TIFR
Department of Chemical Sciences
School of Natural Sciences

Calender

July 31, 2018 at 11.30 am in AG-69

Title :

GroEL Chaperonin Assisted Protein Folding: studied by PETFCS and SmFRET 

Abstract :

Many newly synthesized unfolded polypeptides require assistance by molecular chaperones in order to reach their active folded states. The GroEL/GroES chaperonin system is one of the most important bacterial chaperonin systems, which fulfills an essential function in assisting the folding of cytosolic proteins. GroEL is a homo-tetradecameric double-ring assembly of 60 kDa subunits with two opposing central cavities stacked back to back. Upon binding of ATP and the co chaperone GroES, GroEL transiently encapsulates newly synthesized or misfolded substrate proteins, which then can fold to the native state while being shielded from the crowded cytosolic environment. The mechanism of GroEL remains controversial whether GroEL acts as a passive cage, merely providing an aggregation preventing micro compartment, or whether GroEL actively accelerates the refolding of a subset of substrate proteins by modulation of the folding energy landscape. 

We resorted to a variety of single molecule fluorescence techniques to address this controversy. A novel and sensitive dual color fluorescence cross-correlation spectroscopy assay shows the absence of transient aggregates at single molecular concentration. Using a single molecule FRET (SmFRET) based assay, we show that the acceleration of substrate protein folding by GroEL is preserved under single molecule conditions, where aggregation is excluded. We apply photoinduced electron transfer fluorescence quenching correlation spectroscopy (PETFCS) to demonstrate that the acceleration of substrate protein folding is achieved by encapsulation of a dynamic folding intermediate inside the GroEL cavity. Furthermore, we provide evidence that modulation of the folding energy landscape is a result not only of steric confinement during encapsulation, but also of the net negative charge of the GroEL cage wall. Taken together, these results represent a substantial advance in our understanding of the mechanism of the prokaryotic chaperonin system and our findings suggest that GroEL, by an active chaperonin mechanism, promotes substrate protein folding by entropic destabilization of folding intermediates.

 

July 30, 2018 at 4.00 pm in AG-69

Title :

Direct observation of the Mechanical Foldase Activity of Trigger Factor Chaperone by Magnetic tweezers

Abstract :

Proteins fold under mechanical forces in a number of biological processes, ranging from muscle contraction to co-translational folding at the mouth of the ribosome. As force hinders the folding reaction, chaperones must play a crucial role in this scenario. Nevertheless, to date, it has not been possible to monitor the direct influence of a chaperone on a protein folding under force. Here, we introduce single molecule magnetic tweezers to study the folding dynamics of protein L in presence of the prototypical molecular chaperone Trigger Factor (TF) over the range of physiological forces (4 to 10 pN). Our results show that TF modulates the folding of protein L by prominently increasing the probability of folding against the force and accelerating the refolding kinetics. Moreover, we find that the ability of TF to catalyze the folding reaction depends on the pulling force; as the force increases, higher concentrations of TF are needed for rescue folding, although no effect is observed above 12 pN even with saturating amounts of TF. Here, we propose for the first time that chaperones such as TF can work as foldases under force, playing a relevant role in many biological processes such as protein translation.

July 18, 2018 at 2.30 pm in AG-69

Title :

Charge Transport and Catalysis Reactions at the Electrified Interfaces

Abstract :

Possibility of studying the properties of molecules or nanostructures at single enity level offers huge opportunities to tune structure property relationships at nanoscale. The problem with current state-of-the-art nanomaterials and energy research involving charge or electron transport at electrode|molecule interface as a key process is centered in the fact that no single experimental technique can independently provide complete information on nanoscale structure-property relationships. The development of fast, cost effective and structure sensitive characterization methods at single entity level is the target of much current nanotechnology research.

