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Robust total X-ray scattering workflow to study correlated motion of proteins in crystals
Open accessPreprint — published as 10.1038/s41467-023-36734-3 · Paper page
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 developed a general workflow that enables robust subtraction of lattice disorder. The workflow introduces two new 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. 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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Highly accurate protein structure prediction with AlphaFold
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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
- Venue
- Nature Communications
- Publisher
- openRxiv
- Published
- 2022-08-22
- Volume
- 14
- Issue
- 1
- Pages
- 1228-1228
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC9984388
- OpenAlex
- W4323048702
- Cited by
- 20
- References
- 1
- Citations by year
- 2026: 3 · 2025: 2 · 2024: 6 · 2023: 9
- FWCI
- 1.47
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- 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 (1829070, 1-P30-GM124166-01A1)
- U.S. Department of Health and Human Services (F32GM117757, GM 122086, GM124847, 1-P30-GM124166-01A1)
- Empire State Development Corporation
- National Institutes of Health (GM124166, GM122086)
- National Institute of General Medical Sciences (F32GM117757, 1-P30-GM124166, 1‐P30‐GM124166‐01A1, GM‐124166, DMR-1829070, R01GM122086, GM122086, GM124847, R35GM124847, P30GM124166)
- Division of Materials Research (DMR-1829070, 1829070)
- 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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