Title :

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

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.

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.

Title :

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

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.

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.

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 

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.

Title :

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

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 

Title :

Carbon dioxide capture: Insights from Raman spectroscopy

Abstract :

Increasing carbon dioxide levels stemming from various anthropogenic sources have led to adverse climatic conditions. CO₂ sequestration becomes vital to mitigate global warming. Metal organic frameworks (MOFs) have immense potential to sequester CO₂ owing to their porous and flexible architecture exhibiting high guest selectivity. While the as-synthesized structure can be predicted by X-ray diffraction, knowing in-situ structural dynamics during gas adsorption is a challenge. In the first part of the talk, I will discuss how adsorption or desorption of gases modulates the structure of MOFs. Investigating these dynamics frameworks are crucial for designing new materials with higher CO₂ uptake. 

Furthermore, it is necessary to reduce captured CO₂ into fuels and one of the ways to achieve this is by using metal nanostructures. In addition to catalysing chemical reaction, plasmonic nanoparticles also amplify the signal of adsorbed molecules enabling their detection via surface enhanced Raman spectroscopy (SERS). In the second half of the talk, I will show different types of plasmonic nanostructures and further illustrate that silver nanoparticles exhibit high SERS enhancement and hence is a suitable catalyst for studying single molecule reaction. 

References. 

1.P. Kanoo, S. K. Reddy, G. Kumari, R. Haldar, C. Narayana, S. Balasubramanian, T. K. Maji. Chem. Commun. 2012, 48, 8487-8489. 

2.G. Kumari, K. Jayaramulu, T. K. Maji, C. Narayana. J. Phys. Chem. A 2013, 117, 11006-11012. 

3.G. Kumari, C. Narayana. J. Phys. Chem. Lett 2012, 3, 1130-1135. 

Title :

Organometallic Catalysis for Energy & Environment: What we can achieve

Abstract :

We are living in the age where we have witnessed critical rise in all types of pollution and the depletion of limited supply of fossil fuel. A lot of it is caused by the way our industries manufacture their products and our dependence on fossil fuel for the production of energy. In order to restore the balance of clean environment we need to develop production methods that are environmentally-benign, atom-economic and sustainable. This lecture will focus on some of the strategy in Green Catalysis that can be utilized for the production of industrially useful chemicals and energy storage materials from inexpensive and readily available starting materials. For example: (a) Based on our recent discovery,¹ utilization of alkali or alkaline earth-metal catalysts instead of transition-metal catalysts can make the overall process cheaper and sustainable. (b) Development of reversible chemical hydrogen storage materials such as those based on glycerols or amine-boranes². (c) Chemical recycling of robust plastics such as nylons, polycarbonates and polyurethanes using ruthenium catalyzed hydrogenative depolymerization method. 

1.A. Kumar, T. Janes, S. Chakraborty, P. Daw, N. von Wolff, R. Carmieli, Y. Diskin-Posner, D. Milstein, Angew. Chem. Int. Ed., 2019, 58, 3373. 

2.A. Kumar, N. Beatie, S. A. Macgregor, A. S. Weller, Angew. Chem. Int. Ed., 2016, 55, 6551.

Title :

Organometallic Catalysis for Energy & Environment: What we have achieved

Abstract :

Catalysis plays a major role in the production of food, pharmaceuticals and energy. We have been working in the area of green homogeneous catalysis using pincer complexes of transition-metals. We have developed several interesting methods that are environmentally-benign and sustainable for the production of industrially useful chemicals from the cheap and inexpensive starting materials using pincer complexes of earth-abundant metals such as manganese. These methods are based on hydrogenation or dehydrogenation reactions which makes the overall process highly atom-economic. Utilization of manganese in place of precious metals such as ruthenium makes the overall process cheaper and more sustainable. Some of these examples will be discussed in the lecture, such as: 

1.We reported the first example of the direct synthesis of amides by the dehydrogenative coupling of amines with either alcohols or esters using an earth-abundant metal catalyst.

2.We reported the first example of the direct hydrogenation of organic carbonates to methanol using an earth-abundant metal catalyst. As organic carbonates can be readily prepared from CO₂ and alcohols, this method can be utilized as an alternative route for the conversion of low-pressure CO₂ to methanol.

3.We discovered a fundamentally new Liquid Organic Hydrogen Carrier (LOHC) based on coupling of diols and diamines for the development of a reversible hydrogen storage material.

1.(a) A. Kumar, N. A. E. Jalapa, G. Leitus, Y. Diskin Posner and D. Milstein, Angew. Chem. Int. Ed., 2017, 56, 14992. (b) N. A. E. Jalapa, A. Kumar, G. Leitus, Y. Diskin Posner and D. Milstein, J. Am. Chem. Soc., 2017,139, 11722. 

2.A. Kumar, T. Janes, N. A. E. Jalapa, D. Milstein, Angew. Chem. Int. Ed., 2018, 57, 12076. 

3.A. Kumar, T. Janes, N. A. E. Jalapa, D. Milstein, J. Am. Chem. Soc., 2018, 140, 7453.

Title :

Defect Engineering in Dendritic Fibrous Nano Silica-based Material for CO₂ Methanation

Title :

Microsecond conformational dynamics of biopolymers studied by two-dimensional fluorescence lifetime correlation spectroscopy

Abstract :

Many biological functions of biopolymers (protein/DNA/RNA) are realized with their spontaneous structural fluctuation. Therefore, the elucidation of the energy landscape of biopolymers and their structural dynamics is essential. Single molecule spectroscopy is a powerful tool to investigate this problem, and the single molecule Förster resonance energy transfer (smFRET) technique is widely utilized. However, conventional smFRET detects only millisecond and slower dynamics. In this presentation, I’ll introduce recently developed two-dimensional fluorescence lifetime correlation spectroscopy (2D FLCS)^1,2 that distinguishes the conformers by their fluorescence lifetime and detects their interconverstion dynamics with a microsecond time resolution. Next, I will introduce a new method that combines dynamic fluorescence quenching (DQ) and 2D FLCS. In comparison to FRET which detects relatively large structural change, DQ is more sensitive to the local solvent accessibility of the attached dye. A major advantage of this method is that it requires only single-dye labeling compared to FRET which requires double-labeling. By applying this DQ 2D FLCS to a singly-labeled DNA hairpin, we succesfully resolved the open and closed forms in the equilibrium and detected their microsecond interconversion dynamics. I’ll also show the application of 2D FLCS on preQ₁ riboswitch, an important antibiotic drug target, to resolve its heterogeneous folding dynamics and distinct ligand binding mechanisms.

[1, 2] Ishii, K. & Tahara, T. Journal of Physical Chemistry B, 2013 117, 11414 & 11423.