TIFR
Department of Chemical Sciences
School of Natural Sciences

Calender

October 21, 2016 at 2.30 pm. in AG-66

Title :

Design and Synthesis of Polymeric Materials: Structure-Property Relationship via Self-assembly and Biomedical Applications

Abstract :

Design and validation of pericyclic reactions for sensing conformational stretching in polymer materials.

The naphthalene and anthraquinone based fluorescent reporter molecules were synthesized in multistep for monitoring pericyclic reactions in polymers. These reporter molecules were incorporated into polymer backbones by click reactions. The reaction was monitored optically and optimized using organic chemistry characterization techniques. The mechanical force felicitate to bonds to come into proper orientation for claisen reaction to occur. The overall goal of the research is to design, implement, and validate functional groups designed to react specifically within stressed polymer materials to signal the onset of mechanical failure.

 

Design and synthesis of Novel Alternating sulfone copolymers for biomedical applications

Interest in stimulus-responsive polymers and materials has been increasing in recent years. In particular, efforts to apply these polymers for biomedical applications have focused on changing the structure of assemblies and particles in response to both endogenous molecules and externally-applied energy sources to release drugs, activate contrast agents, or initiate fluorescent signal. Sulfur dioxide has been shown to copolymerize with certain vinyl monomers in a specifically alternating manner, provided that the vinyl group is immediately adjacent to an electron-donating group; examples include vinyl acetate, vinyl carbonate, and olefins. The resulting copolymer possesses a low ceiling temperature. The depolymerisation of poly(vinyl acetate-alt- sulfur dioxide) as initiated by chemical stimuli such as reactive oxygen species (ROS) and mechanical stimuli was studied as a proof of concept. Then, a novel class of hydrolytically depolymerizable macromolecules, poly(O-vinyl carbamate-alt-sulfones), were synthesized via free radical polymerization with excellent functional group tolerance. The polymers were then found to form nanoparticles capable of encapsulating both Rhodamine B and Alexa Fluor 488, and the resulting particles were labile at pH > 6. Finally, these particles were found to retain their contents in mucus at pH 5 but release it at pH 8, resulting in an increase in diffusivity of encapsulated fluorophores from very small to matching that of free dye. Current efforts are focused on adapting the polymers and their particles for mucosal drug delivery.

 

During doctoral studies, my research focussed on the self assembling behavior of various pyrene labeled polymers having different architecture like homopolymers, block, and random copolymers, where the pyrene labeling was varied from 1-100%. The photophysical properties were studied using various fluorescence techniques like steady-state and life time decay analysis as well as time resolved emission spectra (TRES). The applicative aspect of the pyrene labeled polymers was also shown by rhodamine dye encapsulation and release studies as a function of temperature and its temperature triggered release was also used as a handle to understand the microstructural changes inside the polymer microcapsule.

 

Thus, the thesis analyses the following important aspects:

 

1.    Exploration of fundamental aspects of the self assembly of different pyrene labelled polymers like block, random or homopolymers by the detailed photophysical analyses

 

2.    Applicative aspects of the pyrene labeled polymers: probed by rhodamine B encapsulation and release.

 

3.    Self assembly behavior in H-bonded versus non-H-bonded polymers at very dilute concentrations: differences and similarities.

 

 4.       Architectural differences among the polymers: probed by TRES and temperature dependent fluorescence.

October 17, 2016 at 4.00 pm in AG-69

Title :

Design and development of optical probes for imaging signal mediating phospholipids

October 3, 2016 at 4.00 pm in AG-69

Title :

 An energy landscape perspective of biomolecular structure and dynamics

 Abstract :

 During the last decade, the concept of energy landscapes has emerged as a unifying theme in seemingly disparate disciplines, such as biomolecular folding and aggregation, self-assembly, and glassy dynamics, and have provided fundamental insight into the thermodynamics and kinetics of complex systems. For many practical applications, it is often sufficient to consider a coarse-grained description of the landscape, in terms of stationary points (energy minima and transition states). This coarse-graining eliminates the need for dynamical sampling, and stationary points on the underlying landscape can be located in a time-independent fashion, exploiting tools of geometry optimisation. This approach offers several key advantages over conventional rare event sampling techniques, particularly for complex landscapes featuring broken ergodicity, and characterised by multiple relaxation time scales. My talk will discuss the methodological aspects of the computational energy landscape framework, and highlight some recent applications to the study of biophysical problems of contemporary interest, such as RNA folding, conformational switching between alternative folds in DNA and peptides, and structural heterogeneity in intrinsically disordered proteins.

