TIFR
Department of Chemical Sciences
School of Natural Sciences

Calender

September 12, 2014 at 2.30 pm in AG-80

Title :

Structural Biochemistry : Insights into Biological Reactions

Abstract :

A combination of X-ray crystallographic and biochemical techniques can be employed to develop insights into several aspects of biological function like mechanism of catalysis, structure-function relationships, protein-protein interactions in enzymes and protein-DNA regulation. The three-dimensional structure enables one to visualize protein structures at the atomic level and enhances our understanding of protein function and combined with other tools can facilitate understanding of the allosteric changes necessary for catalysis.

In this talk we discuss two enzyme systems: the first problem deals with deciphering the structure-activity and evolutionary relationships of enzymes involved in nucleobase
deamination. The enzyme under investigation, NE0047 was established to be a guanine deaminase with moonlighting activity towards ammeline. Subsequently, the allosteric mechanism of action and structural basis of substrate specificity was determined. By utilizing the information obtained, the enzyme was further engineered so that it can function either exclusively as a guanine deaminase or serve as a specific ammeline deaminase with no cross reactivity.

The second work deals with understanding the mechanism of antibiotic regulation and
resistance in Streptomyces. Streptomyces species contribute to two-third of the naturally occurring antibiotics. Production of antibiotics and resistance pathways in these species are dictated by interplay of transcriptional regulatory proteins. These proteins belong to the tetracycline family of efflux pump regulators and possess a ligand binding and a DNA binding site, both of which remain elusive. To decipher the structural mechanism of action, here we present the crystal structure of CprB (a putative regulator) in complex with its consensus DNA element. The binding of the DNA induces the restructuring of the CprB dimeric interface, thereby inducing a pendulum like motion. This facilitates transcription regulation via conformationally switching of the protein to the repressed form. Furthermore, it was established that CprB is a pleotropic regulator that also autoregulates it own expression. The identity of the ligand that induces transcriptional activation of CprB was additionally explored and it was concluded that CprB likely possess dual triggers. It may be induced by quorum sensing molecules in early stages of growth and antibiotic intermediates in late growth phase.

September 8, 2014 at 4.00 pm in AG-69

Title :

Understanding the Photophysical Behavior of Some Exciting Biologically Relevent Probes in Homogeneous Medium and Micro-heterogeneous Environments - A Fluorescence Based Study

Abstract :

Proposed discussion will be revolve around a particular study containing the synthesis ofsome new and exciting biologically relevant probes and their derivatives having some specific applications to explore the basic photo physics of this compounds in homogeneous as well as micro-heterogeneous environment using different florescence based spectroscopic techniques.Inthis particular talk the dynamics and binding of these probes with some confined geometries, ranging from ‘‘spheres’’ (micelles) and ‘‘cones’’ (cyclodextrins) to the more complex, three-dimensional networks of structures (proteins) will be discussed extensively. The photodynamic in the “cavity-free” homogeneous media will also be discussed. The discussion will also include the verification of experimental findings through substantial quantum chemical calculations using ab-initio methods and/or density functional theory (DFT) based computations.

August 25, 2014 at 4.00 pm in AG-69

Title :

Perturbative Approximations to Spin Flip Coupled Cluster Singles Doubles - Application to Bond Breaking Problem

Abstract:

Spin flip equation of motion coupled cluster (EOM-SF-CC) can correctly treat situations involving electronic degeneracies or near degeneracies, e.g, bond breaking, di- and tri-radicals etc. However, for large systems EOM-SF-CC (even in single and double excitations) is
computationally prohibitively expensive. Therefore, earlier approximations to EOM-SF-CC methods such as spin flip configuration interaction singles with perturbative doubles (SF-CIS(D)) has been proposed. In this talk, I will present a new perturbative approximation to EOM-SF-CC, which has been found to be more accurate than the earlier SF-CIS(D). The capabilities, advantages and timings of the new approach will be demonstrated through bond breaking problems, oxirane ring opening and cyclo-butadiene automerization reaction.

