Project description:Background: Systemic light chain amyloidosis is a protein misfolding disorder characterized by deposition of clonal immunoglobulin light chains in vital organs. To date, little is known about the contribution of light chain constant domain mutations in thermodynamic stability and amyloidogenicity.Methods: In 89 patients, RNA-based full-length light chain repertoire sequencing with Oxford Nanopore was performed, in addition to Illumina sequencing and mass spectrometric detection of light chain protein in serum and amyloid deposits. Computational methods for conservation, free energy calculation, and molecular dynamics simulations were applied to investigate the thermodynamic stability.Results: Monoclonal light chain detection rate was 95.4%, and sequences showed 100% identity with Illumina in all patients. Light chain protein was specifically detectable by mass spectrometry in serum and amyloid deposits. Lambda constant domain mutations were present in 10%, while no kappa constant domain mutations were detected. Fold free energy change and molecular dynamics simulations indicate potential light chain stabilizing or destabilizing effects of detected constant domain mutations.Conclusion: Current findings highlight the importance of routinely implementing full-length light chain sequencing in plasma cell dyscrasias, particularly light chain amyloidosis to account for the potential impact of constant domain mutations on light chain stability and amyloidogenicity.

2026-05-06 | PXD077140 | Pride

Proteomes of Wenzhouxiangella isolate grown on three substrates

Project description:A new haloalkaliphilic species of Wenzhouxiangella, strain AB-CW3 was isolated from a system of alkaline soda lakes in the Kulunda Steppe. Its complete, circular genome was assembled from combined nanopore and illumina sequencing and its proteome was determined for three different experimental conditions: growth on Staphylococcus cells, casein, or peptone. AB-CW3 is an aerobic bacterium feeding mainly on proteins and peptides.

2020-11-03 | PXD021036 | Pride

LC-MS/MS of autotrophic culture KS, that performs nitrate reduction coupled to iron(II) oxidation (NDFO)

Project description:Nitrate-reducing iron(II)-oxidizing bacteria are widespread in the environment contribute to nitrate removal and influence the fate of the greenhouse gases nitrous oxide and carbon dioxide. The autotrophic growth of nitrate-reducing iron(II)-oxidizing bacteria is rarely investigated and poorly understood. The most prominent model system for this type of studies is enrichment culture KS, which originates from a freshwater sediment in Bremen, Germany. To gain insights in the metabolism of nitrate reduction coupled to iron(II) oxidation under in the absence of organic carbon and oxygen limited conditions, we performed metagenomic, metatranscriptomic and metaproteomic analyses of culture KS. Raw sequencing data of 16S rRNA amplicon sequencing, shotgun metagenomics (short reads: Illumina; long reads: Oxford Nanopore Technologies), metagenome assembly, raw sequencing data of shotgun metatranscriptomes (2 conditions, triplicates) can be found at SRA in https://www.ncbi.nlm.nih.gov/bioproject/PRJNA682552. This dataset contains proteomics data for 2 conditions (heterotrophic and autotrophic growth conditions) in triplicates.

2021-05-17 | PXD023186 | Pride

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