Biology subjects

Sekhar, A.

Publications and source records attributed to Sekhar, A..

7 recordsLinked to original sources

bioRxiv2026

Morpheus-3D: Structural Diversity-Guided Detection and Localization of Protein Fold Switching

Proteins that reversibly adopt multiple stable folds challenge the classical sequence-structure paradigm, yet their discovery remains limited because fold switching is difficult to detect experimentally and current computational methods fail to resolve the underlying conformationally plastic regions. Here we present Morpheus-3D, a sequence-based framework that quantifies residue-level tertiary structural diversity using entropy profiles derived from the Foldseek 3Di structural alphabet. By capturing variation in tertiary interaction environments rather than secondary structure alone, Morpheus-3D identifies fold-switching proteins while simultaneously localizing the sequence regions responsible for structural transitions. The framework outperforms existing predictors, accurately recovers experimentally characterized switching regions, generalizes to recently discovered natural and engineered fold-switching proteins absent from training, and detects conformational plasticity inaccessible to secondary-structure-based approaches. Application to 57 representative proteomes reveals that fold-switching potential is widespread but enriched in regulatory, pathogenic, and environmentally adaptive lineages. Integration with ancestral sequence reconstruction further un-covers evolutionary trajectories through which conformational plasticity emerges. To make these predictions directly accessible, we implemented Morpheus-3D as an interactive web platform (https://morpheus.slicearrow.com/), in which per-residue entropy profiles, sequence and three-dimensional structure are displayed together and respond as one, allowing predicted fold-switching regions to be mapped onto the structure and exported for downstream analysis. Morpheus-3D provides a scalable framework for discovering metamorphic proteins and investigating the origins, mechanisms, and evolution of structural plasticity directly from sequence.

biophysics↗

bioRxiv2026

Revealing taxonomic signals in plant volatiles with phytochemistry, machine learning and trait mapping

Plant volatiles have long been used as taxonomic characters, especially in chemotaxonomy. Exploring the utility of chemotaxonomy has been widely regarded critical for drug discovery, despite the knowledge that phytochemicals are often evolutionarily labile. Despite this, the use of chemotaxonomy has been restricted primarily due to the complex interpretations behind translating chemical characters into phylogenetically operational characters. In this paper, we propose a method that integrates phytochemistry, machine learning, and trait mapping to examine whether plant volatiles retain signals for classification across broad taxonomic ranks and which components of the volatile metabolites carry these signals. Leveraging a global dataset comprising 2,139 volatiles across 429 plant species, we trained classifiers on presence-absence data and molecular fingerprints that can predict species to their taxonomic ranks. Incorporating structural features improves performance, suggesting that plant volatiles may encode lineage-specific chemical signatures. Rather than single diagnostic markers, combinations of volatiles informed taxonomic predictions, indicating biosynthetic constraints within volatile clusters. Fingerprint-derived clusters showed a lineage-dependent pattern when mapped onto phylogeny. The proposed method provides an integrated approach to revisit chemotaxonomy and trait evolution to understand the chemical diversity across lineages. This approach can also support comparative chemical prediction, especially for understudied closely related plant groups.

plant biology↗

bioRxiv2026

Structure of a sparsely populated chimeric intermediate that facilitates fold-switching of a metamorphic protein

Metamorphic proteins challenge the structure-function paradigm by switching between distinct folds. However, the conformational states sampled along the fold-switching pathway have remained elusive because they are transient and unstable. Using multinuclear chemical exchange saturation transfer and relaxation dispersion nuclear magnetic resonance, combined with chemical shift-based structure determination and protein engineering, we visualized the atomic-resolution structure of an invisible state of the metamorphic chemokine lymphotactin. This state is a chimera that integrates the secondary and tertiary structure of one fold with the quaternary assembly of the other. Locking lymphotactin into a single conformation abolishes access to this state, supporting its role as an on-pathway intermediate in metamorphosis. The stabilization of such hybrid intermediates is likely to have facilitated the evolution of fold switching and represent a powerful strategy for protein design.