 

During this presentation, I will try to show the experimental framework (experimental technique and methodologies development) that I am planning to implement/develop in my future laboratory to address the key issue of nanoscale structure-property relationships under in-operando conditions.1-4

 

References:

 

1. Kaliginedi et al., Nanoscale. 2015, 7 (42), 17685-17692.

2. Rudnev, A., Kaliginedi et al., Science Advances. 2017, 3, e1602297.

3. Seth, C., Kaliginedi et al., Chemical Science. 2017, 8, 1576-1591.

4. Atesci, H., Kaliginedi et al., Nature Nanotechnology. 2018, 13, 117.

July 17, 2018 at 2.30 pm in AG-69

Title :

Charge transport at Electrode|Molecule interface: From Molecular Electronics to Energy Research Applications

Abstract :

The idea of building electronic devices using single molecule as an active component was first proposed by Aviram and Ratner in the early seventies.1 Indeed, molecules are of great interest for application in electronic devices because of their small size, recognition properties, ability of self-organization, possibility of chemical modification and customisation. Thus, the ability to measure and control charge transport across metal|molecule|metal junction is of considerable fundamental interest and represents a key step towards the development of molecular electronic and spintronics devices.2-6

 

In addition to the applications in molecular electronics and spintronics research, studying charge or electron transport properties at metal|molecule interfaces under the influence of external stimuli like light, temperature, electrochemical potential or magnetic field will have a variety of applications in other research fields like (i) energy research (for example, solar cells, where the charge or electron transfer at metal|molecule interfaces plays a crucial role in determining the efficiency of the solar cell); (ii) photocatalysis and electrocatalysis (activity of a catalyst depends on the effective charge transport at electrode|catalyst interface); (iii) Sensors (sensitivity and selectivity of a sensor may depend on the effective charge transport at electrode|sensor moiety interface) and etc.5,7

 

In the first part of my presentation, I will introduce working principle of measurement techniques (i.e STM break junctions (STM-BJ), mechanically controllable break junction (MCBJ) and conducting probe AFM (CP-AFM) techniques) and data analysis procedures used to extract conductance properties of molecular junctions.2 Using the results from several case studies, I will try to demonstrate a frame work for building structure-property correlations of metal|molecule|metal junctions at single and multi-molecular level.2-6 In the later part of my presentation, I will discuss the molecular conductance measurement results which will have direct consequences in electrocatalysis and energy researh.3,5,7

 

References:

 

1. Aviram, A.,Ratner, M., Chem. Phys. Lett. 1974, 29, 277.

2. Kaliginedi et al., Journal of American chemical society. 2012, 134, 5262–5275.

3. Rudnev, A., Kaliginedi et al., Science Advances. 2017, 3, e1602297.

4. Seth, C., Kaliginedi et al., Chemical Science. 2017, 8, 1576-1591.

5. Atesci, H., Kaliginedi et al., Nature Nanotechnology. 2018, 13, 117.

6. Kaliginedi et al., PCCP. 2015, 16, 23529.

7. Kaliginedi et al., Nanoscale. 2015, 7, 17685.

July 16, 2018 at 4.00 pm in AG-69

Title :

Circular permutations in azurin: Creating new termini for pulling along different directions

July 11, 2018 at 2.30 pm in AG-69

Title :

Plant Viruses for the Delivery of Platinum Anticancer Therapeutics

Abstract :

Platinum-based anticancer drugs such as cisplatin, carboplatin, and oxaliplatin are used in the treatment of nearly half of the population of the cancer patients undergoing chemotherapy. These drugs, however, lack selectivity and have dose-limiting toxicities, low bio-availability, rapid clearance from the body, and may encounter drug resistance mechanisms, leading to the recurrence of the cancer. Therefore, efficient loading of drugs in novel delivery agents has the potential to substantially improve therapy by directly targeting the diseased tissue and avoiding unwanted side effects.  Given that the development of new drugs is expensive, reducing toxicity caused by existing drugs by packaging them into delivery vehicles is attractive and can be achieved by controlled and targeted methodologies. Although presently available nano-sized delivery agents impart safety, their limited efficacy and inability to penetrate tissue adequately are some of the limitations. Consequently, development of new drug delivery methods has been a subject of recent burgeoning interest.

