Biology subjects

Vedula, S.

Publications and source records attributed to Vedula, S..

4 recordsLinked to original sources

bioRxiv2025

Experiment-guided AlphaFold3 resolves accurate protein ensembles

AlphaFold3 predicts highly accurate protein structures from sequence, but tends to collapse to a single dominant conformation, even when the underlying structure is inherently heterogeneous. Moreover, its predictions are oblivious to experimental conditions that can alter local sequence conformation. In this work we show that AlphaFold3 can be guided to match data obtained by NMR spectroscopy, X-ray crystallography and cryo-EM experiments, and combinations thereof. Our approach can also incorporate data that explicitly report on dynamics, such as site-resolved order parameters. We demonstrate that this methodology can generate ensembles of conformations having less distance restraint violations than traditionally resolved NMR structures and uncover unmodelled alternate conformations detectable in electron density. This methodology paves the way for the development of experimentally aware predictive models that capture the ensemble nature of protein structures.

molecular biology↗

bioRxiv2025

Plasma membrane folate transport in fungi and plants is mediated by members of the oligopeptide transporter (OPT) family

Folates are essential for all organisms. They are acquired either through de novo biosynthesis or from the diet. Yeast, fungi and plants make their own folates and it has not been clear if plasma membrane folate transporters exist in these organisms. Using a synthetic lethal screen in Saccharomyces cerevisiae we observed that deletions in a gene encoding the previously identified glutathione transporter, OPT1, was synthetically sick with a disruption in folate biosynthesis. Uptake experiments confirmed that Opt1p/Hgt1p can transport folinic acid and the naturally abundant methyl tetrahydrofolate. As S. cerevisiae Opt1p was able to transport both folate and glutathione, we used alanine-scanning mutants of the residues in the transmembrane domains of the channel to identify the residues required specifically for the uptake of folates and distinct from those required for glutathione. We further examined the oligopeptide transporter family of other organisms for the presence of folate transporters. In C. albicans, CaOPT1, the orthologue of S. cerevisiae OPT1 efficiently transported folate but not glutathione, while the previously characterized glutathione transporter, CaOPT7 could not transport folate. Aspergillus fumigatus has eight homologues of the oligopeptide transporter family, of which OptB and OptH could transport folates. In the plant Arabidopsis thaliana, the Opt1 homologs AtOpt2, AtOpt4, and AtOpt6 could transport folates. This discovery of folate transporters across fungi and plants fills a critical gap in our understanding of folate metabolism, and can benefit the exploitation of these pathways in pathogenic fungi, and in plants.

genetics↗

bioRxiv2024

The end of protein structure prediction: Improving prediction accuracy in chimeric proteins by windowed multiple sequence alignment

AlphaFold2 has predicted the structures of almost every known protein. A simple means to create proteins beyond those found in nature, is by unnaturally fusing together two known proteins. Here we demonstrate that dependence on multiple sequence alignment, limits the success with which AlphaFold and ESMfold capture such chimeric forms of otherwise well predicted, individual, proteins. Specifically we show that peptides are predicted with significantly reduced accuracy when added to the terminal ends of scaffold proteins. Appending the multiple sequence alignment for the individual peptide tags to that of the scaffold protein often restores prediction accuracy.

bioinformatics↗

bioRxiv2024

Seeing Double: Molecular dynamics simulations reveal the stability of certain alternate protein conformations in crystal structures

Proteins jiggle around, adopting ensembles of interchanging conformations. Here we show through a large-scale analysis of the Protein Data Bank and using molecular dynamics simulations, that segments of protein chains can also commonly adopt dual, transiently stable conformations which is not explained by direct interactions. Our analysis highlights how alternate conformations can be maintained as non-interchanging, separated states intrinsic to the protein chain, namely through steric barriers or the adoption of transient secondary structure elements. We further demonstrate that despite the commonality of the phenomenon, current structural ensemble prediction methods fail to capture these bimodal distributions of conformations.

biochemistry↗