Department of Chemical Sciences
School of Natural Sciences


April 11, 2014 at 2.30 pm in AG-80

Title :

Molecular Machinery Involved in the Process of Small RNA Mediated Gene Regulation

Abstract :

Micro-RNA (miRNA) and small interfering-RNA (siRNA) are short (~22-nucleotide), single-stranded RNA molecules that regulate gene expression by promoting degradation or translational inhibition of target mRNAs. They influence diverse biological functions through the repression of target genes during normal development and pathological responses. A hallmark of small-RNA mediated gene silencing is a class of approximately 22-nucleotide RNAs that are processed from double-stranded RNA precursors by Dicer. The current model suggests that Dicer selects cleavage sites by measuring a set distance from the 3′ overhang of the double-stranded RNA terminus. Our structural studies on human Dicer in complex with siRNA having different overhang lengths at 5’- and 3’-ends along with in vitro and in vivo functional studies showed that Dicer recognizes both 3’- as well as 5’-ends for proper cleavage of siRNA/miRNA. The 5'-end recognition by Dicer, demonstrated for the first time by us, is important for precise and effective biogenesis of siRNA/miRNA. This study has provided practical benefits to the design of small-RNAs for gene silencing. We also solved the crystal structure of a large complex of Trax–translin heteromers, also known as C3PO, which has been proposed to activate the RNA-induced silencing complex by facilitating endonucleolytic cleavage of the siRNA passenger strand. Our studies establish that Trax adopts the translin fold, possesses catalytic centers essential for C3PO's endoribonuclease activity and interacts extensively with translin to form an octameric assembly. This study provides important insights into the catalytic mechanism of C3PO and its conserved role in human RISC activation. Just as miRNAs and siRNAs bind to the Argonaute proteins, another class of small RNAs encoded in the genome, the Piwi-interacting RNAs (piRNAs), that are 2′-O-methylated at their 3′ ends, bind to the Piwi proteins. Germline-specific piRNAs and Piwi proteins play a critical role in genome defense against transposable elements. Our work on Piwi proteins demonstrated the structural basis for piRNA 2'-O-methylated 3' end recognition by the PAZ domain of Piwi proteins.

April 10, 2014 at 4.00 pm in AG-80

Title :

Structural Insights into Non-vesicular Trafficking of Lipids by Lipid Transfer Proteins and Bacterial Toxin-Antitoxin Systems

Abstract :

Phosphorylated sphingolipid Ceramide-1-Phosphate (C1P) is a key regulator of cell growth, survival, migration and inflammatory responses, but non-vesicular mechanisms involved in its intracellular sensing, transfer and presentation remained unexplored till recently. We have identified a widely-expressed protein, CPTP (Ceramide-1-Phosphate Transfer Protein) in humans, which specifically transfers C1P. Our co-crystal structures established that C1P binding occurs via a surface-localized phosphate head-group recognition center connected to a hydrophobic pocket. Down-regulation of CPTP dramatically alters C1P steady-state levels, decreasing at the plasma membrane while elevating at the trans-Golgi where C1P is produced by ceramide kinase. The elevated C1P triggers proinflammatory eicosanoid generation associated with cellular inflammation, thus highlighting its physiological importance. We have also carried out structure-function studies on lipid transfer proteins involved in cell survival such as “accelerated cell death 11 (ACD11)” protein from Arabidopsis and “heterokaryon incompatibility C2 protein (HET-C2)” from the fungus Podospora anserina which has provided insights on roles of lipid transfer process in cell survival.

             Almost all bacteria and many archaea contain genes (encoding toxins) whose expression inhibit cell growth and may lead to cell death when overproduced, reminiscent of apoptotic genes in eukaryotes. These toxins are co-expressed and neutralized with their cognate antitoxins from TA (toxin-antitoxin) operons in normally growing cells. MazF (toxin) / MazE (antitoxin) system is one of the most extensively characterized TA systems. Under stress conditions, labile anti-toxins (MazE) are readily degraded by proteases allowing MazF (toxin) to cleave mRNA in a sequence specific manner. Recently, we solved the structure of Bacillus MazF in complex with ssRNA containing its target site as well as in complex with its cognate antitoxin MazE. This study has provided for the first time structural basis of recognition and cleavage of mRNA by MazF in a sequence specific manner during stress conditions and also demonstrated how antitoxin inactivates the toxin in normally growing cells.

