TIFR
Department of Chemical Sciences
School of Natural Sciences

Calender

February 23, 2017 at 2.30 pm in AG-80

Title :

A Theoretical Model to explain the DNP Induced NMR Signals Using TEMPOL at 3.4 T

Abstract :

Dynamic nuclear polarization (DNP) is one of the most efficient methods to increase the sensitivity of NMR and MRI by transferring polarization from electron spins to nuclear spins.  For radicals in solid solutions the nuclear signal enhancements during microwave irradiation are interpreted either using the thermal mixing (TM) mechanism or a combination of the solid-effect (SE) and cross-effect (CE) mechanisms.  Although the SE and CE based analysis of the lineshape of the enhancement as a function of the MW frequency has been possible, it was only realized recently that these lineshapes are correlated to the electron polarization distribution in the sample. To quantify this correlation a theoretical model was introduced based that describes the electron spectral-diffusion (eSD) mechanism and its contribution to DNP through the new indirect-CE (iCE) mechanism. 

February 21, 2017 at 2.30 pm in AG-69

Title :

Directed Evolution of Thermally Stable Cytochrome P450: An Approach for Alkane Hydroxylation

February 20, 2017 at 4.00 pm in AG-69

Title :

Bi-ion : A new electroactive species for batteries

February 17, 2017 at 2.30 pm in AG-69

Title :

Cryo-electron microscopy (cryo-EM) studies of mammalian mitochondrial and Mycobacterium smegmatis ribosomes

Abstract :

Ribosomes the protein synthesis machinery are large macromolecular complexes. The mammalian mitochondrial ribosomes (mitoribosomes) are responsible for synthesizing 13 membrane proteins that form essential components of the complexes involved in oxidative phosphorylation (or ATP generation) for the eukaryotic cell. The mitoribosome contains significantly smaller rRNAs and a large mass of mitochondrial ribosomal proteins (MRPs), including large mito-specific amino acid extensions and insertions in MRPs that are homologous to bacterial ribosomal proteins and an additional 35 mito-specific MRPs. The cryo-EM structures of the mitoribosome have yielded the architecture of small subunit of the mitoribosome and existence of the previously eluded E-site within the mitoribosome. The mitoribosomes are susceptible to the antibiotics that targets the bacterial ribosomes because the mitoribosomes are believed be of prokaryotic origin. A docking study of antibiotics in to bacterial and mitochondrial ribosomes have provided rational to the differential affinity of these antibiotic. 

 

Mycobacterium smegmatis is widely used as a model organism to study pathogenic mycobacteria, such as Mycobacterium tuberculosis. About one third of M. smegmatis mRNAs are leaderless, lacking a 5’UTR and therefore also lacking a Shine-Dalgarno sequence. How ribosomes initiate protein synthesis from leaderless mRNAs is unknown. We have obtained a 5 Å resolution cryo- EM map of the M. smegmatis 70S ribosome, with some core regions resolved to 4 Å. Our map reveals two unique features of the mycobacterial ribosome: (i) an altered conformation of the previously identified steeple feature on the large (50S) ribosomal subunit (ii) a novel protein density mass is found below the origin of the rim of the small (30S) ribosomal subunit platform that appears to correspond to an α-helical structure of up to ~33 amino acid residues. While we continue to improve the resolution of our cryo-EM map, we are also using mass spectroscopy to identify the α-helical density. I will summarize the results of these studies that I have been involved in, and will outline my future research plan on the protein synthesis in Plasmodium falciparum ribosome that I would like to pursue as an independent investigator.