 References:

1.      A. K. Dutta, S. Pal And D. Ghosh, Perturbative approximations to single and double spin flip equation of motion coupled cluster singles doubles methods, J. Chem. Phys., 139, 124116  (2013).

2.      D. Ghosh, Perturbative approximation to hybrid equation of motion coupled cluster / effective fragment potential method, J. Chem. Phys., 140, 094101 (2014).

 

August 22, 2.30 pm in AG-80

Title :

Self Assembly of Topologically Complex Architectures and DNA Based Materials

Abstract :

Dynamic Combinatorial Chemistry (DCC) is a concept where reversible chemistry under thermodynamic control is used to generate complex dynamic libraries. In this talk I will describe the application of DCC towards the supramolecular self-assembly of amino acid derived building blocks into hydrogen-bonded nanotubes with the ability to encapsulate fullerenes. Moving on, I will also illustrate the importance of the hydrophobic effect in the formation of topologically complex molecules such as molecular knots and links.

 

In the second part of my talk, I will extend the principles of supramolecular chemistry to the self-assembly of multilayered 2D and 3D DNA nanostructures: DNA origami. DNA nanostructures have significant applications in biomedicine due to their biodegradability and their ability to be site specifically functionalized allowing for precise interactions with target molecules and cells. Currently, the biomedical applications of DNA nanostructures are, however, hindered due to their structural instability and nuclease degradability in physiological buffers. After a brief introduction to the field of DNA origami I will give an update on the development of a novel oligolysine based method that provides intracellular stability to DNA nanostructures for biomedical applications such as the design of a DNA based cancer adjuvant.


August 21, 2.30 pm in AG-80

Title :

Molecular Knots and Antimicrobial Peptides

Abstract :

Molecules with complex topologies, such as molecular links and knots, are often found in nature, but remain extremely difficult to synthesize using the current methods of chemistry. Over the past 30 years, the only strategy for the synthesis of molecular knots has been reliant on metal templation.1 Through our work on dynamic disulfide chemistry, we established that the hydrophobic effect can provide a powerful alternative synthetic strategy that enabled us to synthesize a variety of different knots, some of which had remained elusive until now: Hopf links,2,3 Solomon links,4 trefoil knots,5 and figure eight knots.4 In some cases, the hydrophobic effect overcomes electrostatic interactions between electron-rich and electron-deficient aromatic units, leading to the formation of unconventional structures that seem to contradict the current models of donor-acceptor interactions. A mechanism that succeeds in rationalizing and predicting their formation was proposed. This mechanism represents a major advance in understanding the role of hydrophobic effect in the assembly of complex architectures


In the second part of my talk, I will outline my current work on human defensins 5 and 6 (HD5-6), small (2-5 kDa) cysteine-rich host-defense peptides, which are key contributors to innate immunity and provides the first line of defense for detection and response to microbial invasion.6 Paneth cells protect the intestinal epithelium against infection and colonization of pathogenic or opportunistic microbes by secreting a mixture of antimicrobial peptides and proteins that includes HD5 and HD6. Although both peptides exhibit a common tertiary structure, they possess unique functional attributes. HD5 has broad-spectrum antibacterial activity in vitro. In contrast, HD6 provides only negligible antimicrobial activity in vitro but forms nanonets-like higher-order oligomeric structures that entrap bacteria in the intestinal lumen in order to prevent invasion. In the oxidized forms, both defensins contain three conserved and regiospecific intramolecular disulfide bonds. We explored the redox properties of these disulfide bonds and their role to maintain the peptides antimicrobial function. These peptides can interact with various metals, notably zinc,7 an important metal controlling the immune response.