April 7, 2014 at 4.00 pm in AG-69

Title :

Spectroscopic Studies of Interactions of Some Biologically Important Small Molecules with Proteins

Abstract :

Like other biological macromolecules such as polysaccharides and nucleic acids, proteins are essential parts of organisms and participate virtually in every process within cells. The work is based on studies of the interactions of erythroid membrane skeletal protein, Spectrin and Hb along with serum protein from human (HSA) and from bovine (BSA) and another soluble protein of non-erythroid origin, the lysozyme (Lyz) with small organic molecules like the phosphate metabolite ATP, hemin and other small molecules of therapeutic importance e.g. 4-Nitroquinoline (4NQO), Merocyanine 540 (MC 540) and Imatinib mesylate. To study these interactions we have been using spectroscopic tools like absorption, fluorescence, circular dichroism, synchronous fluorescence, time-resolved fluorescence and theoretical modelling.

            SAs are the most important studied proteins in this field but the structural comparison between HSA and BSA was not studied previously.  This aspect has been highlighted in this thesis while discussing the interactions of MC 540 with both HSA and BSA. The discrepancies between the spectroscopic data obtained with HSA and BSA while interacting with MC 540 depict that although both the SAs have 80% structural similarities but the conformational flexibility is greater in HSA than that of BSA that has further been confirmed by the results obtained from time-resolved fluorescence and induced CD experiments. 

The Hb is the most studied blood protein and its structural changes have strong impact on blood-related or hematological diseases. In case of thalassemia, the prosthetic heme group of Hb is sometimes displaced from heme pocket. This type of phenomenon of heme loss could be stimulated in acidic pH. In erythrocyte cells, the membrane contains different types of phospholipids and cholesterol. Therefore, a detailed discussion on the impact of phospholipids on Hb has been done in my Ph. D. work. The heme loss and the release of oxygen from Hb occur simultaneously. The oxygen affinity of Hb decreases, in some diseased conditions as well as due to interaction with ATP. This aspect has been studied in detail by the spectroscopic techniques. Besides Hb, the Spectrin is also an erythrocyte membrane skeletal protein. The interaction of Spectrin with different phospholipids and drugs were studied previously. Here we have reported our findings regarding the interactions between Spectrin and an antileukemic drug, Imatinib as well as between Spectrin and another antileukemic as well as good fluorescent molecule, MC 540.     


March 24, 2014 at 4.00 pm in AG-69

Title :

'Turn On' Optical Probes for Sensing Manganese

March 20, 2014 at 2.30 pm in AG-80

Title :

Biophysical and Biochemical Studies on Structural characteristics of Plasmodium falciparum P2

March 10, 2014 at 4.00 pm in AG-69

Title :

Elucidating the Copper Binding Properties of Peptide Fragments of the CuA Center in Cytochrome c Oxidase

March 3, 2014 at 4.00 pm in AG-69

Title :

Photoinduced Electron Transfer in DNA Repair: A Computational Study

Abstract :

UV radiation (200-400 nm) causes damage of DNA, mostly producing the cyclobutane
pyrimidine and (6-4)-pyrimidine-pyrimidone (PP) photodimers. (6-4) photolyase is a DNA repair enzyme that selectively repairs (6-4)PP photodimer, using visible light. This repairprocess is a complex photocycle comprising of several electron transfer (ET) steps possibly coupled to proton transfer, controlled by the protein. The key repair steps are the forward electron transfer (FET) and the back electron transfer (BET) which involve the FADH−chromophore and the (6-4)PP. Experimentally, the ET rates of these steps have been estimated, but the overall repair mechanism remains elusive.

We wish to predict the ET rates with in the photolyase repair site and evaluate the roles of various factors that may influence these ET rates. Towards this, we have set up a multiscale computational apparatus based on a combination of QM, hybrid QM/MM and MD methodologies. With this approach, we have computed the energies of the FADH− - (6-4) PP (Donor-Acceptor) complex in different electronic states, formally describing the electron transfer reaction. We then evaluate the effects of the protonation state of key residues, the solvent and DNA counterions on these states and also account for the effect of the protein dynamics. Using these complex energy estimates, we predict the FET and BET rates employing the semi classical Marcus formalism and compare them against the experimental observations.

February 19, 2014 at 2.30 pm in AG-69

Title :

Characterization of the Non-Covalent Interactions of Propofol Using Mass Resolved Spectroscopy

Astract :

Propofol is probably the most widely used anaesthetic and became sadly famous several years ago as the cause of dead of the pop star Michael Jackson. The molecule exerts its action by docking on the GABAA receptors in the central nervous system. But why does it like to interact with the receptor, and how is its trip until it reaches the active site? Using a combination of laser spectroscopy and quantum mechanical calculations, under a reductionist approach, we will try to shed light on the forces that govern such odyssey.


