The Making of a Footprint in Protein Footprinting: A Review in Honor of Michael L. Gross

Abstract

Within the past decade protein footprinting in conjunction with mass spectrometry has become a powerful and versatile means to unravel the higher order structure of proteins. Footprintingbased approaches has demonstrated the capacity to inform on interaction sites and dynamic regions that participate in conformational changes. These findings when set in a biological perspective inform on protein folding/unfolding, protein-protein interactions, and protein-ligand interactions. In this review, we will look at the contribution of Dr. Michael L. Gross to protein footprinting approaches such as hydrogen deuterium exchange mass spectrometry and hydroxyl radical protein footprinting. This review details the development of novel footprinting methods as well as their applications to study higher order protein structure.

Developments in Hydrogen/Deuterium Exchange Mass Spectrometry

“…There were multiple more specific reviews of MS-based methods for structural biology, which included HDX MS, as applied to specific entities including macromolecular complexes − and protein interfaces as drug targets, amyloid fibrils, viral proteins, , G-protein coupled receptors, , vaccine development, and protein therapeutics . Several reviews compare and contrast HDX MS with footprinting methods such as covalent labeling, − and one review compared HDX MS and cryoEM . These combination-type reviews point again to the penetration of HDX MS applications into many other areas of science and away from isolation as an analytical curiosity.…”

Hydrogen-Deuterium Exchange Mass Spectrometry: A Novel Structural Biology Approach to Structure, Dynamics and Interactions of Proteins and Their Complexes

“…Still, HDX-MS is a good choice for studying hydrogen bonding networks and folding in proteins, especially when only a limited amount of sample is at one’s disposal. Applied in conjunction with other methods, like chemical cross-linking, HDX-MS helps elucidate structure and conformational dynamics in individual proteins and large protein complexes [ 102 ]. When analyzing protein complexes, binding or interaction sites can also be identified.…”

“…Selected protein modifications, like glycosylation and disulfide bonding, hinder proteolysis and/or mass analysis [ 26 ]. An exciting field of development is ’millisecond pulsed labeling’ that can reveal information about intrinsically disordered proteins and allosteric effects, and has the ability to detect co-existing folding states [ 66 , 102 , 110 , 111 , 112 , 113 , 114 ]; for millisecond labeling, microfluidic devices need to be applied [ 111 , 112 , 113 , 114 ].…”

Advances in mass spectrometry‐based footprinting of membrane proteins

“…Another is chemical labeling or footprinting that, via proteomic analysis of a labeled protein, offers sufficient spatial resolution to answer many structural biology questions. Labeling approaches include chemical crosslinking (XL) [12][13][14][15], hydrogen/deuterium exchange (HDX) [16][17][18][19], and chemical labeling [20] (often referred to as "covalent labeling" to distinguish it from HDX, but HDX also involves formation of "covalent" bonds where the bonding is reversible) [21][22][23]. Hydroxy radical footprinting (HRFP)can be accomplished by synchrotron radiolysis [24], fast photochemical oxidation of proteins (FPOP) [25,26], oxidation by plasma-generated OH radicals [27], photolysis of hydrogen peroxide by a discharge lamp from GenNext Technologies, Inc.…”