 

February 16, 2017 at 2.30 pm in AG-80

Title :

The cryo- electron microscopy (cryo-EM) structure of the group II intron at 3.8 Å resolution

Abstract :

Single-particle cryo-electron microscopy (cryo-EM) is an emerging technique in the field of structural biology. With the recent advancement in electron detection technology and improved image processing algorithms, now it is possible to achieve atomic resolution structure of macromolecular complexes.  We have been applying cryo-EM to illustrate the architecture of ribonucleoprotein complexes, such as bacterial group II introns and ribosomes. Bacterial group II introns are large catalytic RNAs related to nuclear spliceosomal introns and eukaryotic retrotransposons. They self-splice, yielding mature RNA, and integrate into DNA as retroelements. A fully active group II intron forms a ribonucleoprotein complex comprising the intron ribozyme and an intron-encoded protein that performs multiple activities including reverse transcription, in which intron RNA is copied into the DNA target. Recently, the first cryo-EM structure of Lactococcus lactis group IIA intron, in complex with an intron-encoded protein, was resolved at 3.8 Å resolution and its protein-depleted form at 4.5-Å resolution. Molecular analysis of the cryo-EM structure of the group II intron reveals functional coordination of the intron RNA with the protein. Interestingly, the protein structure revealed a close relationship between the reverse transcriptase catalytic domain and telomerase, whereas the active splicing center resembles the spliceosomal Prp8 protein. These extraordinary similarities hint at intricate ancestral relationships and provide new insights into splicing and retromobility. I will highlight the recent development in the cryo- EM field and summaries our findings on group II introns.

February 15, 2017 at 2.30 pm in AG-80

Title :

DNA Based Emerging Technologies for Biological and Bioengineering Applications

Abstract :

Structural DNA nanotechnology explores various nanoscale structural and functional properties of DNA to manipulate matter at nanoscale for diverse applications1. Three dimensional architectures based on DNA polyhedra have raised particular interest in biomedical applications2. DNA polyhedra possess an internal void bounded by a welldefined three-dimensionally structured surface3,4. I will present the first successful delivery of quantum dots (QDs) as the internal payload of DNA icosahedra that are monofunctionalized with specific, endocytic ligands like folic acid, Galectin-3 (Gal35), Shiga toxin B-subunit (STxB6) and transferrin. Single particle tracking of Gal3/STxB-bearing, QDloaded icosahedra reveal new observations of compartment dynamics along the endocytic pathways7. QD-loaded DNA polyhedra bearing ligands of unique stoichiometry represent a new class of high-precision molecular imaging tools for quantitative approaches to complex biological phenomena arising from receptor clustering. Similarly, DNA caged magnetic particles were produced to purify galectin-3 enriched endocytic vesicles. Quantitative mass-spectrometry revealed new and pathway specific cargo molecules and trafficking machinery on the pre-early endosomal structures arising from Gal3 induced carriers. Using inhibitors and siRNA based screens I have validated the key cargo and cytosolic candidates involved in CLIC biogenesis and its endocytic trafficking. Our multidisciplinary and innovative approach using DNA nanotechnology and lattice light sheet microscopy has contributed immensely to fundamental understanding of formation of distinct endocytic pits via clathrin- independent carriers and the molecular anatomy of these carriers. Further, our results highlight the emerging potential of DNA devices in cell biology and biomedical applications that could enable probing and programming various biological systems as well as developing next generation tools probe and program the living systems for advanced bioengineering and biomedical applications.

References

1. Modi, S., Bhatia, D., Simmel, F. C. & Krishnan, Y. J. Phys. Chem. Lett. 1, 1994–2005.

2. Bhatia, D., Surana, S., Chakraborty, S., Koushika, S. P. & Krishnan, Y.. Nat.Commun. 2, 339 (2011).

3. Bhatia, D., Sharma, S. & Krishnan, Y. 22, 475–484 (2011).

4. Bhatia, D., Chakraborty, S. & Krishnan, Y. Nat Nanotechnol 7, 344–346 (2012).

5. Lakshminarayan, R., Wunder, C. & Becken, U..Nat. Cell Biol. 16, 595–606 (2014).

6. Johannes, L. & Römer, W. Nat. Rev. Microbiol. 8, 105–16 (2010).

7. Bhatia. D., et al., Nat Nananotehnol 11, 1112-1119 (2016).

 