 

Viruses are very simple in structure and composition, and they can be considered as biology-derived nanocarriers, naturally evolved to carry and delivery cargos to target cells. Moreover, they can transfect host cells with a very high efficiency. However, their immunogenic nature hinders their development as drug carriers. In this regard, plant viruses form an emerging platform technology as they offer several advantages over mammalian vectors.

In this talk, I will highlight the use of tobacco mosaic virus (TMV) for the delivery of platinum anticancer therapeutics. It has been shown previously by our research group that the highly potent analogues of cisplatin, phenanthriplatin (1) and its aqua-form (2), are differentially taken up in the TMV channel. Whereas ~1000 molecules of 1 are loaded in TMV, 2 is taken up in higher quantities (~2000 molecules per TMV particle). Studies on delineating the mechanism of their differential uptake and their stabilization in the TMV channel will be discussed in detail. Furthermore, I will also discuss on the heat-transition of TMV nanorods to nanospheres (SNPs) in the presence of 1, which leads to significant uptake of 1 in the bulk of SNPs, and their mechanism of formation. These SNPs are stable in the fetal bovine serum (FBS) medium and they do not release 1 at pH 7.4 and pH 5, which may further prevent the toxicity arising due to off-target release of drugs. To an added advantage, the release of 1 is only triggered by proteolytic enzyme like trypsin which is a constituent of endosome. SNP delivery system presents a comparable to better anticancer efficacy in the panel of cancer cell lines. These investigations inform the design of future drug analogues that can be efficiently encapsulated, stabilized in different morphologies of TMV, and delivered to the tumor site.

 

References

1.A. E. Czapar, Y. Zheng, I. A. Riddel, S. Shukla, S. G. Awuah, S. J. Lippard, N. F. Steinmetz, ACS Nano, 2016, 10, 4119-4126.

2.A. A. Vernekar, G. Berger, A. E. Czapar, F. A. Veliz, D. Wang, N. F. Steinmetz, S. J. Lippard, J. Am. Chem. Soc., 2018, 140, 4279-4287.

3.A. A. Vernekar, F. A. Veliz, N. F. Steinmetz, S. J. Lippard, (SNP work will be submitted soon).

July 10, 2018 at 2.30 pm in AG-69

Title :

Bioinorganic Chemistry Approach to Nanozymes for Cellular Redox Regulation

Abstract :

Organic/metal organic compounds that mimic the functional role of enzymes have been extensively investigated. Recently, few nanomaterials such as gold nanoparticles, ferromagnetic nanoparticles and graphene-based materials have been innovatively shown to exhibit unprecedented biochemical catalysis by mimicking certain enzymes (nanozymes). Owing to their simplicity of preparation and storage and stability, nanozymes have been investigated for their application in many fields such as biosensing, immunoassays, cancer diagnostic, therapeutic and pollutant removal, etc. Despite current interest on nanozymes, tackling with some of the difficulties associated with them such as selectivity, cooperativity with other enzymes, limited surface area due to functionalization, biocompatibility and activity in cells, etc. is a challenging task.

 

In this seminar, I will discuss about the novel antioxidant and phosophotriesterase nanozymes. We have recently reported the graphene-hemin hybrid material for its remarkable peroxynitrite reductase and isomerase antioxidant activities. Noncovalent interactions of hemin and reduced graphene oxide (RGO) resulted in synergistic activity to effectively scavenge peroxynitrite, which is a potent reactive nitrogen species (RNS) found in vivo.

