Ramanathan Sowdhamini

Ramanathan Sowdhamini
Tata Institute of Fundamental Research | TIFR · National Centre for Biological Sciences

About

503
Publications
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Publications

Publications (503)
Article
Full-text available
Resource-poor areas with moisture deficit lands following aerobic and direct seeded rice (DSR) methods of cultivation face severe problems of iron deficiency. In this study, Bengal and Assam Aus rice panel was phenotyped at the seedling stage using an iron-deprived hydroponic medium for various shoot and root traits. A novel iron deficiency scoring...
Article
Moringa oleifera is a plant well-known for its nutrition value, drought resistance and medicinal properties. cDNA libraries from five different tissues (leaf, root, stem, seed and flower) of M. oleifera cultivar Bhagya were generated and sequenced. We developed a bioinformatics pipeline to assemble transcriptome, along with the previously published...
Article
Olfactory receptors are important transmembrane proteins that enable organisms to perceive odours and react to them. Structural understanding of insect olfactory receptors is scarce. In this review, we discuss different transmembrane helix prediction methods, consensus methods, topology prediction methods which can enable topology prediction of the...
Article
Full-text available
The repertoire of RNA-binding proteins (RBPs) in bacteria play a crucial role in their survival, and interactions with the host machinery, but there is little information, record or characterisation in bacterial genomes. As a first step towards this, we have chosen the bacterial model system Escherichia coli, and organised all RBPs in this organism...
Article
Full-text available
Domain-domain interactions in multi-domain proteins play an important role in the combined function of individual domains for the overall biological activity of the protein. The functions of the tethered domains are often coupled and hence, limited numbers of domain architectures with defined folds are known in nature. Therefore, it is of interest...
Article
Full-text available
Chemical signaling is ubiquitous and employs a variety of receptor types to detect the cacophony of molecules relevant for each living organism. Insects, our most diverse taxon, have evolved unique olfactory receptors with as little as 10% sequence identity between receptor types. We have identified a promiscuous volatile, 2-methyltetrahydro-3-fura...
Article
Full-text available
Reversible phosphorylation maintained by protein kinases and phosphatases is an integral part of intracellular signalling, and phosphorylation on tyrosine is extensively utilised in higher eukaryotes. Tyrosine phosphatases are enzymes that not only scavenge phosphotyrosine but are also involved in wide range of signalling pathways. As a result, mut...
Data
Supplementary_Material – Supplemental material for Genome-Wide Search for Tyrosine Phosphatases in the Human Genome Through Computational Approaches Leads to the Discovery of Few New Domain Architectures
Article
Full-text available
The number of protein structures is increasing due to the individual initiatives and rapid development of structure determination techniques. Structure-based sequence alignments of distantly related proteins enable the investigation of structural, evolutionary and functional relationships between proteins and their domains leading to their common e...
Article
Full-text available
Background Protein-protein interactions are crucial for normal biological processes and to regulate cellular reactions that affect gene expression and function. Several previous studies have emphasized the roles of residues at the interface of protein-protein complexes in conferring stability and specificity to the complex. Interface residues in a...
Article
Full-text available
Plants are essential facilitators of human life on planet earth. Plants play a critical functional role in mediating the quality of air, availability of food and the sustainability of agricultural resources. However, plants are in constant interaction with its environment and often hampered by various types of stresses like biotic and abiotic ones....
Presentation
Work Submitted for The IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 3-6 December 2018, Madrid, Spain.
Presentation
Work selected for a POSTER presentation at the RSGDREAM2018: RECOMB/ISCB Conference on Regulatory and Systems Genomics with DREAM Challenges 2018 NYU Langone Health, New York, NY, United States, December 8-10, 2018
Conference Paper
Full-text available
MuPhenome: A curated catalog of microbiome correlates with clinical phenotypes
Chapter
Phytochemicals in the form of secondary metabolites produced by plants have been used for therapeutic purposes, some of the well-known examples being artemisinin for treatment of malaria, vinblastine and vinblastine and vincristine for treatment of cancer. Plants produce several such secondary metabolites having anticancer, cardioprotectant, anti-i...
Presentation
Work accepted as a poster presentation of ISCB-LA SOIBIO EMBnet 2018 | Nov 5 – 9, 2018 | Viña del Mar, Chile
Presentation
Work selected for The Molecular Biophysics Unit, Indian Institute of Science (IISc) - in-house SYMPOSIUM 2018.
Article
Flavivirus causes arthropod-borne severe diseases that sometimes lead to the death. The Flavivirus species including Dengue virus, Zika virus and yellow fever virus are transmitted by the bite of Aedes mosquitoes. All these viral species target the people living in their respective endemic zone causing a high mortality rate. Recent studies show tha...
Preprint
Background RNA-binding proteins (RBPs) have been extensively studied in humans over the past few years. Multiple reports have been made in the literature for genome-wide survey for this class of proteins in the human genome using different tools and techniques. Due to the inherent difference in the nature of the methods used in identifying human RB...
Presentation
Work submitted for the International Conference on Microbiome Research 2018 (ICMR 2018), 19 - 22 November , Pune, India.
