TIFR
Department of Chemical Sciences
School of Natural Sciences

Calender

February 16, 2015 at 4.00 pm in AG-69

Title :

Photocatalytic Application of Atomic Layer Deposited (ALD) TiO2 on Fibrous Nano-Silica (KCC-1)

February 12, 2015 at 4.00 pm in AG-80

Title :

Single Molecular Spectroscopy of Single Live Cell

Abstract :

The 2014 Nobel Prize in Chemistry has been awarded for the development of Single Molecule Spectroscopy. We will discuss some recent application of this technique to the study of a single live cell. In a confocal microscope, the size of the focused spot (~200 nm = 0.2 m) is one-hundredth of the dimension of a cell. Thus one can probe different regions/organelles in a cell. Utilizing this, we will describe several new phenomena inside a live cell [1-5]. Specifically, we have discovered found substantial differences between a cancer cell and a normal cell [1-4]. The gold nano-clusters preferentially enter or stain a cancer cell compared to a non-malignant cell [1]. The red-ox processes (thiol-disulfide interconversion) lead to intermittent structural oscillations leading to fluctuations in fluorescence intensity in a single live cell [2-3]. Such oscillations are absent for a cancer cell [2]. The number of lipid droplets are much higher in a cancer cell. We detected stochastic resonance during gene silencing in a cancer cell [5].

References
1.  S. Chattoraj, et al.  "Fluorescent Gold Nano-Cluster inside a Live [UTF-8?]Cell,” J. Phys. Chem. C 118

     (2014, in press).
2.  S. Chattoraj, et al.  "Role of Red-Ox Cycle in Structural Oscillations and Solvation Dynamics in Mitochondria,"

     J. Phys. Chem. B 118 (2014, in press).
3.  S. Ghosh, et al. "Solvation Dynamics and Intermittent Oscillation of a Cell Membrane: " J. Phys. Chem. B 118

     (2014) 2949-2956.  
4.  R. Chowdhury, et al. "Confocal Microscopy of Cytoplasmic Lipid Droplets in a Live Cancer  Cell”

     Med. Chem. Comm. 5 (2014) 536-539.
5.  S. Chattoraj, et al. "Dynamics of Gene Silencing in a Live Cell," J. Phys. Chem. Lett. 5 (2014) 1012-16.

February 9, 2015 at 4.00 pm in AG-69

Title :

Examining Protein Ligand Interactions Using Single Molecule Force Spectroscopy

February 3, 2015 at 2.30 pm in AG-69

Title

Investigations Of Thermal Properties Of Carbon Nanotubes And Metal Oxide Nanomaterials Using Raman Spectroscopy And Molecular Dynamics Simulations

Abstract :

Single-walled carbon nanotubes (SWCNTs) are cylindrical tubes formed from covalently bonded carbon atoms and are described mathematically by performing a rolling operation on the honeycomb planar lattice of a single graphite layer. In the current study, we have examined closely the thermal expansion properties of these quasi one-dimensional objects using experimental Raman spectroscopy and Molecular Dynamics simulations. The Raman measurements have been performed employing a Thermo Scientific DXR spectrometer and a heated cell over a range of temperatures (27-200 deg C), while the Molecular Dynamics simulations utilize the powerful and versatile software package - Large-scale Atomic Molecular Massively Parallel Simulator (LAMMPS). The Raman spectra of the SWCNTs were investigated under thermal loading via two methods, namely laser heating and the externally heated cell, in an effort to demonstrate the bond softening and resultant red-shift of the various Raman features of SWCNTs. In addition, metal oxide nanomaterials can provide insight into the changes in structure and properties that result from the chemisorption of oxygen in the lattice and the way energy is stored in nanomaterials. We have examined the characteristics of graphitic and metal oxide nanomaterials using Resonant Raman Spectroscopy at 514, 532 and 780 nm laser excitations using the DXR Smart Raman spectrometer and a Renishaw inVia Raman Microscope. Computational atomistic analysis of the associated phonon thermodynamics has been performed with the goal of determining the effect that temperature has on the vibrational frequencies of the nanomaterials. In many future applications of graphitic nanomaterials, the electronic devices will have to endure high temperatures during manufacturing and/or operation, whereby the induced strain and thermal expansion characteristics may serve as significant quality/reliability control factors.Intriguing results from both experimental measurements and simulation studies help to shed light on the thermal properties of SWCNTs and metal oxide nanomaterials that have important ramifications for their use in electronic devices.  