 

In another related study, we found that vanadium pentoxide (V2O5), an oxidant, reveals an unexpected antioxidant role in its nano-form and exerts tremendous cytoprotective effects. The vanadia nanozyme exhibit excellent glutathione peroxidase (GPx)-like catalytic antioxidant activity and prevents oxidative damage to cells from reactive oxygen species (ROS) without affecting the expression level of other antioxidant enzymes. This work demonstrates the first experimental evidence that the biological property of a metal ion in its nano-form can be completely different from that of a bulk material. In a similar line, I will also briefly highlight about MnFe2O4 nanooctahedrons as oxidase and vacancy-engineered nanoceria as phosphotriesterase nanozymes for antibody-free detection of major biomarkers of oxidative stress and detoxification of sarin gas-related nerve agents, respectively.

 

References:

1.       A. A. Vernekar, G. Mugesh, Chem. Eur. J. 2012, 18, 15122-15132.

2.       A. A. Vernekar, G. Mugesh, Chem. Eur. J. 2013, 19, 16699-16706.

3.       A. A. Vernekar, D. Sinha, S. Srivastava, U. P. Prasath, P. D’Silva, G. Mugesh, Nature Commun. 2014, 5, 5301.

4.       A. A. Vernekar, T. Das, S. Ghosh, G. Mugesh, Chem. Asian J. 2016, 11, 72-76.

5.    A. A. Vernekar, T. Das, G. Mugesh, Angew. Chem. Int. Ed.2016, 55, 1412-1416.

July 9, 2018 at 4.00 pm in AG-69

Title :

When Nano Break H2O

Abstract :

While H2O (water) is life to all living organisms on earth, it is also one of the key technological components of hydrogen economy. In an electrolysis cell, water can be decomposed into hydrogen and oxygen due to an electric current passing through it. Although hydrogen evolution reaction (HER) is the major reaction of interest, oxygen evolution reaction (OER) is the most energy intensive step. To overcome the activation barrier of splitting water, a catalyst is needed. The more active and stable the catalyst, more effective is the splitting. One of our major research interests is to develop nanoheterostructured electrocatalysts for OER and HER,1,2 thereby leading to overall water splitting.3 The best performances are obtained not only by designing a suitable catalyst but also by optimizing the substrate on which the catalyst nanoparticles are supported, among which flexible substrates are fascinating.4 When the electrolyzer is integrated to solar cells, water photolysis with high solar-to-hydrogen efficiency also becomes possible.

 

References :

 

1.Datta, A.; Kapri, S.; Bhattacharyya, S. J. Mater. Chem. A 2016, 4, 14614-14624.

2.Debnath, B.; Kumar, A.; Salunke, H. G.; Bhattacharyya, S. J. Phys. Chem. C 2017, 121, 25594-25602.

3.Kumar, A.; Bhattacharyya, S. ACS Appl. Mater. Interfaces 2017, 9, 41906-41915.

 

4.Sahasrabudhe, A.; Dixit, H.; Majee, R.; Bhattacharyya, S. Nat. Commun. 2018, 9, 2014.

 

June 25, 2018 at 4.45 pm in AG-69

Title :

Investigations on photocatalytic H2 generation using modified TiO2 and g-C3N4 semiconductors

Abstract :

