Biology subjects

Mesdaghi, S.

Publications and source records attributed to Mesdaghi, S..

9 recordsLinked to original sources

bioRxiv2025

Can AlphaFold3 predict unseen amyloid polymorphs?

Amyloid fibrils are highly ordered, aggregation-prone protein assemblies implicated in numerous neurodegenerative diseases. Their formation arises from protein misfolding, producing structurally distinct polymorphs that have historically been difficult to predict computationally. While AlphaFold2 excels at predicting monomeric globular proteins, it struggles with protein complexes. Here, we show that AlphaFold3 provides a new opportunity to model amyloid structure and capture polymorph heterogeneity. Using TM-score based clustering of known -synuclein fibril structures, we establish a polymorph nomenclature and demonstrate that AlphaFold3 can reproduce known fibril architectures and predict alternative conformations. These results highlight AlphaFold3s potential for studying amyloid proteins, enabling systematic investigation of amyloid polymorphism.

bioinformatics↗

bioRxiv2025

The promise of AlphaFold for gene structure annotation

BackgroundAs sequencing technology improves, more genomes become available. Most lack annotation, automated methods are error prone, and few genomes are ever manually curated due to time and cost. Protein structure prediction software may provide new angles for assessing and improving gene models without requiring experimental data. In this paper, we explore whether scores from protein structure prediction can aid in scoring gene model quality. We chose three species (Fusarium graminearum, Toxoplasma gondii, and Aspergillus fumigatus) from the VEuPathDB database which have collectively undergone more than 1000 manual curation events. We modelled translations of the gene models with AlphaFold 3, before and after curation, collecting various scores. Then we carried out structure searching of the PDB with Foldseek and sequence-based domain identification using InterProScan. We profiled the scores produced by these methods to identify those best for gene model assessment. ResultsAlphaFold 3 scores strongly favoured manually improved over pre-improvement models, supporting 75% of manually-curated changes in F. graminearum, 65% in T. gondii, and 84% in A. fumigatus (the lower percentage in T. gondii attributed to a high level of disorder). Further, combining scores across multiple tools (AlphaFold 3, Foldseek and InterProScan) provided additional improvements in model scoring. ConclusionOverall, the most discriminative scores combined outputs of AlphaFold 3 and Foldseek. Our results therefore highlight the potential of scores derived from deep learning-based protein structure prediction for scoring gene models in the absence of experimental data. Future work should focus on intrinsically disordered regions and developing integrated tools to apply this approach.

bioinformatics↗

bioRxiv2025

From paleness to albinism: Contribution of OCA2 exon 10 skipping to hypopigmentation

Pathogenic variants in the OCA2 gene result in oculocutaneous albinism. In humans and several other mammalian species, OCA2 is transcribed into two coding mRNAs, a major transcript that encodes the full-length protein and a minor transcript that skips in-frame exon 10 and has no identified function. By contrast, rodents and non-mammalian vertebrates only express the major transcript. Several rare variants of human OCA2 have been reported to be pathogenic due to increased exon 10 skipping. To understand the vulnerability of human OCA2 to exon 10 skipping and its impact on pigmentation, we first functionally tested a series of rare missense variants spread across exon 10. We found that each variant significantly influences the skipping ratio either positively or negatively. By combining human and murine sequences in functional assays, we found that the skipping ratio depends on particular exonic and intronic combinations. Next, we focused on the most frequent exonic single nucleotide variant of human OCA2, rs1800404-T (c.1065G>A/p.Ala355=), located in exon 10. We show that this variant significantly promotes exon 10 skipping on its own and exhibits an additive effect in cis to previously identified splicing variants likely contributing to their pathogenicity. Association studies reveal that rs1800404-T is tightly associated with lighter skin and hair pigmentation in a representative European population, as has been observed in other populations around the world. Our structural models of the skipped transcript-derived protein support causality by predicting that it could exert a dominant-negative effect, which is consistent with a dose-dependent hypopigmentation response in both pathological and physiological contexts. Overall, the modulation of OCA2 exon 10 skipping by both benign and pathogenic variants provides a basis for improving the genetic diagnosis of albinism, and paves the way for research into the molecular and evolutionary mechanisms behind human pigmentation diversity.

