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.

High-Resolution Hydroxyl Radical Protein Footprinting: Biophysics Tool for Drug Discovery

2018 ◽  
Vol 47 (1) ◽  
pp. 315-333 ◽  
Author(s):  
Janna Kiselar ◽  
Mark R. Chance
Keyword(s):  
Protein Structure ◽  
High Resolution ◽  
Hydroxyl Radical ◽  
Solvent Accessibility ◽  
Side Chains ◽  
Protein Footprinting ◽  
Hydroxyl Radical Protein Footprinting ◽  
Wide Range ◽  
Hydroxyl Radical Footprinting

Hydroxyl radical footprinting (HRF) of proteins with mass spectrometry (MS) is a widespread approach for assessing protein structure. Hydroxyl radicals react with a wide variety of protein side chains, and the ease with which radicals can be generated (by radiolysis or photolysis) has made the approach popular with many laboratories. As some side chains are less reactive and thus cannot be probed, additional specific and nonspecific labeling reagents have been introduced to extend the approach. At the same time, advances in liquid chromatography and MS approaches permit an examination of the labeling of individual residues, transforming the approach to high resolution. Lastly, advances in understanding of the chemistry of the approach have led to the determination of absolute protein topologies from HRF data. Overall, the technology can provide precise and accurate measures of side-chain solvent accessibility in a wide range of interesting and useful contexts for the study of protein structure and dynamics in both academia and industry.

scholarly journals Protein structure characterization with mass spectrometry

2004 ◽  
Vol 18 (1) ◽  
pp. 37-47 ◽  
Author(s):  
Richard Kriwacki ◽  
Nichole Reisdorph ◽  
Gary Siuzdak
Keyword(s):  
Mass Spectrometry ◽  
Protein Structure ◽  
Chemical Modification ◽  
Protein Identification ◽  
Higher Order ◽  
Order Structure ◽  
Mass Analysis ◽  
Analysis Techniques ◽  
Protein Mass ◽  
Mass Mapping

Mass spectrometry is now commonly being used to determine both the primary and higher order structures of proteins. The basis for these investigations lies in the ability of mass analysis techniques to detect changes in protein conformation under differing conditions. These experiments can be conducted on proteins alone (with no modifying substance present) or in combination with proteolytic digestion or chemical modification. In addition to primary structure determination, proteases and chemical modification have long been used as probes of higher order structure, an approach that has been recently rejuvenated with the emergence of highly sensitive and accurate mass analysis techniques. Here, we review the application of proteases as probes of native structure and illustrate key concepts in the combined use of proteolysis, chemical modification, and mass spectrometry. For example, protein mass maps have been used to probe the structure of a protein/protein complex in solution (cell cycle regulatory proteins, p21 and Cdk2). This approach was also used to study the protein/protein complexes that comprise viral capsids, including those of the common cold virus where, in addition to structural information, protein mass mapping revealed mobile features of the viral proteins. Protein mass mapping clearly has broad utility in protein identification and profiling, yet its accuracy and sensitivity is also allowing for further exploration of protein structure and even structural dynamics.

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