 

February 2, 2015 at 4.00 pm in AG-69

Title :

Strategies to Reduce Rate of Charge Recombination

Abstract :

Modulating excitons generated as a result of photoinduced electron transfer in crowded environments is vital for the development of photo-functional materials.1 The hetero-junctions (HJs) in organic photovoltaics are termed as “transport highways” for the charge carriers to the respective electrodes.2Careful design and organization of molecular architectures at the HJs in organic solar cells dictates the fate of excitons generated. Molecular organization relies on interplay between various inter/intra molecular interactions such as multi-pole electrostatic interactions, dispersion and inductive effects, p-p interactions, hydrogen bonding etc. which determines electronic and optical properties associated with these materials. Myriads of models have been proposed in enhancing the survival times of the excitons generated at the HJs. Mullen and co-workers3 substantiated that compromise and dominance of various inter and intra molecular interactions operating in donor (D) - acceptor (A) self-assembled systems could generate segregated D-D/A-A stacks, D-A interdigitating alternate stacks etc. Aida and co-workers4 demonstrated the photochemical generation of spatially separated charge carriers through co-axial nanotubular arrangement of D and A. Wasielewski et al.5extended the survival time of charge separated states through self-assembled D-A tetramers, trefoils, dimers and hydrogen bonded foldamers.Recent report from our group6 demonstrated the importance of supramolecular vesicular scaffold in reducing the rate of charge recombination of the charge separated states.7Recently we are successful in synthesizing near-orthogonal D-A helical and columnar stacks wherein the latter undergo self-assembly in CHCl3 to form spherical aggregates which couldhelp in sustaining the charge transfer intermediates for longer timescales through D-A stacks. The following scheme represents the different models of D-A self-assembled systems reported and under investigation.

References:

1.   Engel, G. S.; Calhoun, T. R.; Read, E. L.; Ahn, T.-K.; Mancal, T.; Cheng, Y.-C.; Blankenship, R. E.; Fleming, G. R., Nature 2007,446 (7137), 782-786.

2.   Wang, M.; Wudl, F., J. Mater. Chem. 2012,22 (46), 24297-24314.

3.   (a) Dössel, L. F.; Kamm, V.; Howard, I. A.; Laquai, F.; Pisula, W.; Feng, X.; Li, C.; Takase, M.; Kudernac, T.; De Feyter, S.; Müllen, K., J. Am. Chem. Soc. 2012,134 (13), 5876-5886;(b) Samorì, P.; Fechtenkötter, A.; Reuther, E.; Watson, M. D.; Severin, N.; Müllen, K.; Rabe, J. P., Adv. Mater. 2006,18 (10), 1317-1321;(c) Mativetsky, J. M.; Kastler, M.; Savage, R. C.; Gentilini, D.; Palma, M.; Pisula, W.; Müllen, K.; Samorì, P., Adv. Funct. Mater. 2009,19 (15), 2486-2494.

4.   (a) Yamamoto, Y.; Fukushima, T.; Suna, Y.; Ishii, N.; Saeki, A.; Seki, S.; Tagawa, S.; Taniguchi, M.; Kawai, T.; Aida, T., Science 2006,314 (5806), 1761-1764;(b) Li, W.-S.; Saeki, A.; Yamamoto, Y.; Fukushima, T.; Seki, S.; Ishii, N.; Kato, K.; Takata, M.; Aida, T., Chem.-Asian J. 2010,5 (7), 1566-1572.

5.   (a) Gunderson, V. L.; Smeigh, A. L.; Kim, C. H.; Co, D. T.; Wasielewski, M. R., J. Am. Chem. Soc. 2012,134 (9), 4363-4372;(b) Lefler, K. M.; Kim, C. H.; Wu, Y.-L.; Wasielewski, M. R., J. Phys. Chem. Lett. 2014,5 (9), 1608-1615;(c) Lefler, K. M.; Co, D. T.; Wasielewski, M. R., J. Phys. Chem. Lett. 2012,3 (24), 3798-3805;(d) Wu, Y.-L.; Brown, K. E.; Wasielewski, M. R., J. Am. Chem. Soc. 2013,135 (36), 13322-13325.