genetics↗

bioRxiv2024

AlphaFold 2, but not AlphaFold 3, predicts confident but unrealistic beta-solenoid structures for repeat proteins

AlphaFold 2 has revolutionised protein structure prediction but, like any new tool, its performance on specific classes of targets, especially those potentially under- represented in its training data, merits attention. Prompted by a highly confident prediction for a biologically meaningless, scrambled repeat sequence, we assessed AF2 performance on sequences comprised perfect repeats of random sequences of different lengths. AF2 frequently folds such sequences into {beta}-solenoids which, while ascribed high confidence, contain unusual and implausible features such as internally stacked and uncompensated charged residues. A number of sequences confidently predicted as {beta}-solenoids are predicted by other advanced methods as intrinsically disordered. The instability of some predictions is demonstrated by Molecular Dynamics. Importantly, other Deep Learning-based structure prediction tools predict different structures or {beta}-solenoids with much lower confidence suggesting that AF2 alone has an unreasonable tendency to predict confident but unrealistic {beta}-solenoids for perfect repeat sequences. The potential implications for structure prediction of natural (near-)perfect sequence repeat proteins are also explored.

bioinformatics↗

bioRxiv2024

Investigating Medin Cleavage Accessibility in MfgE8: Conformational Insights Derived from Molecular Dynamics Simulations and AlphaFold2 Models

Recent studies have indicated that the human amyloidogenic protein medin is associated with a range of vascular diseases, including aortic aneurysms, vascular dementia, and Alzheimers 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. The exact mechanism of medin production from MfgE8 is unknown, with crystal structures of homologous C2 domains suggesting that the cleavage sites are buried, requiring a conformational transition for medin production. Molecular dynamics simulations can explore a wide range of conformations, from small-scale bond rotations to large-scale changes like protein folding or ligand binding. This study employed a combination of full-atom and coarse-grained molecular dynamics simulations, along with CONCOORD- and AlphaFold2-generated models, to investigate MfgE8 conformations and their implications for medin cleavage site accessibility. The simulations revealed that MfgE8 tends to adopt a compact conformation with the RGD motif, important for cell attachment within the N-terminal domain, and the medin region in the C-terminal domain close in proximity. Formation of this compact structure is facilitated by interdomain electrostatic interactions that promote stability and in turn decrease the solvent-accessible surface area of the medin region and particularly the C-terminal medin cleavage site. This data enhances current knowledge on medin generation to propose that alterations in local environmental conditions, possibly through changes in glycosylation or other post-translational modifications are required to induce MfgE8 to unfold partially or fully: this would result in enhanced accessibility of the cleavage sites and therefore enable medin generation.

bioinformatics↗

bioRxiv2024

Deep-learning protein structure predictions suggest likely molecular functions for three uncharacterised polytopic membrane proteins from the P. falciparum apicoplast

Malaria is a burdensome disease to humanity caused chiefly by the still poorly understood parasite genus Plasmodium. Much of the pathogenic success of these and other related parasites is due to the presence of the apicoplast, a comparatively poorly characterised biosynthetic organelle containing many proteins of unknown function. Here we present AlphaFold2 protein structure predictions together with further in silico analyses to infer molecular functions for the three uncharacterised transmembrane apicoplast proteins PF3D7_0622700, PF3D7_0908100 and PF3D7_1021300. The targets PF3D7_0622700 and PF3D7_0908100 are shown herein to belong to the polytopic Major Facilitator and Cation-Proton Antiporter and Anion Transporter superfamilies respectively, confirming previous suspicions for PF3D7_0908100 of a transporter function. Importantly, our docking screens further suggest pyridoxal-5-phosphate may be transported by PF3D7_0622700, and PF3D7_0908100 likely transports a larger negatively charged metabolite. These findings will help direct experimental assays to confirm what apicoplast metabolites these proteins may transport. PF3D7_1021300 is proposed to possess a six transmembrane alpha-helix domain of a currently unknown fold which may also possess a transporter molecular function. This work highlights the power of high accuracy protein structure predictions to illuminate proteins of unknown structure and function.

