scholarly journals Mass Spectrometry-Based Protein Footprinting Characterizes the Structures of Oligomeric Apolipoprotein E2, E3, and E4

Biochemistry ◽  
2011 ◽  
Vol 50 (38) ◽  
pp. 8117-8126 ◽  
Author(s):  
Brian Gau ◽  
Kanchan Garai ◽  
Carl Frieden ◽  
Michael L. Gross
Keyword(s):  
Mass Spectrometry ◽  
Protein Footprinting

Current Trends in Biotherapeutic Higher Order Structure Characterization by Irreversible Covalent Footprinting Mass Spectrometry

2019 ◽  
Vol 26 (1) ◽  
pp. 35-43 ◽  
Author(s):  
Natalie K. Garcia ◽  
Galahad Deperalta ◽  
Aaron T. Wecksler
Keyword(s):  
Mass Spectrometry ◽  
Protein Structure ◽  
Protein Interactions ◽  
Quaternary Structure ◽  
Solvent Accessibility ◽  
Higher Order ◽  
Structure Characterization ◽  
Order Structure ◽  
Protein Footprinting ◽  
Wide Range

Background: Biotherapeutics, particularly monoclonal antibodies (mAbs), are a maturing class of drugs capable of treating a wide range of diseases. Therapeutic function and solutionstability are linked to the proper three-dimensional organization of the primary sequence into Higher Order Structure (HOS) as well as the timescales of protein motions (dynamics). Methods that directly monitor protein HOS and dynamics are important for mapping therapeutically relevant protein-protein interactions and assessing properly folded structures. Irreversible covalent protein footprinting Mass Spectrometry (MS) tools, such as site-specific amino acid labeling and hydroxyl radical footprinting are analytical techniques capable of monitoring the side chain solvent accessibility influenced by tertiary and quaternary structure. Here we discuss the methodology, examples of biotherapeutic applications, and the future directions of irreversible covalent protein footprinting MS in biotherapeutic research and development. Conclusion: Bottom-up mass spectrometry using irreversible labeling techniques provide valuable information for characterizing solution-phase protein structure. Examples range from epitope mapping and protein-ligand interactions, to probing challenging structures of membrane proteins. By paring these techniques with hydrogen-deuterium exchange, spectroscopic analysis, or static-phase structural data such as crystallography or electron microscopy, a comprehensive understanding of protein structure can be obtained.

scholarly journals Probing Conformational Changes of Human DNA Polymerase λ using Mass Spectrometry-Based Protein Footprinting

2009 ◽  
Vol 390 (3) ◽  
pp. 368-379 ◽  
Author(s):  
Jason D. Fowler ◽  
Jessica A. Brown ◽  
Mamuka Kvaratskhelia ◽  
Zucai Suo
Keyword(s):  
Mass Spectrometry ◽  
Dna Polymerase ◽  
Conformational Changes ◽  
Protein Footprinting ◽  
Human Dna ◽  
Dna Polymerase Λ

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

2021 ◽  
Author(s):  
Niloofar Abolhasani Khaje ◽  
Alexander Eletsky ◽  
Sarah E. Biehn ◽  
Charles K. Mobley ◽  
Monique J. Rogals ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Protein Structure ◽  
Computational Modeling ◽  
Solvent Exposure ◽  
Uncharacterized Protein ◽  
Single Experiment ◽  
Protein Footprinting ◽  
Hydroxyl Radical Protein Footprinting ◽  
Unknown Structure

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.

scholarly journals Trifluoroethanol Partially Unfolds G93A SOD1 Leading to Protein Aggregation: A Study by Native Mass Spectrometry and FPOP Protein Footprinting

Biochemistry ◽  
2020 ◽  
Vol 59 (39) ◽  
pp. 3650-3659
Author(s):  
Ben Niu ◽  
Brian C. Mackness ◽  
Jill A. Zitzewitz ◽  
C. Robert Matthews ◽  
Michael L. Gross
Keyword(s):  
Mass Spectrometry ◽  
Protein Aggregation ◽  
Native Mass Spectrometry ◽  
Protein Footprinting ◽  
G93a Sod1
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