Proper evaluation of chemical cross-linking-based spatial restraints improves the precision of modeling homo-oligomeric protein complexes

The Cortisol Levels, Histology, and Fine Structure of Various Tissues of Fish Gambusia affinis (Baird and Girard, 1853) after Exposure to Lead

Background

Aquatic organisms demonstrate a high vulnerability to mortality when exposed to Pb, even at low concentrations. The objective of this investigation is to ascertain the histopathological alterations and cortisol concentrations in diverse tissues of Gambusia affinis, with a specific focus on the eggs and larvae, following exposure to varying concentrations of PbCl2.

Methods

Adult specimens of G. affinis measuring 5-6 cm in length were obtained from a commercial fish breeding facility. A total of 8 fish with a 1 : 1 ratio of 4 pairs of broodstock were placed in an 8-liter aquarium. Following the adaptation phase, the broodstock underwent a spawning process that lasted for a duration of 7 days. Throughout the spawning process, assessments were conducted on the progression of the abdominal growth of the broodstock. Eggs ready to hatch and Gambusia larvae were taken and exposed to 0.1 mg/L PbCl2, 1 mg/L PbCl2, and control (without PbCl2) for 24 hours, with three replications. At the end of the experiment, histopathological analysis was conducted using the hematoxylin Ehrlich-eosin staining method and scanning electron microscopic (SEM) observation. The levels of Pb in gills were determined by employing atomic absorption spectrophotometer. The cortisol concentration in organ samples of fish was determined through the utilization of a cortisol ELISA Kit.

Results

The findings of this investigation demonstrated an important bioaccumulation occurrence of Pb within the gills of Gambusia fish that were specifically subjected to 0.1 and 1 mg/L PbCl2. The histological structures of eggs and larvae that were subjected to PbCl2 exhibited impairment in comparison to the control group. The present study observed a significant elevation in cortisol levels among fish specimens that were subjected to PbCl2 exposure.

Conclusions

The findings of this investigation suggest that the occurrence of Pb is linked to a rise in cortisol concentrations in various organs of G. affinis larvae. Furthermore, the research indicates that the exposure to Pb has a notable impact on the histological alterations in the eggs and larvae of Gambusia fish, implying that they are undergoing stress as a result of the Pb exposure.

What's the defect? Using mass defects to study oligomerization of membrane proteins and peptides in nanodiscs with native mass spectrometry

Many membrane proteins form functional complexes that are either homo- or hetero-oligomeric. However, it is challenging to characterize membrane protein oligomerization in intact lipid bilayers, especially for polydisperse mixtures. Native mass spectrometry of membrane proteins and peptides inserted in lipid nanodiscs provides a unique method to study the oligomeric state distribution and lipid preferences of oligomeric assemblies. To interpret these complex spectra, we developed novel data analysis methods using macromolecular mass defect analysis. Here, we provide an overview of how mass defect analysis can be used to study oligomerization in nanodiscs, discuss potential limitations in interpretation, and explore strategies to resolve these ambiguities. Finally, we review recent work applying this technique to studying formation of antimicrobial peptide, amyloid protein, and viroporin complexes with lipid membranes.

Structural and dynamic insights into α-synuclein dimer conformations

Parkinson disease is associated with the aggregation of the protein α-synuclein. While α-synuclein can exist in multiple oligomeric states, the dimer has been a subject of extensive debates. Here, using an array of biophysical approaches, we demonstrate that α-synuclein in vitro exhibits primarily a monomer-dimer equilibrium in nanomolar concentrations and up to a few micromolars. We then use spatial information from hetero-isotopic cross-linking mass spectrometry experiments as restrains in discrete molecular dynamics simulations to obtain the ensemble structure of dimeric species. Out of eight structural sub-populations of dimers, we identify one that is compact, stable, abundant, and exhibits partially exposed β-sheet structures. This compact dimer is the only one where the hydroxyls of tyrosine 39 are in proximity that may promote dityrosine covalent linkage upon hydroxyl radicalization, which is implicated in α-synuclein amyloid fibrils. We propose that this α-synuclein dimer features etiological relevance to Parkinson disease.

Leveraging crosslinking mass spectrometry in structural and cell biology

Crosslinking mass spectrometry (crosslinking-MS) is a versatile tool providing structural insights into protein conformation and protein-protein interactions. Its medium-resolution residue-residue distance restraints have been used to validate protein structures proposed by other methods and have helped derive models of protein complexes by integrative structural biology approaches. The use of crosslinking-MS in integrative approaches is underpinned by progress in estimating error rates in crosslinking-MS data and in combining these data with other information. The flexible and high-throughput nature of crosslinking-MS has allowed it to complement the ongoing resolution revolution in electron microscopy by providing system-wide residue-residue distance restraints, especially for flexible regions or systems. Here, we review how crosslinking-MS information has been leveraged in structural model validation and integrative modeling. Crosslinking-MS has also been a key technology for cell biology studies and structural systems biology where, in conjunction with cryoelectron tomography, it can provide structural and mechanistic insights directly in situ.

Modeling and Structure Determination of Homo-Oligomeric Proteins: An Overview of Challenges and Current Approaches

Protein homo-oligomerization is a very common phenomenon, and approximately half of proteins form homo-oligomeric assemblies composed of identical subunits. The vast majority of such assemblies possess internal symmetry which can be either exploited to help or poses challenges during structure determination. Moreover, aspects of symmetry are critical in the modeling of protein homo-oligomers either by docking or by homology-based approaches. Here, we first provide a brief overview of the nature of protein homo-oligomerization. Next, we describe how the symmetry of homo-oligomers is addressed by crystallographic and non-crystallographic symmetry operations, and how biologically relevant intermolecular interactions can be deciphered from the ordered array of molecules within protein crystals. Additionally, we describe the most important aspects of protein homo-oligomerization in structure determination by NMR. Finally, we give an overview of approaches aimed at modeling homo-oligomers using computational methods that specifically address their internal symmetry and allow the incorporation of other experimental data as spatial restraints to achieve higher model reliability.

A non-redundant dataset of inter-residue lysine-lysine solvent accessible surface distances in homo-oligomeric protein complexes

This article contains inter-residue solvent accessible surface distances between lysines in a comprehensive dataset homo-oligomeric protein complex structures, downloaded from 3D Complex database. Solvent Accessible Surface Distances were calculated with Jwalk algorithm. To avoid unnecessary redundancy due to symmetry, we calculated only distances originating from the first subunit of each protein complex. Redundancy was further reduced by including only the shortest of the two possible inter-subunit alternatives in the final non-redundant dataset. For each protein complexes we also calculated weight ob subunits, number of lysines radius of gyration and average distances.

This data can be used for structural analyses of homo-oligomeric protein complexes and for further optimization of distance-based restraints, such as those based on data obtained from chemical cross-linking coupled with mass spectrometry.