bioinformatics↗

bioRxiv2023

Deep Learning-based structural and functional annotation of Pandoravirus hypothetical proteins

Giant viruses, including Pandoraviruses, contain large amounts of genomic dark matter - genes encoding proteins of unknown function. New generation, deep learning-based protein structure modelling offers new opportunities to apply structure-based function inference to these sequences, often labelled as hypothetical proteins. However, the AlphaFold Protein Structure Database, a convenient resource covering the majority of UniProt, currently lacks models for most viral proteins. Here, we apply a panoply of predictive methods to protein structure predictions representative of large clusters of hypothetical proteins shared among four Pandoraviruses. In several cases, strong functional predictions can be made. Thus, we identify a likely nucleotidyltransferase putatively involved in viral tRNA maturation that has a BTB domain presumably involved in protein-protein interactions. We further identify a cluster of membrane channel sequences presenting three paralogous families which may, as seen in other giant viruses, induce host cell membrane depolarization. And we identify homologues of calcium-activated potassium channel beta subunits and pinpoint their likely Acanthamoeba cellular alpha subunit counterparts. Despite these successes, many other clusters remain cryptic, having folds that are either too functionally promiscuous or too novel to provide strong clues as to their role. These results suggest that significant structural and functional novelty remains to be uncovered in the giant virus proteomes.

bioinformatics↗

bioRxiv2022

Structural Insights into Pink-eyed Dilution Protein (Oca2)

Recent innovations in computational structural biology have opened an opportunity to revise our current understanding of the structure and function of clinically important proteins. This study centres on human Oca2 which is located on mature melanosomal membranes. Mutations of Oca2 can result in a form of oculocutanous albinism which is the most prevalent and visually identifiable form of albinism. Sequence analysis predicts Oca2 to be a member of the SLC13 transporter family but it has not been classified into any existing SLC families. The modelling of Oca2 with AlphaFold2 and other advanced methods shows that, like SLC13 members, it consists of a scaffold and transport domain and displays a pseudo inverted repeat topology that includes re-entrant loops. This finding contradicts the prevailing consensus view of its topology. In addition to the scaffold and transport domains the presence of a cryptic GOLD domain is revealed that is likely responsible for its trafficking from the endoplasmic reticulum to the Golgi prior to localisation at the melanosomes and possesses known glycosylation sites. Analysis of the putative ligand binding site of the model shows the presence of highly conserved key asparagine residues that suggest Oca2 may be a Na+/dicarboxylate symporter. Known critical pathogenic mutations map to structural features present in the repeat regions that form the transport domain. Exploiting the AlphaFold2 multimeric modelling protocol in combination with conventional homology modelling allowed the building of a plausible homodimer in both an inward- and outward-facing conformation supporting an elevator-type transport mechanism.

bioinformatics↗

bioRxiv2020

In silico prediction of structure and function for a large family of transmembrane proteins that includes human Tmem41b

Recent strides in computational structural biology have opened up an opportunity to understand previously mysterious uncharacterised proteins. The under-representation of transmembrane proteins in the Protein Data Bank highlights the need to apply new and advanced bioinformatics methods to shed light on their structure and function. This study focuses on such a family; transmembrane proteins containing the Pfam domain PF09335 ( SNARE_ASSOC/ VTT / Tvp38). One prominent member, Tmem41b, has been shown to be involved in early stages of autophagosome formation and is vital in mouse embryonic development. Here we use evolutionary covariance-derived information not only to construct and validate ab initio models but also to make domain boundary predictions and infer local structural features. The results from the structural bioinformatics analysis of Tmem41b and its homologues show that they contain a tandem repeat that is clearly visible in evolutionary covariance data but much less so by sequence analysis. Furthermore, cross-referencing of other prediction data with the covariance analysis shows that the internal repeat features 2-fold rotational symmetry. Ab initio modelling of Tmem41b reinforces these structural predictions. Local structural features predicted to be present in Tmem41b are also present in Cl-/H+ antiporters. These results together strongly point to Tmem41b and its homologues as being transporters for an as-yet uncharacterised substrate and possibly using H+ antiporter activity as its mechanism for transport.

bioinformatics↗