February 14, 2017 at 2.30 pm in AG-69

Title :

Inhibition of formation of alpha-synuclein amyloid fibrils by Triphala, a herbal preparation

February 13, 2017 at 4.00 pm in AG-69

Title :

EUV Laser Photoelectron Spectroscopy of Mass Selected Neutral Clusters and Molecules

Abstract :

Over the past 15 years our research interests have focused on four main and related areas: 1. properties, chemistry, catalytic, and photo-catalytic behavior of neutral, inorganic, isolated clusters, MmM’nXpHq (M,M’ = metals, X = O, S, C); 2. initial release of stored chemical energy from isolated energetic molecules (e.g., RDX, HMX, CL -20, high N- content species, …); 3. small molecule, neutral clusters (e.g., (NH3)n, (H2O)n, (NH3BH3)n, (SO2)n, …) and their ion chemistry; and 4. structure, energetics, ion fragmentation reactions of “simple” bio-related molecules (e.g., amino acids, saccharides, neurotransmitters, and DNA bases). These studies have evolved from characterization of energy levels and intermolecular interactions, to ultrafast kinetics and dynamics of molecular cluster reactions, to the study of inhomogeneous catalytic and photo-catalytic cluster reactions. Clusters and molecules are identified through mass spectrometry, UV/Vis electronic spectroscopy, and most recently photo-electron spectroscopy (PES) employing visible, UV, VUV, extreme ultraviolet (EUV, soft x-ray) lasers. Decomposition reactions for the initial release of molecular stored chemical energy have been time resolved at less than 100 fs. In order to acquire, analyze, and interpret the experimental data obtained on these systems, we have had to develop an essential theoretical/calculational component for our program. This seminar reviews our initial synthesis and reaction studies through mass spectrometry of neutral catalytic and photo-catalytic inorganic clusters, small molecule cluster ion reactions, and generation of new cluster species. These results serve as motivation for constructing a new PES apparatus employing visible, UV, VUV, and EUV photons for photo-detachment of anionic and neutral species in order to acquire spectroscopic data on the systems of interest. We will discuss these new results for FexSyHz clusters, energetic materials, and bio-related saccharides and DNA bases. The importance of the new spectroscopic (PES) data for these systems is that they enable the evaluation of theoretical techniques in order that proper algorithms and approaches may be employed to generate results that are not presently experimentally accessible, such as cluster and molecular structure, reaction mechanisms, and general electronic state specific potential energy surfaces. 

February 7, 2017 at 2.30 pm in AG-69

Title :

Modulation of the Electronic Structure and Phonon Transport of SnTe for High Thermoelectric Performance

Abstract :

Lead chalcogenides are the best performers for thermoelectric power generation at mid-high temperatures; however, environmental concern about Pb limits its use in large-scale thermoelectric applications. SnTe, a IV-VI narrow band gap semiconductor, can be an alternative of PbTe due to its similar crystal structure and valence band characteristics.1 The journey of SnTe, as a potential thermoelectric material begins with In doped SnTe where In creates resonance level. This has been further optimized via lattice thermal conductivity reduction in SnTe1-xSex.2 Another constraint of SnTe is the large energy separation between the light and heavy hole valence bands which restricts the contribution of heavy hole mass to the Seebeck coefficient. Doping of Mg and Ag in SnTe significantly tunes the electronic structure of SnTe, which decreases energy difference between the light hole and heavy hole valence bands, leading to enhanced Seebeck coefficient and thermoelectric efficiency.3,4 Co-doping of the In and Ag in SnTe yields synergistic enhancement in Seebeck coefficient and power factor over a broad temperature range because of the introduction of resonance state and convergence of valence bands.1 Moreover, pristine SnTe exhibits κlat of ~2.88 Wm-1K-1 at room temperature, while theoretical limit for minimum lattice thermal conductivity (κmin) is ~0.5 Wm-1K-1. We have successfully reduced lattice thermal conductivity of SnTe near to its theoretical minimum limit, κmin, via Sb alloying which spontaneous form nanodomains of Sb-rich layered intergrowth SnmSb2nTe3n+m compounds.5