September 20, 2016 at 2.30 pm in AG-69

Title :

Nano-bioconjugation of Mutant Cytochrome P450cam for Biocatalysis

September 19, 2016 at 4.00 pm in AG-69

Title :

Catalysis for Sustainable Development

Abstract :

Catalysis plays a key role in chemical industry. More than 90% of all chemical reactions use catalysts. It is projected that the world demand for catalysts may grow by 4.8% per year, to a value of about US$ 20.6 billion in 2018. This growth will be primarily led by polymer and chemical industries. Additionally, it is speculated that the majority of the share of this growth would occur from developing areas such as the Asia/Pacific and Africa/Mideast regions. Raw material availability is one of the issues the chemical industry is facing. While most of our energy and chemical needs are derived from non-renewable fossil feedstocks (petroleum, natural gas and coal), time has come to switch the chemical processing from the conventional to the non-conventional, renewable feedstocks. There is a great challenge to tune the catalysts for such transformations. My talk addresses catalytic conversion of biomass and carbon dioxide into fuels and chemicals. India has a surplus amount of inedible biomass and at the same time bound to follow the COP-21 resolution for reduction in carbon emissions. Utilization of biomass and CO2 would perhaps lead to low carbon footprint. The influence of catalyst hydrophobicity in biomass transformations and acid/base bi-functionality in CO2 conversions would be discussed.   

September 15, 2016 at 2.30 pm in AG-80

Title :

Alkyl Chain Tethered Dansyl, 1-Naphthyl and Acridinyl Fluorophores: Synthesis and Photophysical Studies

Abstract :

Conjugated fluorescent molecular probes are known to be efficient in probing structural and dynamical information of a variety of aggregates and organized systems. As these find a definite location into the organized assembly they cause less perturbation to the system. The main advantage of this type of probes is to design such probes as per the demand of the site to be investigated. 1  The hydrophobic tail contains dansylamide, 1-naphthol and 9-aminoacridine derivatives have been synthesized and evaluates towards their fluorescent probe properties. The long hydrophobic chain containing dansylamide derivative (DAN-PA) shows better sensitivity towards solvent polarity as compared to the short hydrophobic chain analogue (DAN-ACYL). DAN-PA can monitor premicellar aggregation of sodium deoxycholate (NaDC) in water. DAN-PA is also found useful to understand the micellization process of surfactants like NaC, SDS and CTAB. 2 DAN-PA shows more affinity towards β-CD as compared to DAN-ACYL. Its fluorescence intensity is quite sensitive towards thermotropic phase changes of lipid bilayer membrane. 1-Naphthol (NpOH) is an excited state proton transfer (ESPT) molecular probe which is a weak acid in the ground state (pKa = 9.2), but a strong acid (pKa* = 0.4) in the excited state. 3 In the aqueous medium, the proton transfer of short hydrophobic tail containing p-5C-NpOH is faster than long tail containing p-13C-NpOH. Shorter chain derivative (p-5C-NpOH) is a better ESPT probe to understand the micellization of CTAB, SDS and Tween-20 as compare to p-13C-NpOH because its proton transfer process shows the significant amount of anionic and neutral intensities in the aqueous medium. Acridine is a good DNA binding probe. In acidic pH, it exists in the protonated form (AcH + ) and in alkaline pH, it exists in neutral form (Ac). 4 The decrease in fluorescence intensity of 9-aminoacridine (AC) and its derivative (AC-PA) (the substrate is bound to DNA) is because of static quenching. 9-aminoacridine upon substitution (AC-PA) binds more efficiently to DNA by an order of magnitudes as compared to the un-substituted 9-aminoacridine (AC). DNA melting studies suggest that both 9-aminoacridine (AC) and its derivative (AC-PA) bind with DNA through intercalation binding.

 

References:

1. Rohacova, J., Marin, M. L., and Miranda, M. A., J. Phys. Chem. B, 2010, 114, 4710.

2.Tripathi, A. K., Mohapatra, M., and Mishra, A. K., Phys.Chem.Chem.Phys.,2015, 17, 29985.

3. Mandal, D., Pal, S. K., and Bhattacharyya, K., J. Phys. Chem. A, 1998, 102, 9710–9714.

4. Sayed, M., and Pal, H., Phys. Chem. Chem. Phys., 2015, 17, 9519.

August 9, 2016 at 4.00 pm in AG-80

Title :

Structural and Functional Characterization of an Unusual Ca2+ Binding Protein from E. histolytica

May 9, 2016 at 4.00 pm in AG-69

Title :

Understanding the Role of Specific Hydrophobic Interaction in Amyloid Conformation and Function

 

May 6, 2016 at 2.30 pm in AG-80

Title :

Biophysical Insights into the Ras-Membrane Interactions

Abstract :

