The peroxiredoxins are a well characterised family of toroidal proteins which can self-assemble into a striking array of quaternary structures, including protein nanotubes, making them attractive as building blocks for nanotechnology. Tools to characterise these assemblies are currently scarce. Here, assemblies of peroxiredoxin proteins were examined using native mass spectrometry and complementary solution techniques. We demonstrated unequivocally that tube formation is fully reversible, a useful feature in a molecular switch. Simple assembly of individual toroids was shown to be tunable by pH and the presence of a histidine tag. Collision induced dissociation experiments on peroxiredoxin rings revealed a highly unusual symmetrical disassembly pathway, consistent with the structure disassembling as a hexamer of dimers. This study provides the foundation for the rational design and precise characterisation of peroxiredoxin protein structures where self-assembly can be harnessed as a key feature for applications in nanotechnology.
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http://dx.doi.org/10.1039/c8sc01379a | DOI Listing |
TDP-43 is linked to human diseases such as amyotrophic lateral sclerosis (ALS) and frontotemporal degeneration (FTD). Expression of TDP-43 in yeast is known to be toxic, cause cells to elongate, form liquid-like aggregates, and inhibit autophagy and TOROID formation. Here, we used the yeast model of disorders of inborn errors of metabolism, previously shown to lead to intracellular adenine accumulation and adenine amyloid-like fiber formation, to explore interactions with TDP-43.
View Article and Find Full Text PDFBiochem Biophys Res Commun
January 2025
Center of Protein Studies, Faculty of Biology, Havana University, Havana, Cuba.
Sticholysin I and II (St I/II) belong to the actinoporins family; these proteins form pores in host cell membranes by binding their N-terminal segment to the membrane, leading to protein-lipid (toroidal) pores. Peptides derived from actinoporins pore-forming domains replicate their folding properties and permeabilizing effects. Despite the advances in understanding how these proteins and peptides mediate pore formation, the role of different N-terminal segments in inducing membrane curvature is still unclear.
View Article and Find Full Text PDFJ Chem Phys
October 2024
Biophysical and Computational Chemistry Laboratory, Department of Chemistry, National Institute of Technology Karnataka, Surathkal, Mangalore 575 025, Karnataka, India.
Using a well-developed reaction coordinate in umbrella sampling, we studied the single peptide permeation through a model cancerous cell membrane, varying the hydrophilicity and the charge of the peptides. Two peptides, melittin and pHD108, were studied. The permeation mechanism differs from a barrel-stave-like mechanism to toroidal pore and vesicle formation based on the number and the placement of the hydrophilic amino acids in the peptide.
View Article and Find Full Text PDFChemistryOpen
December 2024
The College of Computer Science and Technology, Jilin University, Changchun, Jilin, China.
The surface area of a molecule, an inherent geometric property of its structure, plays important roles in its solvation and functioning. Here we present an accurate and robust program, sesA, for the analytic computation of solvent-excluded surface (SES) areas. The accuracy and robustness are achieved through the analytic computations of all the solvent-accessible surface (SAS) regions for a surface atom and probe-probe intersections.
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