Biology subjects

Vedula, S.

Publications and source records attributed to Vedula, S..

8 recordsLinked to original sources

bioRxiv2026

The turn less taken: Investigating patterns in β-turn dynamics using large-scale molecular dynamics data

{beta}-turns are among the most common structural motifs in proteins, yet their conformational dynamics and sequence determinants remain incompletely understood. Here we present a data-driven classification and dynamic analysis of {beta}-turn conformations using large-scale molecular dynamics trajectories from the mdCATH database. Clustering of backbone dihedral angles using a cross-bond Ramachandran representation identifies six {beta}-turn types, including a previously uncharacterized hybrid I/I' cluster that combines geometric features of canonical type I and I' conformations. Time-resolved analysis indicates that this hybrid state acts as a transient intermediate state of {beta}-turns. Transitions observed in molecular dynamics simulations closely match NMR ensembles and altlocs detected in X-ray crystal structures, with the most dominant exchanges occurring between type I and II, and between type I' and II' turns. Sequence analysis shows that each turn type exhibits characteristic amino acid preferences at the central residues (i + 1 and i + 2). Within these overall preferences, specific residue pairs display distinct biases toward static or dynamic behavior. Targeted in silico substitutions that interchange dynamic- and static-enriched residue pairs shift the conformational behavior of turns accordingly, providing direct support for these sequence-dynamics relationships. Analysis of flanking secondary-structure environments reveals that structural context further modulates turn flexibility, with strand- and coil-associated turns exhibiting higher dynamic propensity than helix-associated turns. Together, these results reveal how sequence composition and structural context jointly shape the conformational landscape of {beta}-turns.

biochemistry↗

bioRxiv2026

Density-guided AlphaFold3 uncovers unmodelled conformations in β2-microglobulin

Although X-ray crystallography captures the ensemble of conformations present within the crystal lattice, models typically depict only the most dominant conformation, obscuring the existence of alternative states. Applying the electron density-guided AlphaFold3 approach to {beta}2-Microglobulin highlights how ensembles of alternate backbone conformations can be systematically modeled directly from crystallographic maps. This study also highlights how the detection of conformational ensembles is affected by the local quality of electron density and subtle variations in crystallization conditions and lattice packing. These results demonstrate that density-guided AlphaFold3 can uncover conformational heterogeneity missed by conventional refinement, offering a robust, systematic framework to capture the full structural landscape of proteins in crystals and enhancing the interpretive power of macromolecular crystallography. SynopsisElectron-density-guided AlphaFold3 reveals previously unmodeled conformational heterogeneity in {beta}2-Microglobulin and shows how crystal packing influences ensemble detection in X-ray crystallography.

bioinformatics↗

bioRxiv2025

An Evidence-Grounded Research Assistant for Functional Genomics and Drug Target Assessment

The growing availability of biological data resources has transformed research, yet their effective use remains challenging: selecting appropriate sources requires domain knowledge, data are fragmented across databases, and synthesizing results into reliable conclusions is labor-intensive. Although large language models promise to address these barriers, their impact in biomedicine has been limited by unsupported statements, incorrect claims, and lack of provenance. We introduce Alvessa, an evidence-grounded agentic research assistant designed around verifiability. Alvessa integrates entity recognition, orchestration of pre-validated biological tools, and data-constrained answer generation with statement-level verification against retrieved records, explicitly flagging unsupported claims and guiding revision when reliability criteria are not met. We evaluate Alvessa on dbQA from LAB-Bench and GenomeArena, a benchmark of 720 questions spanning gene and variant annotation, pathways, molecular interactions, miRNA targets, drug-target evidence, protein structure, and gene-phenotype associations. Alvessa substantially improves accuracy relative to general-purpose language models and performs comparably to coding-centric agents while producing fully traceable outputs. Using adversarial perturbations, we show that detection of fabricated statements depends critically on access to retrieved evidence. We further demonstrate application to drug discovery, where evidence-grounded synthesis enables identification of candidate targets missed or misattributed by literature-centered reasoning alone. Alvessa and GenomeArena are released to the community to support reproducible, verifiable AI-assisted biological research.

bioinformatics↗

bioRxiv2025

Enterococcus faecalis Influences the Transcription and Metabolism of Pathogenic Escherichia coli when Grown in Co-Culture

UTI involves bacterial growth in the disparate environments of the bladder and within uroepithelial cells. The bladder is a low-nutrient environment that nonetheless supports rapid growth. Phylogenetic group B2 Escherichia coli (Ec) is frequently isolated from urinary tract infection (UTI) patients. Non-B2 strains have also been isolated and are often co-isolated with Enterococcus faecalis (Ef). We characterized the interaction between three co-isolated Ec-Ef pairs and other Ec-Ef combinations in a nutrient-rich medium which was intended to emulate the rapid growth condition of the bladder. In this medium, Ef had little effect on Ec growth but resulted in major transcriptome differences. Ef affected the non-B2 and B2 strains differently. For the non-B2 Ec strains, Ef induced transcript for genes whose products degrade ornithine via putrescine to succinate which is subsequently metabolized by the TCA cycle. For a control B2 Ec strain, Ef induced transcripts for growth rate-associated genes of macromolecular synthesis, and for similar metabolic enzymes, except for those that degrade putrescine to succinate. Unexpectedly, Ef induced transcripts for glyoxylate shunt enzymes in both non-B2 and B2 Ec strains. The bacterial disparate and constantly changing environments during UTI suggest the potential for different types of Ec-Ef interactions. Our results provide evidence for nutrient cross-feeding as one type of Ec-Ef interaction.

microbiology↗

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↗