6.   (a) Cheriya, R. T.; Joy, J.; Alex, A. P.; Shaji, A.; Hariharan, M., J. Phys. Chem. C. 2012,116 (23), 12489-12498;(b) Cheriya, R. T.; Nagarajan, K.; Hariharan, M., J. Phys. Chem. C. 2013,117 (7), 3240-3248.

7.             Cheriya, R. T.; Mallia, A. R.; Hariharan, M., Energy Environ. Sci. 2014,7 (5), 1661-1669.

 

January 27, 2015 at 2.30 pm in AG-69

Title :

Design and Development of Chemical Tools and Animal Models for Probing Mn (II) In Vivo

January 21, 2015 at 2.30 pm in AG-80

Title :

Probing the Molecular Basis of Photo-induced Charge Generation in π-Conjugated  Organic Materials for Photovoltaic Applications

January 19, 2015 at 2.30 pm in Guest House Conference Room

Title :

Bio-compatible Probes for Imaging Mn(II) in vivo

 

January 12, 2015 at 4.00 pm in AG-69

Title

Probing Dynamic Solvation of Water Soluble Molecular Cages through Host-Guest CT States

January 6, 2015 at 2.30 pm in AG-69

Title :

Diels-Alderase: Myth or Reality!

Abstract :

The Diels-Alder (DA) reaction is one of the most common types of cycloaddition reaction which leads to the formation of six-membered ring. The DA reaction plays a pivotal role in the synthesis of diverse polymer and natural products. However, the mechanism through which the DA reaction occurs makes it difficult to elucidate experimentally but can be fully addressed in silico. The DA reaction has found its applications in several aspects of chemistry and it has also been proposed as a key transformation in the biosynthesis of many cyclohexene-containing secondary metabolites. For instance, the key step in the biosynthesis of spinosyn A is a DA reaction which converts the putative macrocyclic lactone into the tricyclic compound (Figure 1) which may be catalyzed by an enzyme. In order to confirm this hypothesis, it is mandatory to demonstrate the concertedness of the transition state and thus, the enzyme would be known as Diels-Alderase. We have used computational methods to locate and characterize the transition state by making use of a theozyme, also known as theoretical enzyme.

 

 

 

Figure 1: Cyclisationreaction.

 

This presentation describes the fundamentals of cycloaddition and DA reactions. This is followed by our sustained efforts to understand these reactions using model systems and then culminating to an enzyme-catalysed reaction.

 

 

 

January 5, 2015 at 4.00 pm in AG-69

Title :

Finding homes to orphan enzymes

Abstract :

My graduate research in the Raushel lab at TAMU focused on the functional annotation of orphan bacterial enzymes and biological pathways. During my graduate studies, I realized the gigantic problem of misannotation of enzymes or lack of thereof in the post-genomic era. Following completion of my graduate studies, I decided to apply my background in biochemistry and mechanistic enzymology, to functionally annotate orphan enzymes in mammalian diseases, and pathophysiology in the Cravatt Lab at TSRI. Here, using a combination of activity based protein profiling, chemoproteomics, and lipidomics, I have identified and functionally characterized an as of yet uncharacterized serine hydrolase enzyme ABHD16A (also BAT5) as the major phosphatidylserine (PS) lipase in mammalian cells and tissues and as the enzyme responsible for biosynthesizing immunomodulatorylyso-PSs in vivo. I validated this annotation of ABHD16A using pharmacological studies performed with first generation small molecule inhibitors of ABHD16A, and from genetic data obtained from ABHD16A-directed shRNA probes, and ABHD16A–/– mice. This functional validation of ABHD16A has potential therapeutic implications in the neurological disorder PHARC (polyneuropathy, hearing loss, ataxia, retinitis pigmentosa, cataract) and other immunological disorders involving deregulated lyso-PS signaling.

