Mapping the allosteric effects that define functional activity of SARS-CoV-2 specific antibodies

Previous studies on the structural relationship between human antibodies and SARS-CoV-2 have focused on generating static snapshots of antibody complexes with the Spike trimer. However, antibody-antigen interactions are dynamic, with significant binding-induced allosteric effects on conformations of antibody and its target antigen. In this study, we employ hydrogen-deuterium exchange mass spectrometry, in vitro assays, and molecular dynamics simulations to investigate the allosteric perturbations linked to binding events between a group of human antibodies with differential functional activities, and the Spike trimer from SARS-CoV-2. Our investigations have revealed key dynamic features that define weakly or moderately neutralizing antibodies versus those with strong neutralizing activity. These results provide mechanistic insights into the functional modes of human antibodies against COVID-19, and provide a rationale for effective antiviral strategies.TeaserDifferent neutralizing antibodies induce site-specific allosteric effects across SARS-CoV-2 Spike protein

HDfleX: Software for flexible high structural resolution of hydrogen/deuterium-exchange mass spectrometry data

Hydrogen/deuterium-exchange mass spectrometry (HDX-MS) experiments on protein structures can be performed at three levels: (1) by enzymatically digesting labelled proteins and analyzing the peptides (bottom-up), (2) by further fragmenting peptides following digestion (middle-down), and (3) by fragmenting the intact labelled protein (top-down), using soft gas-phase fragmentation methods, such as electron transfer dissociation (ETD). However, to the best of our knowledge, the software packages currently available for the analysis of HDX-MS data do not enable the peptide- and ETD-levels to be combined - they can only be analyzed separately. Thus, we developed HDfleX - a standalone application for the analysis of flexible high structural resolution of HDX-MS data, which allows data at any level of structural resolution (intact protein, peptide, fragment) to be merged. HDfleX features rapid experimental data fitting, robust statistical significance analyses and optional methods for theoretical intrinsic calculations and a novel empirical correction for comparison between solution conditions.

Structural Proteomics: Detection of Neurodegenerative Protein Modifications

: For decades now, neurodegenerative disorders have been explored, but their prompt detection is still very strenuous due to the complexity of the brain. This entails the demand for identification and development of clinical biomarkers in order to comply with the criteria of precision, specificity and repeatability. The use of rapidly evolving technologies such as mass spectrometry (MS) in proteomics has opened new ways to speed up the discovery of biomarkers, both for diagnostic and prognostic purposes. The wide range of possibilities for the detection of differentially expressed proteins in specific diseases has been opened by several novel proteomic techniques such as cross-linking mass spectrometry, hydrogen-deuterium exchange mass spectrometry, protein foot printing and more. Still, much research is required to give a deep insight into the complex system of the brain and its related disorders for unraveling prognostic and diagnostic biomarkers, which can be used to either enhance a certain function of our brain or to cure a particular disease/disorder. This review summarizes the latest developments in neuroproteomics and analyzes existing and potential directions for the discovery of biomarkers for neurodegenerative diseases.