Biology subjects

Sudarsanam, K.

Publications and source records attributed to Sudarsanam, K..

4 recordsLinked to original sources

bioRxiv2026

Mapping the structural coverage of Arabidopsis thaliana plant developmental proteins: Insights from Experimental and AlphaFold Approaches

BackgroundPlant development is a multifaceted process governed by intricate protein regulatory networks. High-throughput sequencing methods have vastly expanded plant transcriptomic and proteomic datasets, yet there is a large discrepancy between structural information for plant developmental proteins and the UniProt sequence entries. Advances in X-ray crystallography, NMR spectroscopy, and Cryo-EM have enabled the determination of protein complex structures and their dynamics. AI-driven tools like AlphaFold have revolutionized analysis of protein structural intricacies. However, available three-dimensional structural models predominantly prioritize the human proteome and other mammals over plants. Assessing structural coverage of plant developmental proteins is thus essential to identify research gaps, guide structure-function studies, and advance agriculture. ResultsHere, we focus on mapping the structural coverage of developmental proteins in Arabidopsis thaliana. We observed a substantial disparity in the Protein Data Bank (PDB) representation of Arabidopsis thaliana proteins compared to those of Homo sapiens. Our analysis identified 16,389 reviewed UniProt entries, of which only 1,038 have experimentally determined structures. Functional mapping using PlantGSEA revealed 3,485 proteins associated with plant developmental processes; of which only 337 (9.67%) have experimentally determined structures. In contrast, analysis of the AlphaFold database showed that 69.85% of the 39,278 Arabidopsis thaliana UniProt protein entries have predicted structures. Notably, all 3,485 plant developmental proteins (100%) from Arabidopsis thaliana are covered by AlphaFold models. The substantially higher structural coverage provided by AlphaFold for Arabidopsis thaliana, relative to Homo sapiens, highlights the strength of computational approaches in addressing the challenges of structural studies of difficult-to-crystallize proteins. Furthermore, 79.15% of reviewed A. thaliana protein models exhibit high confidence (pLDDT > 70), indicating reliable structural predictions. Although the experimental structural coverage of Arabidopsis thaliana developmental proteins remains limited, AlphaFold has markedly expanded the accessible structural landscape. ConclusionThis study investigated the structural coverage of Arabidopsis thaliana plant developmental proteins, underscoring the critical need for structural studies using both experimental and AlphaFold approaches. It provides research directions for bridging the knowledge gap in understanding molecular mechanisms of plant development.

bioinformatics↗

bioRxiv2025

Comparing PAS domain coupled intrinsic dynamics in bHLH PAS domain transcription factor complexes

The basic Helix-Loop-Helix-Per-Arnt-Sim (bHLH-PAS) transcription factors (TFs) are regulators of several critical cellular functions such as circadian rhythm, hypoxia response and neuronal development. These proteins contain tandemly repeated PAS domains that mediate heterodimer formation. While PAS domains adopt a conserved fold, recent studies suggest that their interaction interfaces differ distinctly in different TF complexes. However, the implications of these differences on the intrinsic dynamics of PAS domains remain unclear. In this study, we performed a comparative analysis of PAS domain dynamics across multiple bHLH-PAS TF complexes using all-atom Elastic Network Models (ENMs) and molecular dynamics (MD) simulations. We decomposed the intrinsic dynamics of PAS domains into self-coupled (internal domain dynamics) and directly coupled (interaction partner-influenced dynamics) motions using a projection-based approach. Our results show that self-coupled motions are more conserved across PAS domains than structure or sequence alone, while directly coupled motions capture the context-specific influence of partner proteins. Furthermore, hierarchical clustering of the overall covariance-based similarity scores revealed distinct grouping of CLOCK:BMAL1-type and HIF:ARNT-type complexes, which were not captured by sequence or structural comparisons. Root mean square fluctuation profiles derived from both MD and ENM approaches showed strong correspondence, validating the utility of ENMs in capturing biologically relevant dynamics, even in cases where the structural complexes were modelled using AlphaFold3. PAS-B domains were generally found to be less flexible than PAS-A domains for all the complexes analysed. Regions with high directly coupled flexibility were generally localized regions with high interface propensity in class I PAS-B domains, suggesting a higher level of coupled dynamics between PAS-B domains. Our results highlight how PAS domain intrinsic dynamics are shaped by both their internal architecture and complex-specific interactions, offering new insights into the functional diversification of bHLH-PAS transcription factors. Statement of SignificancePAS domains are ubiquitous across all domains of life with diverse functions attributed to them. As part of bHLH-PAS transcription factors (TFs), they enable dimerization of Class I and Class II TFs. In this work, we investigated the effect of dimerization of PAS domains on their flexibility by using a method that allows us to isolate the intrinsic dynamics internal to a target domain and the intrinsic dynamics linked to the crosstalk between domains, from the all-atom elastic network model-based normal modes of the whole TF complex. Our findings reveal a context specific conservation of intrinsic dynamics based on the type of heterodimer complex. We also find a strong agreement between more-detailed MD simulations and the coarse-grained method used.