December 22, 2014 at 4.00 pm in AG-69

Title :

In support of Nitric Oxide Dioxygenase function: Algal Hemoglobins and their Reduction partners

Abstract :

The ubiquity of hemoglobins as a superfamily to life has enthused the field with renewed vigor. Reactions like oxygen binding and nitric oxide (NO) dioxygenation appear to be characteristic to the hemoglobin superfamily, as revealed from investigation of recombinant globins, irrespective of whether they are associated to any particular function like oxygen transport/storage, sensing, electron transport, protection against hypoxia and other possibilities. NO dioxygenase reaction, common in vitro, however, was limited by lack of report of specific enzymes that can convert ferric hemoglobin, formed during reaction of oxy hemoglobin with NO, into ferrous hemoglobin – the species that reacts with NO. Absence of a known cognate reductase would prevent reduction of ferric species of hemoglobin to ferrous form and the oxidation-reduction cycle would be incomplete for NO related function to be fruitful. Assignment of NO dioxygenase activity as a physiological function requires the design of experiments that address reduction mechanisms. We used Chlamydomonas reinhardtii as model system since we have identified 12 globins and 3 putative genes that can potentially function as reductase of ferric hemoglobin. Organism database annotated these reductases as dihydrolipoamide dehydrogenase, cytochrome b5 reductase and monodehydroascorbate reductase. So far, we have characterized 3 hemoglobins and 3 putative cognate reductases using biochemical and biophysical methods. Spectroscopic studies reveal that Chlamydomonas contains both pentacoordinate and hexacoordinate hemoglobins. The enzymes were found to contain flavin domain and could reduce ferric Chlamydomonas hemoglobins in vitro to their functional ferrous state. The interactions between hemoglobins and these reductases might support NO scavenging/detoxification function of globins with potential implications in biotechnology.

December 8, 2014 at 4.00 pm in AG-66

Title : Exploring Energy Landscapes : From Molecules to Nanodevices

Abstract :

The potential energy landscape provides a conceptual and computational framework forinvestigating structure, dynamics and thermodynamics in atomic and molecular science. This talk will summarise new approaches for global optimisation, quantum dynamics, the thermodynamic properties of systems exhibiting broken ergodicity, and rare event dynamics. Applications will be presented that range from prediction and analysis of high-resolution spectra, to conformational changes of biomolecules and coarse-grained models of mesoscopic structures.


Selected Publications:
D.J. Wales, Curr. Op. Struct. Biol., 20, 3-10 (2010)
D.J. Wales, J. Chem. Phys., 130, 204111 (2009)
B. Strodel and D.J. Wales, Chem. Phys. Lett., 466, 105-115 (2008)
D.J. Wales and T.V. Bogdan, J. Phys. Chem. B, 110, 20765-20776 (2006)
D.J. Wales, Int. Rev. Phys. Chem., 25, 237-282 (2006)
D.J. Wales, "Energy Landscapes", Cambridge University Press, Cambridge, 2003

December 2, 2014 at 2.30 pm in AG-69

Title :

Mechanistic Investigation of Membrane Fusion through a Model Caged SNARE Protein

Abstract :

Intracellular membrane fusion is directed by the formation of a specific complex of proteins such as SNARE [Soluble NSF (N-ethylmaleimide-sensitive factor) Attachment Protein Receptor]. There are several mechanisms of SNARE mediated membrane fusion, but the exact nature of these processes remains debated. In particular, little is understood about the molecular mechanisms governing trans-SNARE complex nucleation and zippering in driving fusion. Assembly strength and fusion kinetics in these systems are highly complex, and the downstream events of membrane contact (docking), stalk formation, hemifusion, and fusion pore opening along the fusion pathway is still unclear. Moreover, the exact role of the transmembrane domain (TMD) of synaptobrevin and syntaxin-1A is unknown. In this presentation, I will demonstrate light triggered mechanistic investigation of membrane fusion using artificial caged SNAREs. Caging of a biologically active molecule with a photolabile protecting group at a key functional position can temporarily mask the functionality and inactivate the biomolecule. The activity of the molecule can be restored by uncaging, externally triggered by light of appropriate wavelength. However, caging group strategy has not been applied yet to temporarily block the membrane fusion activity of SNARE protein to get deeper structural insights into the SNARE zippering and assembly pathway. I will illustrate the design of artificial caged SNAREs with photolabile protecting groups to dissect the mechanism of SNAREs in membrane docking, hemifusion, and fusion. I will also provide a method to arrest and study the intermediates such as partially zipped trans-SNARE complexes which is used for light triggered stepwise recognition/two-stage zippering of membrane fusion. Our recent findings of light triggered membrane fusion using artificial caged SNAREs can be a significant starting point to address many compelling questions surrounding the topic of SNARE-induced membrane fusion.

At the end, I will present my future research proposal: 1) Synthetic Transmembrane Peptide-Based Ion Channel and 2) Synthetic Molecular/Supramolecular Machines.