Poster
Full-text available
This poster gives an overview of our discovery of complete olfactory receptor (OR) gene sets from two solitary bee genomes using computational approaches. Although the comparison with other social Hymenopteran and other insect species shows no evidence for increased olfactory receptor repertoires in social species, few subfamilies of olfactory rece...
Article
Full-text available
Glycidyl ethers and their vicinal diols are important building blocks in the organic synthesis of anti-cancer and anti-obesity drugs. Ylehd, an epoxide hydrolase from tropical marine yeast Yarrowia lipolytica, was explored for its enantioselective properties by kinetic, thermodynamic and in silico studies. Kinetic resolution of racemic phenyl glyci...
Preprint
Background The repertoire of RNA-binding proteins (RBPs) in bacteria play crucial role for their survival, and interactions with the host machinery, but there is little information, record or characterisation in bacterial genomes. As a first step towards this, we have chosen the bacterial model system Escherichia coli , and organised all RBPs in th...
Article
Extensive research performed on Toll-like receptor (TLR) signalling has identified residues in the Toll/interleukin-1 receptor (TIR) domains that are essential for its proper functioning. Among these residues, those in BB loop are particularly significant as single amino acid mutations in this region can cause drastic changes in downstream signalli...
Article
The Toll-like receptors (TLRs) are critical components of the innate immune system due to their ability to detect conserved pathogen-associated molecular patterns, present in bacteria, viruses and other microorganisms. Ligand detection by TLRs leads to a signalling cascade, mediated by interactions among TIR domains present in the receptors, the br...
Conference Paper
The phenomenon of protein domain swapping is interesting and acquires importance, since in some cases, it is implicated in neurodegenerative and other diseases. Predictive algorithms, that can attribute a chance of a protein to get engaged in domain swapping, will be of biomedical value. In such domain swapped structures, 'hinge regions' are key li...
Technical Report
Transcriptional factors(TFs) are regulatory molecules having significant role in up regulating the expression of stress gene,This analysis mainly targets to find master transcription factor which are mostly involved in all the major multiple abiotic stress. and control the cascade at the upstream level in the stress gene regulation pathway .This co...
Research
Breeding for the multiple stress tolerant crop is in utmost important for current indian agricultural scenario, upgrading stress tolerance capability of crop defined by stress gene regulation. Transcriptional factors(TFs) are regulatory molecules having vital role in up regulating the expression of stress genes during stress conditions,This analysi...
Data
Supplementary material is available on the publisher’s web site along with the published article.
Article
Full-text available
Significance Mutations in genes encoding sarcomeric proteins are the major cause of primary inherited cardiomyopathies. Troponin T (TnT), encoded by TNNT2 , harbors most of its pathogenic mutants at TNT1 (residues ∼80–180 of TnT). TNT1 is known to interact with tropomyosin (Tm). In this study, we have analyzed TNT1 mutants using in vitro and in sil...
Article
Full-text available
Olfactory/odorant receptors (ORs) probably govern eusocial behaviour in honey bees through detection of cuticular hydrocarbons (CHCs) and queen mandibular gland pheromones (QMP). CHCs are involved in nest-mate recognition whereas QMP acts as sex pheromone for drones and as retinue pheromone for female workers. Further studies on the effect of eusoc...
Article
Full-text available
Background: Pathogenic bacteria have evolved various strategies to counteract host defences. They are also exposed to environments that are undergoing constant changes. Hence, in order to survive, bacteria must adapt themselves to the changing environmental conditions by performing regulations at the transcriptional and/or post-transcriptional lev...
Article
Full-text available
Background: TRIF is a key protein in antiviral innate immunity, operating downstream of TLRs. TRIF activation leads to the production of interferon-β and pro-inflammatory cytokines. There is evidence from experiments to suggest that the N-terminal domain of TRIF binds to its TIR domain to avoid constitutive activation. However, no structure of a c...
Article
Remarkable features that are achieved in a protein-protein complex to precise levels are stability and specificity. Deviation from the normal levels of specificity and stability, which is often caused by mutations, could result in disease conditions. Chemical nature, 3-D arrangement and dynamics of interface residues code for both specificity and s...
Article
Background: The eukaryotic voltage-gated sodium channel(e-Nav) is a large asymmetric transmembrane protein with important functions concerning neurological function. No structure has been resolved at high resolution for this protein. Methods: A homology model of the transmembrane and extracellular regions of an Anopheles gambiae para-like channe...
Article
Full-text available
Background RNA-binding proteins (RBPs) interact with their cognate RNA(s) to form large biomolecular assemblies. They are versatile in their functionality and are involved in a myriad of processes inside the cell. RBPs with similar structural features and common biological functions are grouped together into families and superfamilies. It will be u...
Article
Full-text available
We developed a computational pipeline for homology based identification of the complete repertoire of olfactory receptor (OR) genes in the Asian honey bee species, Apis florea. A. florea is phylogenetically the most basal honey bee species and also the most distant sister species to the Western honey bee Apis mellifera, for which all OR genes had b...