biophysics↗

bioRxiv2024

Structural Insights into Competitive Binding Dynamics between RALF23/33 and PCP-B in Brassicaceae Pollination

Ensuring successful fertilization, viable offspring production, genetic isolation, and maintaining species integrity is pivotal for the survival of flowering plants. Members of Brassicaceae employ a "gatekeeping mechanism" involving interaction between stigmatic membrane-bound Catharanthus roseus receptor-like kinase 1-like (CrRLK1L) receptor, FERONIA, GPI anchored protein LLG2 (LORELEI-LIKE GLYCOPHOSPHATIDYLINOSITOL-ANCHORED PROTEIN 2) and autocrine secreted RALF23/33 (Rapid alkalinization factor) peptide. This binding establishes a barrier for pollen hydration by inducing ROS (Reactive Oxygen Species). Conversely, in the presence of compatible pollen, paracrine-secreted cysteine-rich peptides such as PCP-B{gamma} compete with RALF23/33 for binding to the FERONIA-LLG2 complex, thus reducing ROS levels, ensuring successful pollen hydration and germination. Despite its crucial role, the structural basis of this competitive binding dynamics remains elusive owing to the lack of structural data and the inherent flexibility of these peptides. Using structural modeling, molecular docking, and simulations, this study reveals that PCP-B{gamma} binds to the same negatively charged pocket in the FERONIA-LLG2 complex as RALF23, displacing and interrupting the heterodimerized structure, thus reducing ROS levels to promote pollination. Our study unveils the experimental data-based predicted models, competitive binding dynamics, and mechanism behind this "gatekeeping mechanism," shedding light on the molecular mechanism underlying this pollen hydration barrier in Brassicaceae.

plant biology↗

bioRxiv2024

Structural insights into the recognition of RALF peptides by FERONIA receptor kinase during Brassicaceae Pollination

Ensuring species integrity and successful reproduction is pivotal for the survival of angiosperms. Members of Brassicaceae family employ a "lock and key" mechanism involving stigmatic (sRALFs) and pollen RALFs (pRALFs) binding to FERONIA, a Catharanthus roseus receptor-like kinase 1-like (CrRLK1L) receptor, to establish a prezygotic hybridization barrier. In the absence of compatible pRALFs, sRALFs bind to FERONIA, inducing a lock state for pollen tube penetration. Conversely, compatible pRALFs act as a key, facilitating successful fertilization. Competing pRALFs reduce the sRALFs binding to FERONIA in a dose-dependent manner, enabling pollen tube penetration. Despite its crucial role in Brassicaceae hybridization, the structural basis of this binding remains elusive owing to the highly flexible nature of RALF peptides. Using advanced structural modeling techniques and flexible peptide molecular docking, this study reveals that pRALFs and sRALFs bind to negatively charged pockets in FERONIA with varying binding affinities. Our study unveils the structural basis of this binding, shedding light on the molecular mechanism underlying hybridization barriers in Brassicaceae.

plant biology↗