TIFR
Department of Chemical Sciences
School of Natural Sciences

Calender

August 21, 2019 at 2.30 pm in AG-69

Title :

Picturing the future of healthcare through molecular imaging 

Abstract :

In vivo molecular imaging has the unique advantage of noninvasively assessing cancer metabolism or providing functional real-time information relative to obtaining ex vivo pathological information from tissue biopsies. Two important molecular imaging modalities are Magnetic Resonance Imaging (MRI) and Positron Emission Tomography (PET). 

The first part of the presentation will focus on my research in the development of multiple diamagnetic MRI contrast agents and MRI methods that exploit Chemical Exchange Saturation Transfer (CEST) for the detection of enzyme activity (an important cancer biomarker) within in vivo tumor models of ovarian, colon and pancreatic cancers. This description will also demonstrate CEST MRI methods that have been used to correlate enzyme activity with tumor aggressiveness; to support planning for surgical resection of solid tumors; and to evaluate the early response to enzyme inhibitor treatments.  In conclusion, the first part of the talk represents a new paradigm for molecular imaging that can be translated to the radiology clinic to improve early diagnoses of cancer. 

The second part of the presentation will focus on my contribution to the field of molecular imaging of several infectious diseases such as HIV/SIV, cerebral malaria (CM), Ebola virus disease, and Marburg hemorrhagic fever, using both MRI and PET imaging modalities. The overarching goal of these studies was to develop neuroimaging biomarkers that are useful for detecting CNS involvement prior to display of clinical symptoms. These studies with a transgenic rat model and SIV rhesus macaque models have identified dopaminergic and serotonergic neurotransmitter biomarkers and have evaluated the role of neuroinflammation in an SIV-model of encephalitis. In a related study with a CM mouse model, we used MRI to evaluate the neuropathology of the disease.  We demonstrated, for the first-time, that reversal of clinical symptoms such as edema can occur with a glutamine antagonist, JHU-083, thus suggesting a possible drug candidate for CM therapy. These studies hope to convey to the audience the growing importance of molecular imaging in unraveling early details of the disease pathology, and to recognize potential opportunities for treatment for these diseases. 

 

The remaining talk will focus on harnessing molecular imaging techniques such as MRI for evaluating other biomarkers of the tumor microenvironment such as extracellular tumor pH, as well as new imaging modalities such as Photoacoustic tomography for improvement in cancer surgery. 

 

August 20, 2019 at 2.30 pm in AG-69

Title :

Picturing the future of healthcare through molecular imaging 

Abstract :

In vivo molecular imaging has the unique advantage of noninvasively assessing cancer metabolism or providing functional real-time information relative to obtaining ex vivo pathological information from tissue biopsies. Two important molecular imaging modalities are Magnetic Resonance Imaging (MRI) and Positron Emission Tomography (PET). 

The first part of the presentation will focus on my research in the development of multiple diamagnetic MRI contrast agents and MRI methods that exploit Chemical Exchange Saturation Transfer (CEST) for the detection of enzyme activity (an important cancer biomarker) within in vivo tumor models of ovarian, colon and pancreatic cancers. This description will also demonstrate CEST MRI methods that have been used to correlate enzyme activity with tumor aggressiveness; to support planning for surgical resection of solid tumors; and to evaluate the early response to enzyme inhibitor treatments.  In conclusion, the first part of the talk represents a new paradigm for molecular imaging that can be translated to the radiology clinic to improve early diagnoses of cancer. 

The second part of the presentation will focus on my contribution to the field of molecular imaging of several infectious diseases such as HIV/SIV, cerebral malaria (CM), Ebola virus disease, and Marburg hemorrhagic fever, using both MRI and PET imaging modalities. The overarching goal of these studies was to develop neuroimaging biomarkers that are useful for detecting CNS involvement prior to display of clinical symptoms. These studies with a transgenic rat model and SIV rhesus macaque models have identified dopaminergic and serotonergic neurotransmitter biomarkers and have evaluated the role of neuroinflammation in an SIV-model of encephalitis. In a related study with a CM mouse model, we used MRI to evaluate the neuropathology of the disease.  We demonstrated, for the first-time, that reversal of clinical symptoms such as edema can occur with a glutamine antagonist, JHU-083, thus suggesting a possible drug candidate for CM therapy. These studies hope to convey to the audience the growing importance of molecular imaging in unraveling early details of the disease pathology, and to recognize potential opportunities for treatment for these diseases. 

 

The remaining talk will focus on harnessing molecular imaging techniques such as MRI for evaluating other biomarkers of the tumor microenvironment such as extracellular tumor pH, as well as new imaging modalities such as Photoacoustic tomography for improvement in cancer surgery. 

