What it looks like... determines what it does. In other words, the structure of a biomolecule determines its function. We aim to understand the function of biomolecules by combining results obtained using various techniques such as computational biology, molecular biology, X-ray crystallography, biochemical and biophysical studies. Our current specific goals are to understand the mechanisms of the following:

Protein translation initiation

Figure shows different steps of protein translation in bacteria and eukaryotes (Image source: Schmeing & Ramakrishnan, Nature, 2009; Fraser & Doudna, Nat Rev Microbiol, 2007).

In bacteria, the process of protein translation can be roughly divided into three main stages namely (1) initiation (2) elongation and (3) termination. The initiation of protein translation requires the ribosome to position a unique tRNA (known as initiator tRNA or fMet-tRNAfMet) over the start codon (usually AUG) of mRNA in the P site. The positioning of the ribosome is primarily anchored by base pairing between the 3′ end of 16S RNA and a complementary sequence, upstream of the mRNA start codon (known as the Shine–Dalgarno sequence). In bacteria, three initiation factors (IF1, IF2 and IF3) along with the special initiator tRNA help in the precise positioning of the start codon in the P site of the ribosome. In eukaryotes, the protein translation initiation requires approximately 9-12 initiation factors. In contrary to bacterial systems, in eukaryotes, the initiation comprises of two steps. Firstly, the formation of 48S initiation complexes (IC) consisting of 43S pre-initiation complexes (PIC: 40S ribosomal subunit, eIF2-GTP-fMet-tRNAfMet and probably other initiation factors) and the established codon-anticodon base-pairing in the P-site. In the second step, IC joins with the 60S ribosomal subunit. On most mRNAs, 48S complexes form by a ‘scanning’ mechanism, whereby a 43S PIC attaches to the capped 5′ proximal region of mRNAs. Although most mRNAs use the scanning mechanism, initiation on a few mRNAs is mediated by internal ribosome entry sites (IRESs). However, exactly how the correct tRNA during the initiation and elongation stages of protein translation is selected and/or differentiated remains unclear, as are the roles of the various factors. The mechanism of protein translation initiation is still not clearly understood owing to a paucity of structural data.

Protein translation and antibiotic resistance
Different steps of protein translation and antibiotic resistance (Image source: Wilson, Nat Rev Microbiol, 2014).

Antibiotic resistance is a phenomenon of crucial importance in the treatment of diseases caused by pathogenic microorganisms. Bacteria have evolved various strategies to evade the cytotoxic effects of antibiotics. One of these stragies is alteration of the antibiotic binding site by enzymatic modifications. A major antibiotic binding site is the ribosome and is targeted by a large and chemically diverse group of antibiotics. Nature has evolved an effective and elegant ways of preventing drug binding to the ribosome , one of them is by adding methyl groups to ribosomal RNA at appropriate sites. These modifications are carried out by a group of enzymes called methyltransferases, which functions in a very site-specific manner. Our objectives are to explore more of these methyltransferases and their mechanism of rendering antibiotic resistance.

Membrane dynamics and drug resistance
Maintenance of lipid asymmetry in Gram-negative bacteria (Image source: Malinverni & Silhavy, PNAS, 2009).

Bacterial membrane is a complex and highly asymmetric biological barrier which protects bacteria against a harsh environment. A balanced chemical composition of membrane is essential for the membrane function and its viability. Several mechanisms have been proposed that modulate membrane permeability in normal as well as stress conditions. We are trying to understand the mechanistic insight of an ABC transporter which regulates membrane kinetics. This study would help in designing structure-based inhibitors against multi-drug resistance and hereditary diseases.

ABC transporters and multi-drug resistance

A frequent impediment to the effective treatment of infectious and malignant diseases is the development of multi-drug resistance. Till date, several drug-resistance mechanisms have been suggested. One of the those mechanisms is by effluxing out drugs from the cell. Thus, involvement of ABC transporter proteins superfamily seeks a special interest. We aspire to elucidate the mechanism of efflux pump-mediated drug resistance.
Proposed functionally rotating ordered multidrug binding change mechanism (Image source: Murakami et al., Nature, 2006).