INFECTIOUS DISEASES / Parasitic Diseases
Structure, dynamics and folding of protein-nucleic acids and protein-protein complexes: Metabolomics
Description of Research
Molecular mechanism of protein-nucleic acid interactions
The main theme of the group is to understand molecular mechanism of interactions between protein and nucleic acids that exhibit a wide spectrum of sequence and shape specificity. The understanding of molecular mechanism of the interaction by highly conserved and abundant RRM proteins will help in formulation of a general code of nucleic acid interaction. This is likely to help in understanding how different set of information is decoded from a limited repertoire of genetic code. Nascent mRNAs, the information carriers, in eukaryotes often called the primary transcripts, undergo extensive chemical modification to produce mature mRNAs before they are directed for protein synthesis.
These modifications are performed by a class of proteins called RNA binding proteins. Although the canonical structure of the well-studied RNA-binding domains is generally quite well conserved and restricted, this domain can readily have subtle structural adaptations and is able to recognize a wide spectrum of different RNA and DNA sequences and shapes. The group effectively uses solution-state NMR spectroscopy, X-ray crystallography and other biophysical tools to decipher the molecular mechanism of different protein nucleic acid interactions.
Many RNA recognition motifs (RRMs) are known to unfold and assemble incorrectly, leading to protein aggregates that cause diseases. In this context we study unfolding and aggregation behaviour of RRMs using solution- and solid-state NMR spectroscopy, fluorescence correlation spectroscopy (FCS) and time-resolved fluorescence spectroscopy.
Metabolomics for Bio-marker discovery
We use solution-state NMR for metabolomics analyses. Among the techniques used for studying metabolites high-resolution solution-state NMR spectroscopy has the advantages of being non-destructive, quantitative, robust and highly reproducible. It is a non-equilibrium perturbing technique that provides detailed information on solution-state molecular structures, based on atom-centred nuclear interactions and properties, which can also be used to explore metabolite molecular dynamics and mobility. It allows the simultaneous detection of a wide range of structurally diverse metabolites, providing a metabolic ‘snapshot’ at a particular time point. Metabolite concentrations down to the micromolar range are readily detectable in biofluids (urine, serum, plasma, saliva) and cell or tissue extracts. We have recently identified metabolic dysregulation in Dengue, Chikungunya, HIV and HEV patients and deciphered the metabolic pathways in fungus and plants.
Ray, S., Pandey, N.K., Kushwaha, G.S., Das, S., Ganguly, A.K., Vashi, N., Kumar D., Suar, M. and Bhavesh, N.S. 2022. Structural investigation on SPI-6 associated Salmonella Typhimurium VirG-like stress protein that promotes pathogen survival in macrophages. Protein Sci. 31, 835-849. DOI: 10.1002/pro.4272 PubMed link
Aggarwal, P. and Bhavesh, N.S. 2021. Hinge like domain motion facilitates human RBMS1 protein binding to proto-oncogene c-myc promoter. Nucleic Acids Res. 49, 5943-5955. DOI: 10.1093/nar/gkab363 PubMed link
Kumari, P. and Bhavesh, N.S. 2021. Human DND1-RRM2 forms a non-canonical domain swapped dimer. Protein Sci. 30, 1184-1195. DOI: 10.1002/pro.4083 PubMed link
Pandey, N.K., Verma, G., Kushwaha, G.S., Suar, M. and Bhavesh, N.S. 2020. Crystal structure of the usher chaperone YadV reveals a monomer with the proline lock in closed conformation suggestive of an intermediate state. FEBS. Lett. 594, 3057-3066. DOI: 10.1002/1873-3468.13883 PubMed link
Bhatt, H., Ganguly, A.K., Sharma, S., Kushwaha, G.S., Khan, M.F., Sen, S. and Bhavesh, N.S. 2020. Structure of an unfolding intermediate of an RRM domain of ETR-3 reveals its native-like fold. Biophys. J. 118, 352-365. DOI: 10.1016/j.bpj.2019.11.3392 PubMed link (Featured on the cover page)
Ganguly, A.K., Verma, G., Bhavesh, N.S. 2019. The N-terminal RNA recognition motif of PfSR1 confers semi-specificity for pyrimidines during RNA recognition. J. Mol. Biol. 431, 498-510. DOI: 10.1016/j.jmb.2018.11.020 PubMed link