August 13, 2.30 pm in AG-69

Title :

Design of Nanostructures for Energy and Environmental Applications

August 11, 2014 at 4.00 pm in AG-69

Title :

Engineering Proteins Towards the Development of Optical Sensors for Anionic Phospholipids

 

August 4, 2014 at 4.00 pm in AG-69

Title :

Ultrafast Hole and Electron Transfer Dynamics in Super-sensitized Quantum Dot Solar Cell Materials

July 28, 2014 at 4.00 pm in AG-69

Title :

Regio- and Stereo-selective Approaches for Glycoconjugate Synthesis

Abstract:

Cell surface carbohydrates in the form of glycoconjugates play vital roles in various important life processes. They are structurally complex and diverse. Since they are present in microheterogeneous forms in nature, they cannot be isolated in acceptable amount and purity. Chemical synthesis, however challenging, provides an opportunity for obtaining structurally well defined and chemically pure glycoconjugates for biological studies. Regio- and stereoselective approaches make the synthesis less arduous and more efficient. Recent examples from our studies on the synthesis of complex carbohydrates will be presented.

July 21, 2014 at 4.00 pm in AG-69

Title :

Towards Understanding the Mechanism of Amyloid Beta Mediated Toxicity in Alzheimer's Disease

June 16, 2014 at 4.00 pm in AG-69

Title :

Understanding Bio-molecular Interactions for Novel Drug Discovery: Biophysical Approach

Abstract :

More than the synthesis of a large number of new molecules, the challenge faced by the pharmaceutical industries is to exploit the wealth of these compounds and relate their activity to the mode of interaction with the relevant targets of biological importance. This requires an in-depth understanding of intermolecular interactions responsible for therapeutic intervention. Recent advances in methodologies to unravel the intricate intermolecular interactions have added tremendous amount of understanding in such phenomenon. The talk will address biophysical approach to understand the binding of some antibiotic and anti cancer drugs with serum albumin in view of the importance of drug-protein interactions in drug delivery. This requires a detailed structural, conformational and energetic investigation. The talk will also address the screening of GlaxoSmithKline compound library in search of tuberculosis active compounds which target Mycobacterium tuberculosis topoisomerase-I through stabilized cleaved topoisomerase I - DNA complex mechanism and serve as Mycobacterium tuberculosis topoisomerase I poison to cure XDR and MDR tuberculosis.

May 30, 2014 at 2.30 pm in AG-80

Title :

A Journey from Ordered Mesostructures to Chalcogels: Porous Semiconducting Metal Chalcogenide Aerogels

Abstract :

Mesoporous materials are important in shape selective separations, catalysis, nano-electronics and in the case of metal sulfides, photonics and nanotechnology. Aerogels are another class of low density porous materials. A wide range of binary and mixed metal oxide analogues have been developed in the past. However, non-oxidic counterparts of those are less studied and could be of great interest as well. The goal of the project is to build high surface area metal chalcogenide frameworks and aerogels to create a general methodology. Surfactant directed assembly of metal chalcogenide building units is shown as a method to construct semiconducting mesostructured materials. In addition, a simple metathesis reaction is applied for the first time to generate a broad class of metal-chalcogenide gels and aerogels. The chalcogenide surfaces of these novel semiconductors possess interesting adsorption properties and show promise towards removing heavy metals from water and separating CO2 over H2. Additionally, these aerogels act as efficient hydrodesulfurization and solar fuel catalysts. In this talk an overview of the semiconducting nanoporous project will be presented.

May 29, 2014 at 4.00 pm in AG-80

Title :

Earth-Abundant Thin-Film Solar Cells

Abstract :

Given the remarkable potential of photovoltaic (PV) technology to displace non-renewable electricity generation based on fossil fuels if associated manufacturing costs can be made competitive, there is a tremendous need for low-cost, environmentally benign materials and fabrication processes for preparing high-performance solar cells. In this regard, thin-film heterojunction PVdevices are particularly interesting because of their reduced material utilization and simple cell design. In thin-film devices, a wide range of semiconducting materials can be used as the solar absorber, among which the kesterite Cu2ZnSn(SxSe1-x)4 (CZTSSe) family has been getting significant recent attention due to its earth-abundant and less toxic constituents. Here I will present development of >10% efficiency CZTSSe solar cells based on a novel thin-film deposition approach.

May 27, 2014 at 2.30 pm in AG-69

Title : to be announced

May 26, 2014 at 4.00 pm in AG-69

Title : To be announced