The genome sequencing projects have provided new opportunities and challenges to the field of structural biology. Genomic sequence data provide one step toward a broader and more complete understanding of the molecular basis of life. The next stage of this project is to characterize the structures and function of corresponding gene products, and to integrate this information in expanding our understanding of structure-function relationship, protein folding, evolution, and the general principles of biology.


In pursuit of the above goals, we are using multidimensional solution-state Nuclear Magnetic Resonance (NMR) spectroscopy and X-ray crystallography to understand the structure, dynamics, function and folding of important Biological macromolecules.

 

Molecular mechanism of Protein-RNA interactions 

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The main theme of our group is to understand molecular mechanism of interactions between protein and RNA 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 RNA 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 as the primary transcripts undergo extensive chemical modification to produce mature mRNAs before they are directed for protein synthesis. These modifications performed by a class of proteins called RNA binding proteins. Although the canonical structure of the well-studied RNA-binding domains is generally quite conserved and restricted, this domain can readily have subtle structural adaptations and is able to recognize a wide spectrum of different RNA sequences and shapes. Our group effectively uses solution-state NMR spectroscopy, X-ray crystallography and other experimental tools to decipher the molecular mechanism of different protein RNA interactions.

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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.

 

Intrinsically disordered proteins

Genomic data suggest that about 20-30% of genome codes for Intrinsically Disordered Proteins (IDP) or natively unfolded proteins. In most cases flexible state is necessary for their function and regulation. Therefore, it is structural and dynamical studies of such system are required for understanding their function. NMR spectroscopy, in addition to its normal application for 3D structure determination of folded proteins, is unparalleled in its ability to provide atomic resolution structural and dynamical information of unfolded and flexible proteins and their complexes. We use latest multidimensional NMR methods for atomic resolution characterization of IDPs and their complexes. 

Recently provided molecular insight into interaction between KAHRP and PfEMP1 that takes place at membrane knobs during Plasmodium invasion. In the study using solution-state NMR spectroscopy, calorimetry, confocal microscopy and transmission electron microscopy (TEM) we have identified four positively charged, linear sequence motifs of high intrinsic mobility on KAHRP that interact electrostatically with PfEMP1 in solution to form a fuzzy complex. 

 

Metabolomics

 

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Among the techniques used for study of metabolites high-resolution solution-state NMR spectroscopy has little advantages over other as it is a quantitative nondestructive, noninvasive, non-equilibrium perturbing technique that provides detailed information on solution-state molecular structures, based on atom-centered nuclear interactions and properties. It can also used to explore metabolite molecular dynamics and mobility (such as ligand–protein binding). Further, NMR is a robust and reliable technique for metabonomic applications in which high reproducibility is paramount. It allows the detection of a wide range of structurally diverse metabolites simultaneously, providing a metabolic ‘snapshot’ at a particular time point. Metabolite concentrations down to the few micromolar range are readily detectable. Biofluids particularly urine and serum or plasma or cell or tissue extracts are used as primary sources of metabolic fingerprint data. Using automatic sample handler hundreds of samples per day can be measured on one spectrometer, each taking a total data acquisition time of typically 5 min with minimal sample handling or pretreatment.