This talk would deal with the biophysical study of Ras protein-membrane interactions. Ras proteins existing as four isoforms, act as membrane-associated molecular switches in the early steps of signal transduction pathways associated with cell growth and differentiation. For their biological activity, these proteins need to be anchored to membranes, which is achieved by post-translational lipidation. Deregulated isoform-specific Ras signaling accounts for 30% of all human tumors, thus placing them at the focal point of academic and pharmaceutical research. Despite their enormous potential as drug targets, pharmacological intervention of Ras driven cancers has not been realized till date and is dubbed as a “holy grail” in cancer therapy. Due to the common structures of Ras isoforms, most drugs often lead to undesirable off-target effects. Thus, a major hurdle in drugging Ras in a specific manner has been the lack of detailed molecular level characterization of these proteins in their cellular environments. Using various state-of-the-art spectroscopic and microscopic techniques,comprehensive biophysical characterization of the structural and conformational changes in Ras isoforms, upon incorporation into heterogeneous model membrane systems, was accomplished. The main results elucidate key codecs for Ras isoform diversity, providing critical hints to target Ras in an isoform-specific manner. Moreover, highly decisive and critical roles for lipid membranes in Ras protein biophysics, ranging from dictating Ras orientational flexibility, conformational dynamics, and mechanosensitivity, to modulating the interactions of Ras with other proteins would be demonstrated by the presented work.

May 5, 2016 at 2.30 pm in AG-80

Title :

Small-molecule Mediated Modulation of Signaling Pathways

Abstract :

The talk will focus on small molecule–mediated modulation of signaling pathways. Systematic application of small molecule modulators of protein function for the study of biological networks involved in signaling pathways lies at the heart of an experimental approach termed as Chemical Biology.

Wnt signaling is a branch of a functional network involved in a broad range of biological processes, such as development and homeostasis. It is one of the fundamental oncogenic pathways, and is implicated in multiple cancers. Thus targeting this pathway is an attractive therapeutic approach. Within the framework of biology oriented synthesis (BIOS), screening of the natural product inspired withanolide-based compound collection revealed potent inhibitors of Wnt signaling (IC50 = 100 nM) in human colorectal cancer cells. An assortment of different biochemical, cell biological and proteomic methods-based primary and secondary assays, were used to validate the bioactivity of our „lead compound“ in the Wnt pathway. Our efforts towards identification of the compound’s target protein will be discussed. Through a similar approach in a parallel project, a potent and selective small molecule inhibitor of cytokinesis was identified and validated.

 

May 2, 2016 at 4.00 pm in AG-69

Title :


Fluorescent Sensors for Imaging the Signal Mediating Phospholipids

April 25, 2016 at 4.00 pm in AG-69

Title :

Understanding the Mechanical Properties of Azurin Using Single Molecule Force Spectroscopy and Steered Molecular Dynamics

April 21, 2016 at 2.30 pm in AG-80

Title :

Novel Protein Targets of Multi Drug Resistant Acinetobacter baumannii

Abstract :

In the current scenario, widespread multidrug resistivity in ESKAPE pathogens demands identification of novel drug targets to keep their infections at bay. For this purpose, we have identified histone acetyltransferase Hpa2 and DNA-repair enzyme TAG of A. baumannii. Correct sequence alignment and construction of 3D monomeric and dimeric models of proteins having optimal structural parameters is a troublesome task. To overcome these problems, we have designed an easy and optimized protocol for homology modeling. Improvement in the structural features of protein is an onerous process and generally achieved by paying time and computational cost. Herein, it is achieved by reconciliation of FoldX commands which takes less time in execution. Evaluations performed to validate structural parameters and stability of models attests to its quality.

Hpa2 and TAG protein genes were cloned and heterologously expressed in bacterial expression system. The expressed protein was purified up to 98% homogeneity by a two-step purification protocol involving affinity purification followed by the size exclusion chromatography step. The biophysical studies (CD, Fluorescence and ITC) were carried out to characterize the structural and substrate/inhibitors binding parameters.The oligomeric state of enzymes determined in presence of various substrates as well as in extreme physiological conditions using analytical size exclusion, native PAGE and glutaraldehyde crosslinking assay. The enzyme activity is checked using simplified HPLC based biochemical assay. The Hpa2 and TAG proteins were put onto crystallization trials using commercial Hampton screens. The outcomes of these studies will be presented.  

April 18, 2016 at 4.00 pm in AG-69

Title :

Design of CO2 Sorbents Using Functionalized Fibrous Nanosilica (KCC-1: Insights into the Effect of the Silica Morphology (KCC-1 vs. MCM-41)

April 11, 2016 at 4.00 pm in AG-69

Title :

TiO2 coated fibrous nanosilica (KCC-1) for photocatalysis: Particle formation and size quantization