Structural proteomics and protein complexes - special issue.

Abstract

The field of structural proteomics encompasses a range of techniques that aim to unravel the mysteries of protein structure on a global scale. Through structural proteomics, a plethora of information can be obtained about proteins including how they function and the interacting partners essential for that function. Structural proteomics techniques include, but are not limited to, hydrogen deuterium exchange mass spectrometry (MS), cross-linking MS, ion mobility MS and native MS, which are supported by bioinformatics and computational modelling. The field emerged just over two decades ago and has enjoyed a rapid growth ever since. A recent Web of Science search for the term revealed nine publications and 27 citations in 1999, and 725 publications with over 38,000 citations in 2020. In this Special Issue, we are pleased to present four research articles and one technical brief from leading researchers in the field. Sharon and co-workers [1] describe the application of direct MS to the analysis of antibody-antigen complexes. The work makes use of a variant of native MS, which enables direct analysis of the antibody–antigen complex from the crude growth media, taking advantage of the fact that recombinant antibodies accumulate in the media. The authors were able to investigate various parameters including stability, affinity and specificity. The broad significance of this work derives from the importance of therapeutic antibodies in a range of diseases and more specifically the need for reliable and rapid quality assessment. More specifically, the authors demonstrate that the direct MS approach, which brings the analysis so close to the biology, offers many benefits and potential applications. Borchers and co-workers [2] apply structural proteomics to propose a potential mode of assembly of β-oligomers of the prion protein. These pathological oligomers play a central role in the development of prion diseases. In their article, the authors describe how cross-linking constraints elucidated by cross-linking MS informed subsequent discrete molecular dynamic simulations to provide models for monomer and dimer structures. The model was verified by hydrogen deuterium exchange MS, limited proteolysis and surface modification. The work is a great demonstration of a comprehensive structural proteomics approach combining a range of experimental techniques and computer modelling applied to an important biomedical challenge. Oldham and co-workers [3] reveal how carbene footprinting, a chemical labelling structural proteomics technique, could be used to map a specific interaction between elF4A helicase and an inhibitor, hippuristanol. They were able to map the binding site of the inhibitor to the C-terminal domain of the protein and additionally show conformational changes within the protein that were a direct result of ligand binding. Their work highlights the complementarity of structural proteomics MS techniques to other biophysical techniques. Jones and co-workers [4] focus on a challenge for the structural proteomics community, that is, the analysis of large MS datasets. They focused on data obtained from hydroxyl radical protein footprinting experiments and were able to decrease computational analysis time whilst simultaneously identifying more modified peptides using a novel cloud-based search engine termed Bolt. These leaps forward in computational analysis are essential to enable us to utilise fully the wealth of data structural proteomics provides. Finally, Heck and co-workers [5] use an integrative structural MS approach that combines traditional bottom-up proteomics with native MS and cross-linking MS to elucidate a structural model of the complement C7 protein. The work is a great demonstration of how multiple structural proteomics techniques can be combined to give a wealth of information about lesser characterised protein complex assemblies. We thank all the contributors to this Special Issue and the referees for their comprehensive and prompt reviews, and hope the readers enjoy the articles presented.