 

August 19, 2019 at 4.00 pm in AG-69

Title :

Protein degradation by a double-ring AAA+ protease: in singulo mechanisms of unfolding and translocation

Abstract :

 

ATP powered molecular motors play a crucial role in maintaining protein quality control in a cell and AAA+ proteases maintain protein homeostasis by degrading damaged and unneeded proteins. Single-molecule manipulation tools complement the biochemical experiments and provide deeper insights into the mechanisms of these molecular motors and their interaction with protein substrates. In this talk, I will discuss my recent work on mechanistic investigations of a double-ring AAA+ protease, E.coli ClpAP using single-molecule optical tweezers and determine the role of individual ATPase rings in protein unfolding and translocation. Our single-molecule studies provide new insight into the functional importance of the D1 ring of ClpA and the role of coordination between the two AAA+ rings. Also, the differences in translocation from N- and -C termini indicate that the enzyme can recognize subtle differences in direction of the polypeptide track. In addition, I will elucidate the paramount role of local stability of a substrate in protein degradation and provide clues as to how the placement of degradation signals on a substrate may evolve to minimize the energetic cost of degradation.

References:

Hema Chandra Kotamarthi, Robert Sauer, Tania Baker. “The non-dominant AAA+ ring in the ClpAP protease functions as an anti-stalling motor to accelerate protein unfolding and translocation” (Pre-peer reviewed version at bioarXiv: https://doi.org/10.1101/585554)

Adrian Olivares*, Hema Chandra Kotamarthi*, Benjamin Stein, Robert Sauer, Tania Baker, “Effect of directional pulling on mechanical protein degradation by ATP-dependent proteolytic machines”, Proceedings of National Academy of Sciences, USA, 2017, Vol 114, E6306-E6313. * Equal Contribution.

August 13, 2019 at 2.30 pm in AG-80

Title :

Evaluation of Photocatalytic Activity Over g-C3N4 Coated DFNS and the Role of Interface

July 30, 2019 at 2.30 pm in AG-69

Title :

Small Molecule Activation at Transition Metal Centers: Structure-Function Correlations

Abstract :

Small molecule activation constitutes one of the main frontiers of inorganic and organometallic chemistry, with much effort directed towards the development of new processes for the selective and sustainable transformation of abundant small molecules such as dioxygen (O2), water (H2O), hydrogen peroxide (H2O2) or protons (H+) into high-value chemical feedstocks and energy resources. Because nature mostly uses metal ions to activate these relatively inert molecules and modulate their reactivity, much inspiration for the field has come from bioinorganic chemistry. This talk will focus on some of the recent highlights from our group on homogenously catalyzed bioinspired activation of small molecules, as well as stoichiometric reactions that further our understanding towards such ends. It will cover many aspects of small molecule activation including: organometallic chemistry, spectroscopy, synthesis, and detailed mechanistic studies involving trapping of reactive intermediates. The demonstrated examples will help to emphasize the continuous effort of our group in uncovering the structure-reactivity relationships of biomimetic model complexes, which may allow vital insights into the prerequisites necessary for the design of efficient catalysts for the selective functionalization of unactivated C–H bonds, O2/H2O/H2O2 activations, or H+ reductions by using cheap and readily available first-row transition metals under ambient conditions.

 

July 29, 2019 at 4.00 pm in AG-69

Title :

Computational investigation of the effect   of copper coordination and native disulfide bond   on the mechanical unfolding   pathways of Azurin

July 22, 2019 at 4.00 pm in AG-69

Title :

Can EPR be used to probe solid-liquid phase transitions in confined systems?

Abstract :

Study of systems such as water under confined conditions is actively pursued because of its relevance to real systems, such as cells, microorganisms, etc. In this regard, EPR spectroscopy offers a convenient route due to its excellent sensitivity to micro viscosity and penetrability power.  When used as a probe-based spectroscopy, however, the probe-system interactions need to be thoroughly examined beforehand. In this work, we consider a specific property: solid⇌liquid transition of water, and ask a fundamental question, “Can EPR detect the freezing of water at its conventional freezing point in bulk/confined conditions?”   Our work convincingly demonstrates that the spin probe can itself induce liquid domains in ice, which could be mistaken as a depression in the freezing point. We propose a theory to account for these solute induced perturbations. Finally, it will be discussed how the proposed theory can be applied to the extreme dilution case of a solution containing a single solute molecule.   

References

1.Thangswamy, M.; Maheshwari, P.; Dutta, D.; Rane, V.*; Pujari, P. K. J. Phys. Chem. A 2018, 122, 5177-5189.

