we demonstrate the robustness of this workflow and further demonstrate how it can be interfaced with MD simulations towards obtaining high-resolution insight into functionally important protein motions.
    Mesh-Begriff(e) X-Rays ; Workflow ; Radiography ; Motion ; Vibration
    Sprache Englisch
    Erscheinungsdatum 2023-03-03
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-36734-3
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  6. Artikel: REGALS

    Meisburger, Steve P / Xu, Da / Ando, Nozomi

    IUCrJ

    2021  Band 8, Heft Pt 2, Seite(n) 225–237

    Abstract: Mixtures of biological macromolecules are inherently difficult to study using structural methods, as increasing complexity presents new challenges for data analysis. Recently, there has been growing interest in studying evolving mixtures using small- ... ...

    Abstract Mixtures of biological macromolecules are inherently difficult to study using structural methods, as increasing complexity presents new challenges for data analysis. Recently, there has been growing interest in studying evolving mixtures using small-angle X-ray scattering (SAXS) in conjunction with time-resolved, high-throughput or chromatography-coupled setups. Deconvolution and interpretation of the resulting datasets, however, are nontrivial when neither the scattering components nor the way in which they evolve are known
    Sprache Englisch
    Erscheinungsdatum 2021-02-06
    Erscheinungsland England
    Dokumenttyp Journal Article
    ZDB-ID 2754953-7
    ISSN 2052-2525
    ISSN 2052-2525
    DOI 10.1107/S2052252521000555
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  7. Artikel ; Online: Introduction to diffuse scattering and data collection.

    Pei, Xiaokun / Bhatt, Neti / Wang, Haoyue / Ando, Nozomi / Meisburger, Steve P

    Methods in enzymology

    2023  Band 688, Seite(n) 1–42

    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 ... ...

    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.
    Mesh-Begriff(e) Data Collection ; Crystallography, X-Ray ; Motion ; Software ; Synchrotrons
    Sprache Englisch
    Erscheinungsdatum 2023-08-24
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 1557-7988
    ISSN (online) 1557-7988
    DOI 10.1016/bs.mie.2023.07.007
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  8. Artikel ; Online: Correlated Motions in Structural Biology.

    Xu, Da / Meisburger, Steve P / Ando, Nozomi

    Biochemistry

    2021  Band 60, Heft 30, Seite(n) 2331–2340

    Abstract: Correlated motions in proteins arising from the collective movements of residues have long been proposed to be fundamentally important to key properties of proteins, from allostery and catalysis to evolvability. Recent breakthroughs in structural biology ...

    Abstract Correlated motions in proteins arising from the collective movements of residues have long been proposed to be fundamentally important to key properties of proteins, from allostery and catalysis to evolvability. Recent breakthroughs in structural biology have made it possible to capture proteins undergoing complex conformational changes, yet intrinsic correlated motions within a conformation remain one of the least understood facets of protein structure. For many decades, the analysis of total X-ray scattering held the promise of animating crystal structures with correlated motions. With recent advances in both X-ray detectors and data interpretation methods, this long-held promise can now be met. In this Perspective, we will introduce how correlated motions are captured in total scattering and provide guidelines for the collection, interpretation, and validation of data. As structural biology continues to push the boundaries, we see an opportunity to gain atomistic insight into correlated motions using total scattering as a bridge between theory and experiment.
    Mesh-Begriff(e) Crystallography, X-Ray ; Molecular Dynamics Simulation ; Motion ; Protein Conformation ; Proteins/chemistry
    Chemische Substanzen Proteins
    Sprache Englisch
    Erscheinungsdatum 2021-07-22
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1108-3
    ISSN 1520-4995 ; 0006-2960
    ISSN (online) 1520-4995
    ISSN 0006-2960
    DOI 10.1021/acs.biochem.1c00420
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  9. Artikel ; Online: REGALS

    Steve P. Meisburger / Da Xu / Nozomi Ando

    IUCrJ, Vol 8, Iss 2, Pp 225-

    a general method to deconvolve X-ray scattering data from evolving mixtures

    2021  Band 237

    Abstract: Mixtures of biological macromolecules are inherently difficult to study using structural methods, as increasing complexity presents new challenges for data analysis. Recently, there has been growing interest in studying evolving mixtures using small- ... ...

    Abstract Mixtures of biological macromolecules are inherently difficult to study using structural methods, as increasing complexity presents new challenges for data analysis. Recently, there has been growing interest in studying evolving mixtures using small-angle X-ray scattering (SAXS) in conjunction with time-resolved, high-throughput or chromatography-coupled setups. Deconvolution and interpretation of the resulting datasets, however, are nontrivial when neither the scattering components nor the way in which they evolve are known a priori. To address this issue, the REGALS method (regularized alternating least squares) is introduced, which incorporates simple expectations about the data as prior knowledge, and utilizes parameterization and regularization to provide robust deconvolution solutions. The restraints used by REGALS are general properties such as smoothness of profiles and maximum dimensions of species, making it well suited for exploring datasets with unknown species. Here, REGALS is applied to the analysis of experimental data from four types of SAXS experiment: anion-exchange (AEX) coupled SAXS, ligand titration, time-resolved mixing and time-resolved temperature jump. Based on its performance with these challenging datasets, it is anticipated that REGALS will be a valuable addition to the SAXS analysis toolkit and enable new experiments. The software is implemented in both MATLAB and Python and is available freely as an open-source software package.
    Schlagwörter deconvolution ; small-angle x-ray scattering ; time-resolved saxs ; aex-saxs ; high-throughput saxs ; ligand titration ; regularized alternating least squares ; multivariate curve resolution ; singular value decomposition ; pair-distance distribution function ; Science ; Q
    Sprache Englisch
    Erscheinungsdatum 2021-03-01T00:00:00Z
    Verlag International Union of Crystallography
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  10. Artikel ; Online: Diffuse X-ray scattering from correlated motions in a protein crystal.

    Meisburger, Steve P / Case, David A / Ando, Nozomi

    Nature communications

    2020  Band 11, Heft 1, Seite(n) 1271

    Abstract: Protein dynamics are integral to biological function, yet few techniques are sensitive to collective atomic motions. A long-standing goal of X-ray crystallography has been to combine structural information from Bragg diffraction with dynamic information ... ...

    Abstract Protein dynamics are integral to biological function, yet few techniques are sensitive to collective atomic motions. A long-standing goal of X-ray crystallography has been to combine structural information from Bragg diffraction with dynamic information contained in the diffuse scattering background. However, the origin of macromolecular diffuse scattering has been poorly understood, limiting its applicability. We present a finely sampled diffuse scattering map from triclinic lysozyme with unprecedented accuracy and detail, clearly resolving both the inter- and intramolecular correlations. These correlations are studied theoretically using both all-atom molecular dynamics and simple vibrational models. Although lattice dynamics reproduce most of the diffuse pattern, protein internal dynamics, which include hinge-bending motions, are needed to explain the short-ranged correlations revealed by Patterson analysis. These insights lay the groundwork for animating crystal structures with biochemically relevant motions.
    Mesh-Begriff(e) Crystallization ; Molecular Dynamics Simulation ; Motion ; Muramidase/chemistry ; Phonons ; X-Ray Diffraction
    Chemische Substanzen Muramidase (EC 3.2.1.17)
    Sprache Englisch
    Erscheinungsdatum 2020-03-09
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-020-14933-6
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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