Generation of hydrogen from renewable sources like water and solar energy is considered to be an attractive and viable solution for replacing fossil fuels. Photocatalytic water splitting has attracted much attention as it involves conversion of solar energy into useful chemical energy. The major challenge involved in the process is the development of stable and visible light active photocatalyst with required solar to fuel energy conversion efficiency (SFE). In the present work, studies were undertaken to improvise the optical and photocatalytic properties of several photocatalysts; conventionally known UV active TiO2 and novel organic semiconductor, graphitic carbon nitride (g-C3N4). Various strategies such as cationic doping by Cu in TiO2, composite formation with NiO and CuO inducing pn heterojunctions, carbon and TiO2 heterojunction to improve electronic conductivity, surface modification of g-C3N4 by dispersing carbon nanodots (CND) and noble metal (Pt, Pd, Cu, Ag and Au) were adopted to limit the e-/h+ recombination reaction and to enhance the photoresponse under visible light illumination. All samples were thoroughly characterized by relevant techniques and their potential for H2 generation was evaluated under sunlight and UV-visible light in presence of sacrificial reagent. Density functional theory calculations were performed and life time of e-/h+ from PL decay curves was measured to support the activity trend. Parameters such as illumination area, catalyst concentration, form of catalyst (powder/films) and different sacrificial reagents were optimized for maximum H2 yield. Performance of the screened photocatalysts was also tested in up-scaled photoreactors (volume = 0.5, 1 and 2 L). H2 yield @ 16 ml/h/g with apparent quantum efficiency (AQE) of 7.5 % and SFE of 3.9 % over Cu0.02Ti0.98O2-δ (without cocatalyst) was observed under sunlight suggesting that 0.96 m2 illumination area will yield H2 @ 1 L/h photocatalytically. Among modified g-C3N4 photocatalysts, maximum H2 yield of 398 μmol/h over 80 mg of Pt/CND/ g-C3N4 (0.48 wt %) under sunlight with AQE of 4.0 % and SFE of 2.0 % was achieved as compared to almost negligible yield over pristine carbon nitride. The present study is targeted to provide valuable inputs for actual large scale solar photocatalytic H2 production.

June 25, 2018 at 4.00 pm in AG-69

Title :

Development of metal oxide based photocatalysts for the CO2 reduction to fuel

Abstract :

 

Continuous depletion of fossil fuel resources and growing environmental concerns due to the huge CO2 emissions, have focused the need to develop renewable and clean energy resources. CO2 is a major greenhouse gas and cause of global warming. CO2 capture, storage and utilization particularly, catalytic conversions of CO2 to fuels and chemicals have attracted much attention in recent years.  Activation of CO2 requires high amount of energy due to its stability. Harvesting the photon energy and its storage in the form of fuels hold promise to address the current and future demand of energy supply. The photocatalytic conversion of CO2 over heterogeneous photocatalysts is a potential approach to mitigate CO2.

 

Designing of material with suitable band gap and product selectivity remained key challenges. Problems associated are: (i) massive recombination of generated charge carriers and (ii) low yield and less selectivity for product formation and (iii) development of stable visible light active catalyst. Metal oxides with suitable properties can convert solar energy to chemical energy using artificial photosynthesis and it will be a good technique to develop sustainable environment.

 

The talk will cover my work on designing and synthesis of metal oxide catalysts for the photocatalytic reduction of CO2 to fuel. 

 

June 22, 2018 at 2.30 pm in AG-69

Title :

Switching On and Off of Interfacial Water Ordering at Air/Water Interface

Abstract :

Carbon quantum dots (CQDs) are recently famed and well developed class of fluorescent probe and have shown tremendous potential in numerous fields such as biosensing, bioimaging, drug delivery, and optoelectronics. After its accidental discovery, it has created huge excitement due to their unique features like chemical inertness, high water solubility, excellent biocompatibility, resistance to photo bleaching. Mostly it has been extensively studied to exploit its fluorescence properties through displacement assay for various applications by using conventional fluorescence spectroscopy. Fluorescence spectroscopy does not provide any information directly related to the structural changes of the system or its impact on the surrounding aqueous medium during displacement assay process. In my talk, I will provide a thorough discussion about our recent work on interfacial activities of carbon quantum dots and its impact on perturbing the pristine hydrogen bonding network of interfacial water structure at air/water interface. We have used surface specific and chemically sensitive sum frequency generation (SFG) vibrational spectroscopy to probe the air/water interface with the presence of QCDs and various metal ions. SFG is a nonlinear optical spectroscopic tool based on second order nonlinear optical process. It is quite fascinating to observe the role of various intermolecular interactions in terms of hydrogen bonding, electrostatic interaction during the process of interaction of the QCDs with various metal ions at the air/aqueous interface. I will also extend my discussion about the physics of surface protein unfolding and its kinetics through diffusion and intermolecular interactions at a neutral air/water interface.