Article
Full-text available
Background: The study of survival and communication of pathogenic bacteria is important to combat diseases caused by such micro-organisms. Bacterial cells communicate with each other using a density-dependent cell-cell communication process called Quorum Sensing (QS). LuxS protein is an important member of interspecies quorum-sensing system, invol...
Article
Full-text available
A bstract Understanding key protein-protein interaction network mediated by genes responsive to biotic and abiotic stress could help to understand the functional modules and network topologies driven genes responsive to stresses. It still remains to be an open question whether distinct protein-protein interaction networks have functional or regulat...
Presentation
Accepted for short oral presentation (Highlight) at International Conference on Bioinformatics (InCoB2016), Singapore, September 2016.
Article
Full-text available
Myosins are actin-based motor proteins involved in many cellular movements. It is interesting to study the evolutionary patterns and the functional attributes of various types of myosins. Computational search algorithms were performed to identify putative myosin members by phylogenetic analysis, sequence motifs, and coexisting domains. This study i...
Data
Supplementary Figure 1. ML tree of myosin head domains. The tree is collapsed at key nodes and rooted using the midpoint-rooted tree option. Myosin classes are indicated. Nodal support was obtained using RAxML with 1,000 bootstrap replicates. Different colors have been used to indicate different myosin classes. The arrows indicate the direction in...
Article
Full-text available
3D-domain swapping is one of the mechanisms of protein oligomerization and the proteins exhibiting this phenomenon have many biological functions. These proteins, which undergo domain swapping, have acquired much attention owing to their involvement in human diseases, such as conformational diseases, amyloidosis, serpinopathies, proteionopathies et...
Data
Predicted 3D-domain swapped sequences of human proteome. (TXT)
Data
Prediction results on known cases of domain swapping from 3DSwap as validation. (DOC)
Data
Examples of challenging cases for hinge prediction, experimentally identified hinges are marked in blue color (A: Central loop swapping (PDB: 1IXX), B and C: Intertwined dimmers (PDB: 1A64), D: Missing regions (PDB: 2ZEJ), E: Very small hinges (PDB: 5CRO) and F: Elaborate interface (2PJW)) (TIF)
Data
Description of Gene Ontology terms prevalent in human domain swap predicted sequences. (DOC)
Data
Predicted 3D-domain swapped human entries with Pfam domain family associations. (TXT)
Data
Reviewed UniProt sequences of human proteome used as input to prediction models. (TXT)
Article
Full-text available
Protein-protein interactions play a very important role in the process of cellular functionality. Intricate details about the interactions between the proteins in a macromolecular assembly are important to understand the function and significance of protein complexes. We are reporting about a database of protein-protein interactions in huge macromo...
Data
Full-text available
Supplementary Table 1. Number of assemblies that are classified according to the number of protein chains.
Article
Full-text available
Insertions/deletions are common evolutionary tools employed to alter the structural and functional repertoire of protein domains. An insert situated proximal to the active site or ligand binding site frequently impacts protein function; however, the effect of distal indels on protein activity and/or stability are often not studied. In this paper, w...
Data
Validation of models of Loop3 conformers of TdT-long isoform. a) Modeling of Loop3 in TdT-short form (cyan) by iTASSER (green) and PRODAT loop library of SYBYL7.2 (Tripos package) (top scoring models in magenta (loopmodel 8), yellow (loopmodel 12), cream (loopmodel 22) and grey (loopmodel 23)). iTASSER model has been chosen due to presence of helic...
Data
Fluctuations registered between both isoforms at different simulation temperatures. a) Root Mean Square Fluctuations (RMSF) of TdT-short form and TdT-long form in its free and ligand bound state. TdT-short form maintained similar RMSF in both free and ligand bound form but TdT-long form showed higher RMSF in free form than in ligand bound form. Ind...
Data
Essential dynamics depicted as PCA for the mutated TdT-long form. Absence of electrostatic interactions (or salt bridges) in mutated TdT-long form, within Loop3 and Loop1, caused enhanced fluctuations in each of these regions. This is also demonstrated in the covariance/PCA values which were mapped onto the mutated TdT-long form structure along wit...
Data
Similar trends of perturbation observed across different Loop3 conformers. a) PCA from essential dynamics studies of simulations carried out at 311 K mapped onto the different loop conformers of TdT-long form (iTASSER loopmodel, Loopmodel8, Loopmodel 22) and TdT-short isoform (for comparison); b) Distances observed between of residues in Loop1 and...
Data
Correlation matrices for Loop3 conformers of TdT-long form when simulated at 311 K. The top-ranking loop conformers of TdT-long isoform are a) iTASSER loopmodel, b) Loopmodel 8, c) Loopmodel 22 and d) Loopmodel 23 (from PRODAT library of SYBYL, Tripos package). Positive values (red spectrum) indicate correlated motion; negative values (blue spectru...
Data
Illustration of TdT-long docked with its interacting partners. a) TdIF1 and b) PCNA near the thumb region. Binding at similar positions behind the thumb region support the theory that these proteins may competitively bind in order to regulate TdT. [Details referred in S1 File] (TIF)