Emerging Role of Mass Spectrometry‐Based Structural Proteomics in Elucidating Intrinsic Disorder in Proteins

Abstract

Inherent disorder is an integral part of all proteomes, represented as fully or partially unfolded proteins. The lack of order in intrinsically disordered proteins (IDPs) results in an incredibly flexible, floppy, and heterogeneous ensemble, contrary to the well‐structured and unique organization of folded proteins. Despite such unusual demeanor, IDPs are crucial for numerous cellular processes and are increasingly being associated with disease‐causing pathologies. These warrant more intensive investigation of this atypical class of protein. Traditional biophysical tools, however, fall short of analyzing IDPs, thus making their structure‐function characterization challenging. Mass spectrometry (MS) in recent years has evolved as a valuable tool for elucidating the unusual conformational facets of IDPs. In this review, the features of advanced MS techniques such as Hydrogen‐deuterium exchange (HDX)‐MS, native MS, limited proteolysis (LiP)‐MS, chemical cross‐linking (XL)‐MS, and Fast photochemical oxidation of proteins (FPOP)‐MS are briefly discussed. Recent MS studies on IDPs and the unique advantages/shortfalls associated with the above methods while evaluating structural proteomics of IDPs, are illustrated. Eventually the future scope of the MS methods in further decoding the unexplored landscapes of IDPs is presented.

Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems

“… 405 , 406 Of the available structural characterization techniques, HDX-MS is particularly well-suited to the study of IDPs because it can detect and resolve changes in protection resulting from weak or transient hydrogen bonding without perturbing the IPD structural ensemble. 407 …”

“…In the case of IDPs, it is challenging to accurately create and measure the exchange of a truly unstructured reference. 407 The k ch estimates are commonly calculated from values obtained from extensive NMR studies of unprotected amides. In this method, the intrinsic exchange rate for a particular amide is predicted by accounting for its position in the sequence and all relevant solution conditions.…”

Insight to Functional Conformation and Noncovalent Interactions of Protein-Protein Assembly Using MALDI Mass Spectrometry

“…Soft ionization processes, such as electrospray ionization (ESI) and MALDI, are employed for structural analysis of the protein elucidating not only noncovalent interactions but also conformational changes of the proteins. For such purpose, several techniques such as hydrogen/deuterium exchange (HDX), native MS, limited proteolysis, cross-linking, and fast photochemical derivatizations are applied to investigate the relationship function and conformation [16,83].…”

Diethylpyrocarbonate Footprints a Membrane Protein in Micelles

“…Current structural techniques for MPs exist in two major categories: (1) rapid, low-resolution techniques , (e.g., intrinsic fluorescence, circular dichroism (CD), dynamic light scattering (DLS), differential scanning calorimetry (DSC), and activity assays), and (2) time and sample intensive, high-resolution techniques (e.g., X-ray crystallography, NMR, and cryo-electron microscopy (cryo-EM)). Methods from the first category provide an ensemble average of structures without revealing detailed local conformational change.…”