Chapter

Modern Proteomics – Sample Preparation, Analysis and Practical Applications

Volume 919 of the series Advances in Experimental Medicine and Biology pp 397-431

Date:

Protein Structural Analysis via Mass Spectrometry-Based Proteomics

  • Antonio ArtiguesAffiliated withDepartment of Biochemistry and Molecular Biology, University of Kansas Medical Center Email author 
  • , Owen W. NadeauAffiliated withDepartment of Biochemistry and Molecular Biology, University of Kansas Medical Center
  • , Mary Ashley RimmerAffiliated withDepartment of Biochemistry and Molecular Biology, University of Kansas Medical Center
  • , Maria T. VillarAffiliated withDepartment of Biochemistry and Molecular Biology, University of Kansas Medical Center
  • , Xiuxia DuAffiliated withDepartment of Bioinformatics and Genomics, University of North Carolina at Charlotte
  • , Aron W. FentonAffiliated withDepartment of Biochemistry and Molecular Biology, University of Kansas Medical Center
  • , Gerald M. CarlsonAffiliated withDepartment of Biochemistry and Molecular Biology, University of Kansas Medical Center

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Abstract

Modern mass spectrometry (MS) technologies have provided a versatile platform that can be combined with a large number of techniques to analyze protein structure and dynamics. These techniques include the three detailed in this chapter: (1) hydrogen/deuterium exchange (HDX), (2) limited proteolysis, and (3) chemical crosslinking (CX). HDX relies on the change in mass of a protein upon its dilution into deuterated buffer, which results in varied deuterium content within its backbone amides. Structural information on surface exposed, flexible or disordered linker regions of proteins can be achieved through limited proteolysis, using a variety of proteases and only small extents of digestion. CX refers to the covalent coupling of distinct chemical species and has been used to analyze the structure, function and interactions of proteins by identifying crosslinking sites that are formed by small multi-functional reagents, termed crosslinkers. Each of these MS applications is capable of revealing structural information for proteins when used either with or without other typical high resolution techniques, including NMR and X-ray crystallography.

Keywords

Protein structural analysis Hydrogen/Deuterium Exchange (HDX) Limited proteolysis Chemical Crosslinking (CX)