June 18, 2018 at 4.00 pm in AG-69

Title :

Designing Optical Probes for Sensing Signaling Lipids

June 11, 2018 at 4.00 pm in AG-69

Title :

Carbon-Fixation by Plasmonic Catalysts

Abstract :

Mimicking plant photosynthesis requires a synthetic photocatalyst that absorbs sunlight and uses that energy efficiently to convert CO2 into energy-dense hydrocarbons. My talk will make the case that noble metal nanostructures, which exhibit collective free electron resonances called plasmons, may be well-suited to this task. Not only do plasmonic nanoparticles of Au, Ag, and Cu offer a means to absorb visible light efficiently, their strong-light-matter interaction can be paired with their ability to activate small molecules, such as CO2. We have had preliminary success with plasmonic catalysts, which under visible-light-excitation, can drive kinetically challenging multi-electron multi-proton processes such as methane generation. Moreover, the product selectivity is controllable by the nature of the exciting light, which suggests that a novel phenomenon is at work. In order to understand the light-driven pathway for CO2 reduction, we have probed with single-site spatial resolution the dynamics of a plasmonic photocatalyst under operando conditions. From captured intermediates and density functional theory simulations, we are beginning to understand the mechanism which plasmonic excitation activates physisorbed CO2. It is clear that a close interplay between photoexcited states and surfaces is involved in this scheme of artificial photosynthesis. 

June 5, 2018 at 2.30 pm in AG-80

Title :

Applications of coherent Raman scattering microscopy in bioimaging

Abstract :

Much progress in biology and allied sciences is driven by optical microscopy methods. Techniques involving extraneous labels (e.g. fluorescent molecules) with affinity to one or more sample components are widely used, with some implementations even breaching the diffraction limit. Other than the fact that the introduction of these labels changes sample chemistry, availability of suitable labels, issues of photobleaching, and phototoxicity can limit the applicability of these methods.

Spectroscopy techniques, which rely on energy-level transitions of various molecular species in the sample are chemically specific, sensitive, and label-free. Coherent Raman scattering (CRS), namely coherent anti-Stokes Raman scattering (CARS) and stimulated Raman scattering (SRS) have been applied in bioimaging, with short acquisition times and promising results.

In this talk, I will discuss my research at Cardiff University (PhD) and KU Leuven, where I used CARS and SRS microscopy to image biological samples. Using volumetric hyperspectral CARS microscopy [1-3], I studied mitosis in human osteosarcoma (U-2OS) cells, revealing the sub-cellular distribution of various biomolecules. As an outlook to pharmacodynamical studies, I imaged the effects of two anti-cancer drugs in single cells. In addition to these, I will also show some results from an exploratory application of CARS to 3D tissue cultures- organoids. Not only a proof of principle, this work has revealed interesting information previously unresolved with CRS. 

As a classic example of how fluorescent molecules are not always the best choice for bioimaging, I will present results of SRS imaging of lipids in desert locust (Schistocerca gregaria) oocytes which do not stain efficiently using conventional methods.

When applied to statistically significant sample sizes, the methods demonstrated in this research could establish CARS and SRS as novel and extremely useful tools in biomedical/biochemical research. 

 

References

1.Pope I, Langbein W, Watson P, Borri P, Optics Express 21, 7096 (2013)

2.Masia F, Glen A, Stephens P, Borri P, Langbein W, Anal. Chem. 85, 10820 (2013)

3.Karuna A, Masia F, Borri P, Langbein W, Journ. Raman Spec. 47, 1167 (2016)

 

May 29, 2018 at 2.30 pm in AG-69

Title :

Hot Spot Engineering in Gold-DFNS  Plasmonic Nanostructures: Synthesis and Applications as Nano-Heaters