2.Thangswamy, M.; Maheshwari, P.; Dutta, D.; Rane, V.*; Pujari, P. K. J. Phys. Chem. C 2019, 123, 11244-11256.

 

July 18, 2019 at 2.30 pm in AG-80

Title :

Biophysical characterization of DNA damage proteins from Rice Plant

Abstract :

DNA damage in living cells is repaired by two main pathways, homologous recombination (HR) and non-homologous end joining (NHEJ). The proteins involved in HR pathway have been widely studied in eukaryotes. The MRX/N complex which consists of Mre11, Rad50 and Xrs2 in case of yeast and Nbs1 for vertebrates, are the first responders to double strand breaks. This complex scans the DNA double strand for a break, and binds to the broken DNA ends as soon as a break occurs. The Mre11 protein of the MRN complex is highly conserved in eukaryotes. Rad52 (Radiation sensitive 52) belongs to a different group of important genes, and is found to be highly conserved across different species. Until lately, it was believed that RAD52 is absent in plant systems. However, recent genetic studies have pointed out the presence of RAD52 homologues in plants, though these have not yet been characterized biochemically. 

In the current study, the biochemical properties of rice OsMre11 and OsRad52 protein were analysed. These proteins were over-expressed in Escherichia coli over expression host cells and the proteins purified. The identity of purified OsMre11 and OsRad52 protein was confirmed via peptide mass fingerprinting. DNA binding assays showed that the purified proteins were able to bind to different forms of DNA. Purified OsMre11 protein exhibited nuclease properties, which was promoted by presence of manganese as a co- factor. Gel filtration and native PAGE analysis indicated that the OsRad52 protein in its native state probably formed an undecameric structure. Purified OsRad52 mediated the renaturation of complementary single strands into duplex DNA via both agarose gel and FRET based assays. Hence concluding that both OsMre11 and OsRad52 proteins, binds to ssDNA/dsDNA for mediating important functions like nucleolytic cleavage and renaturation during homologous recombination. This study represents the first report on biochemical properties of OsMre11 and OsRad52 protein from important crop like rice, which shall help in dissecting the recombination and repair machinery in plant systems.

 

July 15, 2019 at 4.00 pm in AG-69

Title :

The response of blue copper protein to changes in beta sheet connectivity

 

July 10, 2019 at 2.30 pm in AG-80

Title :

Chemical Protein Synthesis via a Diselenide–Selenoester Ligation Approach

Abstract :

Native chemical ligation (NCL), reported by Kent and co-workers in 1994, has revolutionized the field of chemical protein synthesis, enabling access to numerous site-specifically modified proteins. While NCL is regarded as the most widely used method for the construction of proteins, some intrinsic limitations of this seminal technology have catalysed the search for an alternative approach. Recently, the Payne group developed a selenium-mediated ligation methodology – the diselenide–selenoester ligation (DSL). First disclosed in 2015, DSL offers number of unique and exciting features, greatly expanding the scope of NCL. Typically, these ligations are performed by simply mixing the two suitably functionalized peptide fragments (peptide bearing a C-terminal selenoester and another peptide with an N-terminal diselenide) dissolved in a denaturing buffer without any exogenous thiols or other additives and proceed to completion within 1-10 minutes, even at sterically hindered junctions. Moreover, due to the lower pKa of selenocysteine compared to cysteine, the ligations can be performed over a wide pH range (pH 3–7) and owing to their additive-free nature, allow one-pot deselenization after ligation. Chemical synthesis of therapeutic peptides and proteins bearing site-specific posttranslational modifications (PTMs) using this rapid and highly efficient ligation methodology will be showcased during this seminar.

July 9, 2019 at 2.30 pm in AG-80

Title :

From Protein-Protein Interaction Modulators to Chemical Protein Synthesis: Exploring Unconventional Approaches

Abstract :

Protein-protein interactions (PPIs) are associated with a wide range of crucial biological processes and targeting specific PPIs has been demonstrated to have tremendous therapeutic potential. However, PPIs – once termed as ‘undruggable’ targets, often involve large and flat binding sites along with conformational changes rendering traditional approaches ineffective. The kinetic target-guided synthesis (TGS) serves as an unconventional strategy, having the potential to streamline the development of protein-protein interaction modulators (PPIMs). In this fragment-based approach, the target is directly involved in the assembly of its own bidentate ligand from a library of reactive fragments. The first half of this seminar will focus on the application of kinetic TGS based on the sulfo-click reaction to identify PPIMs of the Bcl-2 family of proteins.

