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

Noncovalent interactions are the keys to the structural organization of biomolecule e.g., proteins, glycans, lipids in the process of molecular recognition processes e.g., enzyme-substrate, antigen-antibody. Protein interactions lead to conformational changes, which dictate the functionality of that protein-protein complex. Besides biophysics techniques, noncovalent interaction and conformational dynamics, can be studied via mass spectrometry (MS), which represents a powerful tool, due to its low sample consumption, high sensitivity, and label-free sample. In this review, the focus will be placed on Matrix-Assisted Laser Desorption Ionization Mass Spectrometry (MALDI-MS) and its role in the analysis of protein-protein noncovalent assemblies exploring the relationship within noncovalent interaction, conformation, and biological function

The influence of a modified lipopolysaccharide O-antigen on the biosynthesis of xanthan in Xanthomonas campestris pv. campestris B100

Steffens T, Vorhölter F-J, Giampa M, Hublik G, Pühler A, Niehaus K. The influence of a modified lipopolysaccharide O-antigen on the biosynthesis of xanthan in Xanthomonas campestris pv. campestris B100. BMC Microbiology. 2016;16(1): 93.Background The exopolysaccharide xanthan is a natural product which is extensively used in industry. It is a thickening agent in many fields, from oil recovery to the food sector. Xanthan is produced by the Gram negative bacterium Xanthomonas campestris pv. campestris (Xcc). We analyzed the lipopolysaccharide (LPS) of three mutant strains of the Xcc wild type B100 to distinguish if the xanthan production can be increased when LPS biosynthesis is affected. Results The Xcc B100 O-antigen (OA) is composed of a linear main chain of rhamnose residues with N-acetylfucosamine (FucNAc) side branches at every second rhamnose. It is the major LPS constituent. The O-antigen was missing completely in the mutant strain H21012 (deficient in wxcB), since neither rhamnose nor FucNAc could be detected as part of the LPS by MALDI-TOF-MS, and only a slight amount of rhamnose and no FucNAc was found by GC analysis. The LPS of two other mutants was analyzed, Xcc H28110 (deficient in wxcK) and H20110 (wxcN). In both of them no FucNAc could be detected in the LPS fraction, while the rhamnose moieties were more abundant than in wild type LPS. The measurements were carried out by GC and confirmed by MALDI-TOF-MS analyses that indicated an altered OA in which the branches are missing, while the rhamnan main chain seemed longer than in the wild type. Quantification of xanthan confirmed our hypothesis that a missing OA can lead to an increased production of the extracellular polysaccharide. About 6.3 g xanthan per g biomass were produced by the Xcc mutant H21012 (wxcB), as compared to the wild type production of approximately 5 g xanthan per g biomass. In the two mutant strains with modified OA however, Xcc H28110 (wxcK) and Xcc H20110 (wxcN), the xanthan production of 5.5 g and 5.3 g, respectively, was not significantly increased. Conclusions Mutations affecting LPS biosynthesis can be beneficial for the production of the extracellular polysaccharide xanthan. However, only complete inhibition of the OA resulted in increased xanthan production. The inhibition of the FucNAc side branches did not lead to increased production, but provoked a novel LPS phenotype. The data suggests an elongation of the linear rhamnan main chain of the LPS OA in both the Xcc H28110 (wxcK) and Xcc H20110 (wxcN) mutant strains

Simulation Study of Photon-to-Digital Converter (PDC) Timing Specifications for LoLX Experiment

The Light only Liquid Xenon (LoLX) experiment is a prototype detector aimed to study liquid xenon (LXe) light properties and various photodetection technologies. LoLX is also aimed to quantify LXe's time resolution as a potential scintillator for 10~ps time-of-flight (TOF) PET. Another key goal of LoLX is to perform a time-based separation of Cerenkov and scintillation photons for new background rejection methods in LXe experiments. To achieve this separation, LoLX is set to be equipped with photon-to-digital converters (PDCs), a photosensor type that provides a timestamp for each observed photon. To guide the PDC design, we explore requirements for time-based Cerenkov separation. We use a PDC simulator, whose input is the light information from the Geant4-based LoLX simulation model, and evaluate the separation quality against time-to-digital converter (TDC) parameters. Simulation results with TDC parameters offer possible configurations supporting a good separation. Compared with the current filter-based approach, simulations show Cerenkov separation level increases from 54% to 71% when using PDC and time-based separation. With the current photon time profile of LoLX simulation, the results also show 71% separation is achievable with just 4 TDCs per PDC. These simulation results will lead to a specification guide for the PDC as well as expected results to compare against future PDC-based experimental measurements. In the longer term, the overall LoLX results will assist large LXe-based experiments and motivate the assembly of a LXe-based TOF-PET demonstrator system.Comment: 5 pages, 7 figure

Cognitive Dysfunction in Huntington's Disease: Mechanisms and Therapeutic Strategies Beyond BDNF

One of the main focuses in Huntington's disease (HD) research, as well as in most of the neurodegenerative diseases, is the development of new therapeutic strategies, as currently there is no treatment to delay or prevent the progression of the disease. Neuronal dysfunction and neuronal death in HD are caused by a combination of interrelated pathogenic processes that lead to motor, cognitive and psychiatric symptoms. Understanding how mutant huntingtin impacts on a plethora of cellular functions could help to identify new molecular targets. Although HD has been classically classified as a neurodegenerative disease affecting voluntary movement, lately cognitive dysfunction is receiving increased attention as it is very invalidating for patients. Thus, an ambitious goal in HD research is to find altered molecular mechanisms that contribute to cognitive decline. In this review we have focused on those findings related to corticostriatal and hippocampal cognitive dysfunction in HD, as well as on the underlying molecular mechanisms, which constitute potential therapeutic targets. These include alterations in synaptic plasticity, transcriptional machinery, and neurotrophic and neurotransmitter signaling. This article is protected by copyright. All rights reserved

