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PreprintCited by 14Protein Structure and DynamicsMass Spectrometry Techniques and ApplicationsEnzyme Structure and Function

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Validated Determination of NRG1 Ig-like Domain Structure by Mass Spectrometry Coupled with Computational Modeling

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Khaje, Niloofar Abolhasani, Eletsky, Alexander, Biehn, Sarah E., Mobley, Charles K., Rogals, Monique J., Kim, Yoonkyoo, Mishra, Sushil K., Doerksen, Robert J., Lindert, Steffen, Prestegard, James, Sharp, Joshua S.·2021·Communications Biology
DOI 10.1101/2021.12.13.472484PMC PMC9098640

Preprint — published as 10.1038/s42003-022-03411-y

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Abstract

High resolution hydroxyl radical protein footprinting (HR-HRPF) is a mass spectrometry-based method that measures the solvent exposure of multiple amino acids in a single experiment, offering constraints for experimentally-informed computational modeling. HR-HRPF-based modeling has previously been used to accurately model the structure of proteins of known structure, but the technique has never been used to determine the structure of a protein of unknown structure leaving questions of unintentional bias and applicability to unknown structures unresolved. Here, we present the use of HR-HRPF-based modeling to determine the structure of the Ig-like domain of NRG1, a protein with no close homolog of known structure. Independent determination of the protein structure by both HR-HRPF-based modeling and heteronuclear NMR was carried out, with results compared only after both processes were complete. The HR-HRPF-based model was highly similar to the lowest energy NMR model, with a backbone RMSD of 1.6 Å. To our knowledge, this is the first use of HR-HRPF-based modeling to determine a previously uncharacterized protein structure.

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Metadata

Authors
Khaje, N. A., Eletsky, A., Biehn, S. E., Mobley, C. K., Rogals, M. J., Kim, Y., Mishra, S. K., Doerksen, R. J., Lindert, S., Prestegard, J., & Sharp, J. S.
Affiliations
  • University of Mississippi (US)
  • University of Georgia (US)
  • The Ohio State University (US)
Corresponding author
Sharp, Joshua S.
ORCID
Venue
Communications Biology
Publisher
openRxiv
Published
2021-12-14
Volume
5
Issue
1
Pages
452-452
ISSN
2399-3642 (ISSN-L)
DOI
10.1101/2021.12.13.472484
PMC
PMC9098640
OpenAlex
W4280516430
Cited by
14
References
1
Citations by year
2026: 5 · 2025: 3 · 2023: 4 · 2022: 2
FWCI
0.73
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • Communications Biology (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
Funders
  • National Science Foundation (1750666, P41GM111135)
  • U.S. Department of Health and Human Services (P20GM130460, R01GM127267, R01GM134335, P41GM111135)
  • National Institutes of Health
  • Directorate for Mathematical and Physical Sciences (CHE 1750666)
  • National Institute of General Medical Sciences (R01GM033225, P41GM111135, R01GM134335, P20GM130460, R01GM127267)
  • Division of Chemistry (CHE-1750666, 1750666)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
Keywords
neuregulin-1, immunoglobulin-like domains, protein structure determination, solvent exposure, protein structure modeling
MeSH terms
Immunoglobulin Domains, Computer Simulation, Proteins, Mass Spectrometry, Hydroxyl Radical, Protein Footprinting

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