Chemical synthesis of proteins serves as a powerful tool for accessing these valuable biomolecules with the ability to introduce chemical modifications site-selectively. Although native chemical ligation (NCL), reported by Kent and co-workers in 1994, has been the cornerstone of chemical protein synthesis, several mechanically distinct and thiol-independent ligation reactions have also emerged in the last decade. For example, the KAHA ligation, reported by the Bode group in 2006, features a chemoselective reaction between a peptide segment bearing a C-terminal a-ketoacid and another peptide with an N-terminal hydroxylamine. Successful application of the KAHA approach through convergent ligations to accomplish total synthesis of a 184-residue ferric heme-binding protein, nitrophorin 4 (NP4) will be discussed in the second half of this seminar.

 

July 8, 2019 at 4.00 pm in AG-69

Title :

Computation of Resonance Magnetic Fields of CW‑EPR Spectra by Reversion of Power Series

Abstract :

Electron paramagnetic resonance (EPR) spectra are generally recorded as a function of the magnetic field, while keeping the energy of transitions fixed.  Calculations of the EPR spectra, however, are almost always performed at a fixed magnetic field of a given spin-Hamiltonian to determine the energies of various transitions. These two methods, in general, do not produce equivalent spectra. In this pedagogical talk, I will first briefly highlight how various approaches have been used to handle this dichotomy by various workers. I will then describe our recent method to calculate the resonance magnetic fields at a fixed frequency.  With some help from the perturbation theory and the mathematics of reversion of polynominals, our method gives the resonance magnetic fields at a fixed frequency in a relatively simple and straightforward manner. 

Ref. Vinayak Rane and Ranjan Das, Applied Magnetic Resonance,  https://doi.org/10.1007/s00723-019-01128-6 

 

 

July 3, 2019 at 11.30 am in AG-80

Title :

Is the early stage of aggregation important in understanding neurodegenerative diseases?

Abstract :

Although majority of the neurodegenerative diseases do not have any cure available, protein aggregation and deposition has been found to be a common phenotype. The heterogeneity of aggregation process and the presence of large number of triggering mechanisms results in the difficulty to devise therapeutic strategies against these toxic inclusions formation. Our laboratory has been investigating these triggers, which contribute to the alteration of folding pathways leading to the early and unexplored stages of aggregation. The conformational heterogeneity of the early intermediates and their transient nature are some of the reasons why traditional techniques do not typically work for the early stage detection. We have been using sensitive biophysical methods to directly detect and characterize the early intermediates and oligomers in vitro and inside live cells using Parkinson’s diseases (PD) and ALS as our models. We are also using cryo-EM to investigate the structural insights into the early intermediates, which are believed to the primary inducer of cellular toxicity. Using a combination of biophysics, biochemistry and microscopy, we are developing protein early intermediates vs toxicity maps to determine the structural insights responsible for the neuronal toxicity.

June 28, 2019 at 2.30 pm in AG-69

Title :

Stability, Non-enzymatic hydrolysis, and Abiological activity of CYP175A1 and its analogues

June 26, 2019 at 2.30 pm in AG-69

Title :

Visible light driven carbon dioxide reduction on plasmonic catalyst

Abstract :

Direct conversion of solar to chemical energy has gained renewed interest in the recent years. Plants uptake atmospheric CO2 to produce sugar by the process of photosynthesis. Recreating this process requires materials which can absorb light and convert it into energy. Plasmonic nanoparticles of silver and gold are excellent candidates for photocatalysis due to their high absorption cross section. In my talk, I will show that under light irradiation, silver nanoparticles catalyze CO2 reduction reaction. Spatially resolved single particle surface enhanced Raman spectroscopy shows formation of intermediate such as HOCO* as well products such as carbon monoxide and formic acid. Further, binding geometry of HOCO* plays decisive role in directing the reaction either towards carbon monoxide or formic acid. 

Although catalytic reaction on plasmonic nanostructures is fairly well studied, the fate of metal nanoparticles post photocatalysis is largely unknown. We found that plasmon-assisted CO2 reduction reaction induces significant directional restructuring on catalyst surface. In the second part of the talk, I will show you how these structural changes in plasmonic catalysts also gives an insight into the mechanism of photocatalytic activation, the distribution of active sites on nanoparticle surface and the definite role of light. 

References. 

1.G. Kumari, X. Zhang, D. Devasia, J. Heo, P. K. Jain. ACS Nano 2018, 12, 8330−8340. 

2.S. Yu, A. J. Wilson, G. Kumari, X. Zhang, P. K. Jain. ACS Energy Lett. 2017, 2, 2058-2070. 

 

3.X. Zhang, G. Kumari, J. Heo, P. K. Jain. Nat. Commun. 2018, 9, 3056