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Cited by 20Enzyme Structure and FunctionProtein Structure and DynamicsAdvanced X-ray Imaging Techniques

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Robust total X-ray scattering workflow to study correlated motion of proteins in crystals

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Meisburger, Steve P., Case, David A., Ando, Nozomi·2023·Nature Communications
DOI 10.1038/s41467-023-36734-3PMC PMC9984388

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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.

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Metadata

Authors
Meisburger, S. P., Case, D. A., & Ando, N.
Affiliations
  • Cornell University (US)
  • Rutgers, The State University of New Jersey (US)
Corresponding author
Ando, Nozomi
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2023-03-03
Volume
14
Issue
1
Pages
1228-1228
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/s41467-023-36734-3
PMC
PMC9984388
OpenAlex
W4323048702
Cited by
20
References
3
Citations by year
2026: 3 · 2025: 2 · 2024: 6 · 2023: 9
FWCI
1.47
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • National Science Foundation (DMR-1829070)
  • U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (1-P30-GM124166-01A1)
  • U.S. Department of Health & Human Services | National Institutes of Health (F32GM117757, GM122086, GM124847)
  • Startup funds from Cornell University
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Physical Sciences › Physics and Astronomy › Radiation › Advanced X-ray Imaging Techniques
Keywords
collective protein motions, protein crystals, rigid body vibration, elastic network model, protein function
MeSH terms
Motion, Radiography, Vibration, X-Rays, Workflow

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