February 18, 2014 at 2.30 pm in AG-69

Title :

Semiconductor Materials for Solar Hydrogen Production Using Water and Abundant Sulfur Compounds

Abstract :

As a clean non-fossil fuel, hydrogen generation by the combination of solar light and semiconductors have drawn great attention as ideal “green” processes for solving global energy and environmental issues. Herein, the recent results of our studies directed to developing semiconducting materials for solar hydrogen production via photodecomposition of water and hydrogen sulfide are presented. Efficient conversion of solar energy to hydrogen via water splitting on photoelectrochemical (PEC) cell is a promising approach. We have developed morphologically modified WO3, doped FeVO4as well as composite CdS/CdSe/ZnS quantum dots decorated titanium dioxide nanotube arrays as photoanode materials, which show significantly improved performances in applications for solar hydrogen generation. The enhancement of photoelectrochemical performances can be attributed to improved electrical conductivities, efficient separation of photoexcited charges and superior charge carrier transport properties of the developed materials. In this talk, hydrogen production from decomposition of H2S using CuAlGaO4as stable and efficient low band gap (1.87 eV) photocatalyst is also presented. Apart from water, H2S which is a toxic gas and produced in large quantities in petroleum refineries has all possibilities for being an alternative source of hydrogen production for both energy and environmental requirements.


February 17, 2014 at 4.00 pm in AG-69

Title :

n-pi* Interaction: Too Weak But Can Compete With Strong Hydrogen Bonding Interaction

February 12, 2014 at 2.30 pm in D-406

Title :

The Role of CH and SH Groups as Hydrogen Bond Donors in Stabilizing Molecular Complexes

February 11, 2013 at 2.30 pm in AG-66


Detecting Reaction Intermediates in Solution and Guiding Cancer Surgery Using Mass Spectrometry


 I wish to describe two recent developments in my laboratory using ambient ionization mass spectrometry, a mass spectrometric technique in which the sample of interest is in open air at room temperature.  The first concerns detection and identification of solution-phase reaction intermediates, the second concerns mass spectrometric imaging.

Palladium complexes catalyze a variety of oxidation reactions, including the Wacker oxidation, the oxidation of alcohols, and oxidative C-C bond-forming reactions.  Simple Pd(II) salts react sluggishly with oxygen, but in the presence of suitable ligands or solvents, Pd complexes are capable of aerobic oxidation reactions.  A key step in these reactions is the oxidation of Pd(0) by O2 to regenerate a Pd(II) intermediate. We have employed a battery of mass spectroscopic techniques such as desorption electrospray ionization mass spectrometry (DESI-MS, millisecond reaction times), electrospray ionization mass spectrometry (ESI-MS, minutes reaction times), and nano-electrospray ionization mass spectrometry (nanospray-MS, minutes reaction times) to search for reaction intermediates formed during the aerobic oxidation of 1,2-diols. By monitoring active reactions with mass spectrometry operating at various timescales, we have directly detected and identified a number of novel intermediates generated in solution during the fast alcohol oxidation and slow aerobic re-oxidation of (neocuproine)Pd(0).  These studies reveal the formation of a novel trinuclear palladium complex, [(neocuproinePd(II))3(m3-O)2]2+.  The identification of this previously unreported species provides new insights on the mechanism of aerobic oxidation mediated by Pd complexes.

Surgical resection is the main curative option for gastrointestinal cancers. The extent of cancer resection is commonly assessed during surgery by pathologic evaluation of (frozen sections) of the tissue at the specimen margin(s). We compare this to an alternative procedure, desorption electrospray ionization mass spectrometric imaging (DESI-MSI), for 62 human cancerous and normal gastric tissue samples. In DESI-MSI, microdroplets strike the tissue sample, the resulting splash enters a mass spectrometer, and a statistical analysis, the Lasso method (multi-class logistic regression with L1 penalty), is applied to classify tissues based on the molecular information obtained directly from DESI-MSI. The results obtained suggest that DESI-MSI/Lasso may be valuable for routinely assessing margins in gastric cancer surgery.

January 31, 2014 at 2.30 pm in AG-80

Title : Understanding the Aggregation Properties of Amyloid Beta Through Solid State NMR and Designed Mutations

Abstract :

Zn+2 can alter the aggregation properties and toxicity of Amyloid beta (Aβ) by selectively precipitating out the soluble oligomers. What does it change? Using Solid State NMR on fibrils Aβ40 grown in the presence of Zn+2, we show that the turn region of the peptide is affected.  We have found that the fibrils of Aβ40 grown in the presence of equal concentration of Zn+2 has a similar hairpin shape but they differs in the turn region. However what we actually need to look at are the biologically active metastable oligomers, (not the fibrils) and focus on the turn region. Using a technique recently developed in the lab for looking at metastable structures, we find that the oligomers are different only in the turn and the terminal regions. This suggests that the conformational change starts at the two hydrophobic arms of the peptide. We are now trying to selectively disturb the stereospecific interaction in the nucleation centre by selective alternation of some amino acids in to their  "dextro" forms, which leaves chemical property of the peptide unchanged.