biophysics↗

bioRxiv2026

Tannic acid fortifies extracellular matrix against dicarbonyl stress

Methylglyoxal (MGO), a highly reactive dicarbonyl metabolite that accumulates in diabetes and aging, causes tissue dyshomeostasis, for which therapeutic interventions are limited. Herein, we investigate the potential of tannic acid (TA) in fortifying organ and organismal health against MGO. Anatomical disruption in vivo of hydra bodies and ex vivo decellularization of murine mesenteries with MGO suggested an impaired interaction between cells and their extracellular matrix (ECM); however, pretreatment of these systems with TA reversed this effect. We confirmed this through subsequent exposure of control and TA-pretreated mammalian cell-secreted endogenous matrix, Collagen I, and basement membrane matrix to MGO. TA prevented loss of ECM biochemical characteristics and restored perturbed cell adhesion and spreading on these substrata induced by MGO. NMR titrations confirmed TA-bound MGO in a 1:5 stoichiometry, potentially quenching its electrophilic properties. Our study posits TA as a novel candidate for protecting organ and organismal architectures against the histopathological effects of dicarbonyl stress.

biochemistry↗

bioRxiv2025

AmyloGram Reveals Amyloidogenic Potential in Stroke Thrombus Proteomes

BackgroundAmyloidogenic proteins play a central role in a range of pathological conditions, yet their presence in thrombi has only recently been recognized. Whether computational prediction tools can identify amyloid-forming potential in thrombus proteomes remains unclear. MethodsAmyloGram is a computational tool that estimates amyloid-forming potential based on n-gram sequence encoding and random forest classification. Using AmyloGram, we analyzed 204 proteins tagged by humans as amyloidogenic in UniProt. We then applied the same approach to proteins identified in thrombi retrieved using mechanical thrombectomy from patients with cardioembolic and atherothrombotic stroke. In addition we used AmyloGram to analyse the amyloidogenicity of 83,567 canonical human protein sequences. ResultsAmong the UniProt-annotated amyloid set, nearly all proteins received AmyloGram scores above 0.7, including 23 of the 24 human proteins. Even the lowest-scoring human protein, lysozyme (scoring 0.675), is known to form amyloid under certain conditions. In thrombi from both stroke subtypes, all detected proteins had AmyloGram scores above 0.7, suggesting a high likelihood of amyloid content. A majority of unannotated proteins also achieve AmyloGram scores exceeding 0.7. ConclusionsAmyloGram reliably identifies known amyloid-forming proteins and reveals that stroke thrombi are enriched for proteins with high amyloidogenic potential. These findings support the hypothesis that thrombus formation in stroke involves amyloid-related mechanisms and warrant further investigation using histological and functional validation.

bioinformatics↗

bioRxiv2025

Morpheus: A fragment-based algorithm to predict metamorphic behaviour in proteins across proteomes

Functionally important "fold-switching" proteins, which do not obey the classical folding dogma, are now thought to be widespread. Algorithms that can accurately annotate fold-switching proteins from sequence information can help uncover the true extent of the "metamorphome". Here, we present Morpheus, a fragment-based classification approach, that works by analysing the diversity of structures within a query protein sequence. Morpheus exhaustively curates and uses fragment structural data from the protein data bank as well as the AlphaFold Protein Structure Database. We employed our algorithm on 57 different proteomes consisting of a total of 601,218 proteins and identified about 10% of these proteins with the ability to fold switch. Additionally, we provide a web server for Morpheus to test for metamorphic propensities for user-defined sequences (http://mbu.iisc.ac.in/[~]anand/morpheus). Besides screening for metamorphic behaviour in proteomes, our work will be useful in de novo design and engineering of such proteins through further experimentation.

bioinformatics↗

bioRxiv2022

Functional regulation of an intrinsically disordered protein via a conformationally excited state

A longstanding goal in the field of intrinsically disordered proteins (IDP) is to characterize their structural heterogeneity and pinpoint the role of this heterogeneity in IDP function. Here, we use multinuclear chemical exchange saturation (CEST) NMR to determine the structure of a thermally accessible globally folded excited state in equilibrium with the intrinsically disordered native ensemble of a bacterial transcriptional regulator CytR. We further provide evidence from double resonance CEST experiments that the excited state, which structurally resembles the DNA-bound form of CytR, recognizes DNA by means of a folding-before-binding conformational selection pathway. The disorder-to-order regulatory switch in DNA recognition by natively disordered CytR therefore operates through a dynamical variant of the lock-and-key mechanism where the structurally complementary conformation is transiently accessed via thermal fluctuations. One-Sentence SummaryThe intrinsically disordered cytidine repressor binds DNA via a folding-before-binding conformational selection mechanism

biophysics↗