Advances in radical probe mass spectrometry for protein footprinting in chemical biology applications

2014 ◽  
Vol 43 (10) ◽  
pp. 3244 ◽  
Author(s):  
Simin D. Maleknia ◽  
Kevin M. Downard
Keyword(s):  
Mass Spectrometry ◽  
Chemical Biology ◽  
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.

Lipid Cell Biology: A Focus on Lipids in Cell Division

2018 ◽  
Vol 87 (1) ◽  
pp. 839-869 ◽  
Author(s):  
Elisabeth M. Storck ◽  
Cagakan Özbalci ◽  
Ulrike S. Eggert
Keyword(s):  
Mass Spectrometry ◽  
Cell Division ◽  
Cell Biology ◽  
Chemical Biology ◽  
Structural Integrity ◽  
Advanced Imaging ◽  
Functional Roles ◽  
Lipid Interactions ◽  
Cellular Processes ◽  
Alkyl Side Chains

Cells depend on hugely diverse lipidomes for many functions. The actions and structural integrity of the plasma membrane and most organelles also critically depend on membranes and their lipid components. Despite the biological importance of lipids, our understanding of lipid engagement, especially the roles of lipid hydrophobic alkyl side chains, in key cellular processes is still developing. Emerging research has begun to dissect the importance of lipids in intricate events such as cell division. This review discusses how these structurally diverse biomolecules are spatially and temporally regulated during cell division, with a focus on cytokinesis. We analyze how lipids facilitate changes in cellular morphology during division and how they participate in key signaling events. We identify which cytokinesis proteins are associated with membranes, suggesting lipid interactions. More broadly, we highlight key unaddressed questions in lipid cell biology and techniques, including mass spectrometry, advanced imaging, and chemical biology, which will help us gain insights into the functional roles of lipids.

scholarly journals A Pragmatic Guide to Enrichment Strategies for Mass Spectrometry-based Glycoproteomics

2020 ◽  
pp. mcp.R120.002277 ◽  
Author(s):  
Nicholas M Riley ◽  
Carolyn R Bertozzi ◽  
Sharon J Pitteri
Keyword(s):  
Mass Spectrometry ◽  
Molecular Biology ◽  
Chemical Biology ◽  
Hydrophilic Interaction Chromatography ◽  
Porous Graphitic Carbon ◽  
Graphitic Carbon ◽  
Hydrophilic Interaction ◽  
Chemical Coupling ◽  
Modern Mass ◽  
Enrichment Strategy

Glycosylation is a prevalent, yet heterogeneous modification with a broad range of implications in molecular biology. This heterogeneity precludes enrichment strategies that can be universally beneficial for all glycan classes. Thus, choice of enrichment strategy has profound implications on experimental outcomes. Here we review common enrichment strategies used in modern mass spectrometry (MS)-based glycoproteomic experiments, including lectins and other affinity chromatographies, hydrophilic interaction chromatography (HILIC) and its derivatives, porous graphitic carbon (PGC), reversible and irreversible chemical coupling strategies, and chemical biology tools that often leverage bioorthogonal handles. Interest in glycoproteomics continues to surge as MS instrumentation and software improve, so this review aims to help equip researchers with necessary information to choose appropriate enrichment strategies that best complement these efforts.

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 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

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.

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