1. Banik, A.; Shenoy, U. S.; Waghmare, U. V.; Biswas, K. J. Am. Chem. Soc. 2016, 138, 13068.

2. Banik, A.; Biswas, K. J. Mater. Chem. A 2014, 2, 9620-9625.

3. Banik, A.; Shenoy, U. S.; Anand, S.; Waghmare, U. V.; Biswas, K. Chem. Mater. 2015, 27, 581.

4. Banik, A.; Biswas, K. J. Solid State Chem. 2016, 242, 43.

5. Banik, A.; Vishal, B.; Perumal, S.; Datta, R.; Biswas, K. Energy Environ. Sci. 2016, 9, 2011-2019.

February 6, 2017 at 4.00 pm in AG-69

Title :

Fibrous Nanosilica: Tunable Synthesis, Its Applications in Catalysis, CO2 Capture and Novel Materials Design

February 3, 2017 at 2.30 pm in AG-69

Title :

Revealing the Nanoscale Order of Dynamic Molecules Within Microscale Assemblies (Part-II)

Abstract :

Living systems differ from inanimate ones by their ability to create and sustain ordered assemblies of molecules at the expense of chemical energy. The ‘parts list’ of biomolecular assemblies is being discovered at a rapid pace, but how these parts come together to form functional cellular mechanisms remains an outstanding question in many fields of biology. For example, the principal components of the cellular contractile machinery that shapes, divides, and moves cells have been known for a long time, viz., actomyosin network, plasma membrane, and adhesion complexes. But the dynamic architecture of this machinery remains challenging to measure, especially in three-dimensional (3D) (patho)physiological environments.

The architecture of the molecular assemblies within cells that adhere to 2D unphysiological substrates often does not provide predictive insights into the assemblies’ function in the 3D physiological environments. We have devised a confocal LC-PolScope, which employs liquid crystal (LC)-based tuning of polarization, to measure nanoscale alignment and orientation of filamentous assemblies in 3D environments. Our data provides new insights into the molecular architecture of the contractile machinery that drives cytokinesis and migration of cells in 3D environments. 

Building upon above advances, the future studies will reveal the molecular architectural basis of the directional forces generated by single cells and a collective of cells within 3D (patho)physiological environments.

 

February 2, 2017 at 2.30 pm in AG-80

Title :

Revealing the Nanoscale Order of Dynamic Molecules Within Microscale Assemblies (Part-I) 

Abstract :

Living systems differ from inanimate ones by their ability to create and sustain ordered assemblies of molecules at the expense of chemical energy. The ‘parts list’ of biomolecular assemblies is being discovered at a rapid pace, but how these parts come together to form functional cellular mechanisms remains an outstanding question in many fields of biology. For example, the principal components of the cellular contractile machinery that shapes, divides, and moves cells have been known for a long time, viz., actomyosin network, plasma membrane, and adhesion complexes. But the dynamic architecture of this machinery remains challenging to measure, especially in three-dimensional (3D) (patho)physiological environments.

