Publications by authors named "Shahram Mesdaghi"
Article Synopsis
- - Albinism is caused by a variety of genes (21 identified), with most cases following an autosomal recessive inheritance pattern, though one form is X-linked; about 70% of cases can be diagnosed through genetic analysis.
- - Of the undiagnosed cases, roughly 15% carry one pathogenic variant but may have undiscovered variants in non-coding regions; this research involved sequencing a group of 122 heterozygous patients.
- - From the study, 12 patients received additional diagnoses based on non-coding variants that affected RNA splicing, highlighting the need to investigate non-coding regions to improve diagnostic rates for genetic diseases like albinism.
Recent studies have indicated that the human amyloidogenic protein medin is associated with a range of vascular diseases, including aortic aneurysms, vascular dementia, and Alzheimer's disease. Medin accumulates in the vasculature with age, leading to endothelial dysfunction through oxidative and nitrative stress and inducing pro-inflammatory activation. Medin is a cleavage product from the C2 domain of MfgE8.
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- The 2022 CASP experiment introduced a new section focused on generating multiple conformations for protein and RNA structures, with partial success for four out of nine targets.
- Enhanced sampling techniques using AlphaFold2 proved to be the most effective for protein structures, successfully capturing significant conformational changes from mutations.
- Challenges remain, particularly with handling sparse experimental data and modeling RNA/protein complexes, but there is optimism that these issues can be resolved.
The results of tertiary structure assessment at CASP15 are reported. For the first time, recognizing the outstanding performance of AlphaFold 2 (AF2) at CASP14, all single-chain predictions were assessed together, irrespective of whether a template was available. At CASP15, there was no single stand-out group, with most of the best-scoring groups-led by PEZYFoldings, UM-TBM, and Yang Server-employing AF2 in one way or another.
View Article and Find Full Text PDFRepeat proteins are common in all domains of life and exhibit a wide range of functions. One class of repeat protein contains solenoid folds where the repeating unit consists of β-strands separated by tight turns. β-solenoids have distinguishing structural features such as handedness, twist, oligomerisation state, coil shape and size which give rise to their diversity.
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- - Recent advancements in computational structural biology are enhancing our understanding of clinically important proteins, with a focus on human Oca2, which is linked to a common form of albinism.
- - Oca2's structure, modeled using techniques like AlphaFold2, reveals it has a unique scaffold and transport domain, along with a previously unidentified cryptic GOLD domain that aids in protein trafficking.
- - Analysis indicates that Oca2 could function as a Na+/dicarboxylate symporter, with significant mutations mapping to its structural features, and models suggest it may operate via an elevator-type transport mechanism.
Summary: Covariance-based predictions of residue contacts and inter-residue distances are an increasingly popular data type in protein bioinformatics. Here we present ConPlot, a web-based application for convenient display and analysis of contact maps and distograms. Integration of predicted contact data with other predictions is often required to facilitate inference of structural features.
View Article and Find Full Text PDFWe report here an assessment of the model refinement category of the 14th round of Critical Assessment of Structure Prediction (CASP14). As before, predictors submitted up to five ranked refinements, along with associated residue-level error estimates, for targets that had a wide range of starting quality. The ability of groups to accurately rank their submissions and to predict coordinate error varied widely.
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- * This research focuses on the transmembrane protein Tmem41b, linked to autophagosome formation and critical in mouse embryonic development, as well as being a viral host factor for SARS-CoV-2.
- * The study's structural analysis indicates that Tmem41b and its related proteins possess unique features, like a tandem repeat and potential transport activity for an unidentified substrate, suggesting their role as transporters in cellular processes.