Unravel the Local Complexity of Biological Environments by MALDI Mass Spectrometry Imaging

Classic metabolomic methods have proven to be very useful to study functional biology and variation in the chemical composition of different tissues. However, they do not provide any information in terms of spatial localization within fine structures. Matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI MSI) does and reaches at best a spatial resolution of 0.25 mu m depending on the laser setup, making it a very powerful tool to analyze the local complexity of biological samples at the cellular level. Here, we intend to give an overview of the diversity of the molecules and localizations analyzed using this method as well as to update on the latest adaptations made to circumvent the complexity of samples. MALDI MSI has been widely used in medical sciences and is now developing in research areas as diverse as entomology, microbiology, plant biology, and plant-microbe interactions, the rhizobia symbiosis being the most exhaustively described so far. Those are the fields of interest on which we will focus to demonstrate MALDI MSI strengths in characterizing the spatial distributions of metabolites, lipids, and peptides in relation to biological questions

Implementing Complementary Approaches to Shape the Mechanism of α-Synuclein Oligomerization as a Model of Amyloid Aggregation

Giampa M, Amundarain M, Herrera MG, Tonali NM, Dodero VI. Implementing Complementary Approaches to Shape the Mechanism of α-Synuclein Oligomerization as a Model of Amyloid Aggregation. Molecules. 2022;27(1): 88.The aggregation of proteins into amyloid fibers is linked to more than forty still incurable cellular and eurodegenerative diseases such as Parkinson’s disease (PD), multiple system atrophy, Alzheimer’s disease and type 2 diabetes, among thers. The process of amyloid formation is a main feature of cell degeneration and disease pathogenesis. Despite being methodologically challenging, a complete understanding of the molecular mechanism of aggregation, especially in the early stages, is essential to find new biological targets for innovative therapies. Here, we reviewed selected examples on α-syn showing how complementary approaches, which employ different biophysical techniques and models, can better deal with a comprehensive study of amyloid aggregation. In addition to the monomer aggregation and conformational transition hypothesis, we reported new emerging theories regarding the self-aggregation of α-syn, such as the alpha-helix rich tetramer hypothesis, whose destabilization induce monomer aggregation; and the liquid-liquid phase eparation hypothesis, which considers a phase separation of α-syn into liquid droplets as a primary event towards the evolution to aggregates. The final aim of this review is to show how multimodal methodologies provide a complete portrait of α-syn oligomerization and can be successfully extended to other protein aggregation diseases

Immersion by Rotation-Based Application of the Matrix for Fast and Reproducible Sample Preparations and Robust Results in Mass Spectrometry Imaging.

Schäfermann J, Kliewer G, Losch J, Bednarz H, Giampa M, Niehaus K. Immersion by Rotation-Based Application of the Matrix for Fast and Reproducible Sample Preparations and Robust Results in Mass Spectrometry Imaging. Journal of mass spectrometry. 2020;55(3): e4488.Automated matrix deposition for matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) is crucial for producing reproducible analyte ion signals. Here we report an innovative method employing an automated immersion apparatus, which enables a robust matrix deposition within 5 minutes and with scalable throughput by using MAPS matrix and non-polar solvents. MSI results received from mouse heart and rat brain tissues were qualitatively similar to those from nozzle sprayed samples with respect to peak number and quality of the ion images. Overall, the immersion-method enables a fast and careful matrix deposition and has the future potential for implementation in clinical tissue diagnostics. This article is protected by copyright. All rights reserved

Spatial evaluation of long-term metabolic changes induced by cisplatin nephrotoxicity

Sahin M, Neumann JM, Riefke B, et al. Spatial evaluation of long-term metabolic changes induced by cisplatin nephrotoxicity. Toxicology letters. 2020;334:36-43.Cisplatin is a widely used chemotherapeutic agent. However, it is causing nephrotoxic side effects including a reduced glomerular filtration rate and acute kidney injury. Although kidneys can recover to an extent from the treatment, long-term damage is possible. While a lot of research is focusing on short-term effects, little is known about adverse metabolic effects in the process of recovery. In this study, male Han Wistar rats were dosed with a single intraperitoneal injection of 3 mg/kg cisplatin. Urine and kidney samples were harvested 3, 8 and 26 days after administration. Tubular injury was demonstrated through urinary biomarkers. Complementing this, mass spectrometry imaging gives insight on molecular alterations on a spatial level, thus making it well suited to analyze short- and long-term disturbances. Various metabolic pathways seem to be affected, as changes in a wide range of metabolites were observed between treated and control animals. Besides previously reported early changes in kidney metabolism, unprecedented long-term effects were detected including deviation in nucleotides, antioxidants, and phospholipids. Copyright © 2020 Elsevier B.V. All rights reserved

Maleic anhydride proton sponge as a novel MALDI matrix for the visualization of small molecules (< 250 m/z) in brain tumors by routine MALDI ToF imaging mass spectrometry

Giampa M, Lissel M, Patschkowski T, et al. Maleic anhydride proton sponge as a novel MALDI matrix for the visualization of small molecules (&lt; 250 m/z) in brain tumors by routine MALDI ToF imaging mass spectrometry. Chemical Communications. 2016;52(63):9801-9804.A novel vacuum stable proton sponge, 4-maleicanhydridoproton sponge (MAPS), was prepared and applied as the matrix in Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging (MALDI-MSI) of an aggressive brain tumor tissue (glioblastoma multiforme). Ionic maps of lactate, 2-hydroxyglutarate and chloride anions (m/z 89, 147, 35, respectively) were obtained using a routine MALDI ToF mass spectrometer