Our recent work has led to fluorescence-based computational microscopy assays that reveal nanoscale architecture of molecules within the context of microscale assemblies. We exploit intrinsic polarization of fluorescence to measure sub-resolution orientation and alignment of molecules. We have developed an instantaneous fluorescence polarization microscope (instantaneous fluorescence PolScope) to analyze the dynamic changes in concentration, position, and orientation of molecules (Mehta et al., PNAS 2016). Instantaneous fluorescence PolScope acquires four polarization-resolved images of dynamic molecules with single molecule sensitivity. The image data is then computationally translated into orientation, concentration, and kinetics of the cytoskeletal networks. This computational microscopy approach revealed nanoscale orientation of actin filaments relative to the retrograde flow of the network at the leading edge of cells migrating on 2D surfaces. Analysis of actin filament orientation at the leading edge has been possible only in fixed cells with electron microscopy. Further, in a multi-institutional collaboration (Swaminathan et al., bioRxiv 2016 and Nordenfelt et al., bioRxiv 2016), synergistic use of fluorescence polarization microscopy and computational analysis revealed that integrin transmembrane receptors are ‘actively aligned’ by their engagement with retrograde flow and extracellular ligand. The active alignment of integrin receptors may be a general mechanism used by cells to sense directional cues within extracellular matrix and is uniquely accessible with fluorescence polarization microscopy in live cells. 

 

January 30, 2017 at 4.00 pm in AG-69

Title :

Towards a Novel Theoretical Approach to Characterize Biomolecular Flexibility

January 25, 2017 at 11.00 a.m. in AG-80

Title :

Allostery in Chaperonins: How and Why?

Abstract :

Chaperonins are large protein assemblies that assist protein folding in an atp-dependent fashion. I will discuss their allosteric mechanisms and how they impact their folding function.

January 24, 2017 at 2.30 pm in AG-80

Title :

Carbonaceous- and Layered-material based Hybrids for Drug Delivery and Catalysis

Abstract :

In this presentation, I will talk about synthesis and characterization of various hybrid materials and their applications in drug delivery and catalysis. Carbonaceous nanospheres derived from glucose show preferential accumulation into the mice brain. We have modified the surface of these spheres with magnetic (Prussian blue and its analogues) nanoparticles and luminescent (lanthanide) probes to make brain theranostic agents. These multifunctional hybrid spheres showed enhanced magnetic and luminescent behaviour. They were biocompatible, entered brain, and showed no toxicity to the mice. The method of fabrication was versatile and could be used to create a number of theranostic systems for brain. Hybrid nanoparticles were synthesized from glucose derived carbon and iron oxide in the form of different morphology. Depending on their shape, these nanoparticles could compartmentalize inside the brain cells in the in vivo conditions. Biconcave shape of nanoparticles showed preferential nuclear entry, whereas nanotube morphology was restricted to the cytoplasm. Also, shape dependent compartmentalized delivery of an activator of an epigenetic enzyme was demonstrated. Smart hybrid nanospheres were prepared using layered clay and polyelectrolytes in a layer-by-layer fashion. These hybrid spheres showed reversible size change (about 60%) in response to pH, in the range of physiologically relevant pH values. Hybrids were also demonstrated for their pH dependent drug release ability. Catalytic behaviour of layered boron nitride and boron nitride supported metals towards oxidative dehydrogenation of propane was studied. Boron nitride (a generally accepted inert material) catalysed the propane oxidative dehydrogenation reaction. The catalytic activity was found to improve with increasing surface area of the catalyst. The catalytic activity was stable for nearly 5 hours and could be regenerated easily by heating in dilute ammonia. Oxidation of surface B-N bonds in oxygen leads to the diminishing catalytic activity, which on heating in ammonia reduced back to their native form regaining the indigenous catalytic activity. Remarkably, the high propene selectivity and yields obtained for these metal free catalysts were comparable to the reported catalysts and could be further increased by using higher surface area boron nitride samples.

References:

1. P Chaturbedy et. al. Journal of Nanobiotechnology (2012), 10, 35.

2. P Chaturbedy et. al. J. Mater. Chem. B (2013), 1, 939-945.

3. P Chaturbedy et. al. Journal of Controlled Release (2015), 217, 151-159.

4. P Chaturbedy et. al. ACS Nano (2010), 4, 5921-5929.

5. P Chaturbedy et. al. Manuscript under preparation (2017).