Native Ubiquitin Structural Changes Resulting from Complexation with β-Methylamino-l-alanine (BMAA)

Surface-Induced Unfolding Reveals Unique Structural Features and Enhances Machine Learning Classification Models

Native ion mobility-mass spectrometry combined with collision-induced unfolding (CIU) is a powerful analytical method for protein characterization, offering insights into structural stability and enabling the differentiation of analytes with similar mass and mobility. A surface-induced dissociation (SID) device was recently commercialized, enabling broader adoption of SID measurements and surface-induced unfolding (SIU). This study evaluates SIU, benchmarking its reproducibility and performance against CIU on a Waters CyclicIMS ion mobility-mass spectrometer. Reproducibility studies were conducted on model proteins, including β-lactoglobulin (β-lac), bovine serum albumin (BSA), and immunoglobulin G1 kappa (IgG1κ). SIU and CIU exhibited comparable reproducibility, with root-mean-square deviation (RMSD) values averaging less than 4% across multiple charge states. Notably, SIU achieved unfolding transitions at lower lab-frame energies, enhancing sensitivity to subtle structural differences and providing additional analytical information, such as unique high arrival time unfolding features and additional unfolding transitions. Furthermore, the differentiation of closely related protein subclasses, such as IgG1κ and IgG4κ, was improved with SIU, as evidenced by the enhancement of supervised machine learning models for IgG subclass classifications. SIU-trained models outperformed or matched CIU-trained models, achieving high cross-validation accuracies (>90%) and robust classifications of biotherapeutics Adalimumab and Nivolumab. This work establishes SIU as a complementary and efficient alternative to CIU, offering improved sensitivity and analytical depth without loss in reproducibility. This work highlights the benefits of including SIU in protein characterization workflows, particularly in high-throughput and machine learning-guided applications.

Accessing Different Protein Conformer Ensembles with Tunable Capillary Vibrating Sharp-Edge Spray Ionization

Capillary vibrating sharp-edge spray ionization (cVSSI) has been used to control the droplet charging of nebulized microdroplets and monitor effects on protein ion conformation makeup as determined by mass spectrometry (MS). Here it is observed that the application of voltage results in noticeable differences to the charge state distributions (CSDs) of ubiquitin ions. The data can be described most generally in three distinct voltage regions: Under low-voltage conditions (<+200 V, LV regime), low charge states (2+ to 4+ ions) dominate the mass spectra. For midvoltage conditions (+200 to +600 V, MV regime), higher charge states (7+ to 12+ ions) are observed. For high-voltage conditions (>+600 V, HV regime), the "nano-electrospray ionization (nESI)-type distribution" is achieved in which the 6+ and 5+ species are observed as the dominant ions. Analysis of these results suggests that different pathways to progeny nanodroplet production result in the observed ions. For the LV regime, aerodynamic breakup leads to low charge progeny droplets that are selective for the native solution conformation ensemble of ubiquitin (minus multimeric species). In the MV regime, the large droplets persist for longer periods of time, leading to droplet heating and a shift in the conformation ensemble to partially unfolded species. In the HV regime, droplets access progeny nanodroplets faster, leading to native conformation ensemble sampling as indicated by the observed nESI-type CSD. The notable observation of limited multimer formation and adduct ion formation in the LV regime is hypothesized to result from droplet aero breakup resulting in protein and charge carrier partitioning in sampled progeny droplets. The tunable droplet charging afforded by cVSSI presents opportunities to study the effects of the droplet charge, droplet size, and mass spectrometer inlet temperature on the conformer ensemble sampled by the mass spectrometer. Additionally, the approach may provide a tool for rapid comparison of protein stabilities.

Roughhousing with Ions: Surface-Induced Dissociation and Electron Capture Dissociation as Diagnostics of Q-Cyclic IMS-TOF Instrument Tuning Gentleness

Native mass spectrometry can characterize a range of biomolecular features pertinent to structural biology, including intact mass, stoichiometry, ligand-bound states, and topology. However, when an instrument's ionization source is tuned to maximize signal intensity or adduct removal, it is possible that the biomolecular complex's tertiary and quaternary structures can be rearranged in a way that no longer reflect its native-like conformation. This could affect downstream ion activation experiments, leading to erroneous conclusions about the native-like structure. One activation strategy is surface-induced dissociation (SID), which generally causes native-like protein complexes to dissociate along the weakest subunit interfaces, revealing critical information about the complex's native-like topology and subunit connectivity. If the quaternary structure has been disturbed, then the SID fingerprint will shift as well. Thus, SID was used to diagnose source-induced quaternary structure rearrangement and help tune an instrument's source and other upstream transmission regions to strike the balance between signal intensity, adduct removal, and conserving the native-like structure. Complementary to SID, electron-capture dissociation (ECD) can also diagnose rearranged quaternary structures and was used after in-source activation to confirm that the subunit interfaces were rearranged, opening the structure to electron capture and subsequent dissociation. These results provide a valuable guide for new practitioners of native mass spectrometry and highlight the importance of using standard protein complexes when tuning new instrument platforms for optimal native mass spectrometry performance.

How does the neurotoxin β-N-methylamino-L-alanine exist in biological matrices and cause toxicity?

The neurotoxin β-N-methylamino-L-alanine (BMAA) has been deemed as a risk factor for some neurodegenerative diseases such as amyotrophic lateral sclerosis/parkinsonism dementia complex (ALS/PDC). This possible link has been proved in some primate models and cell cultures with the appearance that BMAA exposure can cause excitotoxicity, formation of protein aggregates, and/or oxidative stress. The neurotoxin BMAA extensively exists in the environment and can be transferred through the food web to human beings. In this review, the occurrence, toxicological mechanisms, and characteristics of BMAA were comprehensively summarized, and proteins and peptides were speculated as its possible binding substances in biological matrices. It is difficult to compare the published data from previous studies due to the inconsistent analytical methods and components of BMAA. The binding characteristics of BMAA should be focused on to improve our understanding of its health risk to human health in the future.

Neuropathological Mechanisms of β-N-Methylamino-L-Alanine (BMAA) with a Focus on Iron Overload and Ferroptosis

The incidence of neurodegenerative diseases and cyanobacterial blooms is concomitantly increasing worldwide. The cyanotoxin β-N-methylamino-L-alanine (BMAA) is produced by most of the Cyanobacteria spp. This cyanotoxin is described as a potential environmental etiology factor for some sporadic neurodegenerative diseases. Climate change and eutrophication significantly increase the frequency and intensity of cyanobacterial bloom in water bodies. This review evaluates different neuropathological mechanisms of BMAA at molecular and cellular levels and compares the related studies to provide some useful recommendations. Additionally, the structure and properties of BMAA as well as its microbial origin, especially by gut bacteria, are also briefly covered. Unlike previous reviews, we hypothesize the possible neurotoxic mechanism of BMAA through iron overload. We also discuss the involvement of BMAA in excitotoxicity, TAR DNA-binding protein 43 (TDP-43) translocation and accumulation, tauopathy, and other protein misincorporation and misfolding.