Using Deuterium Exchange and Mass Spectrometry to Study Protein Structure

Abstract

Proteins are surely among nature’s most magical molecules. Linear polymers derived from a rather small, well-defined set of amino acids, they orchestrate every cellular process with exquisite selectivity and efficiency. While the order of amino acids, the protein’s primary sequence, is important; it is really the folding of the linear chain that brings together the key functional groups to make the protein biologically active. Mass spectrometry (MS) plays an important role in protein sequence determination, and in the identification of post-translational modification [1, 2], but for higher-order structural information biochemists turn to other types of spectroscopy: NMR, X-ray crystallography, circular dichroism (CD), neutron diffraction. The development of gentle ionization techniques for mass spectrometry, matrix-assisted laser desorption ionization (MALDI) and electrospray ionization (ESI), have tremendously expanded the impact mass spectrometry can have on protein chemistry. The majority of applications of these techniques remains in the area of primary structure determination. Increasingly, however, investigators are realizing that mass spectra can provide important clues about higher-order structure of proteins [3, 4, 5, 6, 7, 8, 9, 10]. The gentleness of the ionization may not disrupt many of the vital non-covalent interactions responsible for protein folding and function. The extreme importance of protein folding, coupled with the shortcomings of all existing methods of its investigation, will lead to an explosive growth in the application of mass spectrometry in this field over the next several years.