Validated determination of NRG1 Ig-like domain structure by mass spectrometry coupled with computational modeling

Niloofar Abolhasani Khaje; Alexander Eletsky; Sarah E Biehn; Charles K Mobley; Monique J Rogals; Yoonkyoo Kim; Sushil K Mishra; Robert J Doerksen; Steffen Lindert; James H Prestegard; Joshua S Sharp

doi:10.1038/s42003-022-03411-y

Validated determination of NRG1 Ig-like domain structure by mass spectrometry coupled with computational modeling

Commun Biol. 2022 May 12;5(1):452. doi: 10.1038/s42003-022-03411-y.

Authors

Niloofar Abolhasani Khaje^{1

2}, Alexander Eletsky³, Sarah E Biehn⁴, Charles K Mobley^{1

5}, Monique J Rogals³, Yoonkyoo Kim³, Sushil K Mishra^{1

6}, Robert J Doerksen^{1

6}, Steffen Lindert⁴, James H Prestegard³, Joshua S Sharp^{7

8

9}

Affiliations

¹ Department of BioMolecular Sciences, University of Mississippi, University, MS, USA.
² Analytical Operations Department, Gilead Sciences, Foster City, CA, USA.
³ Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA.
⁴ Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA.
⁵ Protein Discovery Department, Impossible Foods, Redwood City, CA, USA.
⁶ Glycoscience Center of Research Excellence, University of Mississippi, University, MS, USA.
⁷ Department of BioMolecular Sciences, University of Mississippi, University, MS, USA. jsharp@olemiss.edu.
⁸ Glycoscience Center of Research Excellence, University of Mississippi, University, MS, USA. jsharp@olemiss.edu.
⁹ Department of Chemistry and Biochemistry, University of Mississippi, University, MS, USA. jsharp@olemiss.edu.

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. 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.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.
Research Support, N.I.H., Extramural

MeSH terms

Computer Simulation
Hydroxyl Radical / chemistry
Immunoglobulin Domains
Mass Spectrometry
Protein Footprinting* / methods
Proteins* / chemistry

Substances

Proteins
Hydroxyl Radical

Abstract

Publication types

MeSH terms

Substances

Grants and funding