TIFR
Department of Chemical Sciences
School of Natural Sciences

Calender

July 17, 2017 at 4.00 pm in AG-69

Title :

Modulation of emission signaling pathway through allosteric control on the conformational rigidity of coumarin-imidazole conjugate

Abstract:

The allosteric regulation in the biological system is controlled at the molecular level by recognition events that are triggered by subtle conformational changes of the proteins.1 Although it is very challenging to mimic such complex communication pathways, one can still be inspired by these systems and design prototype that can give into fundamentals of molecular recognition2 in physiological environments. There seems to be a significant lag in the area of chemically controlled conformational switches that modulate new fluorescence signaling pathway through allostery; bridging this gap may lead to novel molecular systems. The design of such molecular systems represents a promising avenue for finding and manipulating allosteric networks3 in the biology. 

 

In this presentation, I will discuss about a prototype based on coumarin-imidazole conjugate which undergo conformational changes through distal intramolecular H-bonding interactions.4 The key factor behind this conformational switching is a cooperative effect that involves coumarin side arm, solvents, and leads to a conformational or dynamic changes in the distal coumarin sidearm through intramolecular H-bonds, affecting its emission output function. So we hypothesized that the combination of distal intramolecular H-bond interactions and allostery results in the observed effects on the fluorescence output signaling pathway. The concept of new emission signaling pathways caused by conformational switching between two states offers a new paradigm to introduce functional allostery in macromolecular backbones. 

 

References

1. (a) Monod, J.; Changeux, J.; Jacob, F. J. Mol. Biol. 1963, 6, 306-329. (b) Changeux, J. P. Ann. Rev.

    Biophys. 2012, 41, 103-133.

2. (a) Mechanisms of cooperativity and allosteric regulation in proteins; University Press: Cambridge, 

    UK, 1990. (b) Laskowski, R. A.; Luscombe, N. M.; Swindells, M. B.; Thornton, J. M. 

    Protein Sci. 1996, 5, 2438-2452. (c) Faulkner, A.; Leeuwen, T. V.; Feringa, B. L.; Wezenberg, S. J. J.

   Am. Chem. Soc. 2016, 138, 13597-13603.

3. Dokholyan, N. V. Chem. Rev. 2016, 116, 6463-6487.

4. Bhattacharjee, I.; Ghosh, N.; Raina, A.; Dasgupta, J.; Ray, D.- Manuscript under communication

 

July 3, 2017 at 4.00 pm in AG-69

Title :

Tessellation Models for Microstructure Evolution

Abstract :

Accurate morphological representation of polycrystalline microstructures is the key to structure-property linkage. Spatial tessellations exhibit great resemblance with the real microstructure evolution, which are driven by nucleation and growth. Voronoi, Avarami and Laguerre tessellations are the most popular models among the spatial tessellation models, but are only a small subset of the wide spectrum of the real microstructure evolution. Specifically, none of these models capture the anisotropy of grain shapes. The current research work proposes generalized ellipsoidal growth, in which grains grow as ellipsoids with specified 3D orientation and with velocities as a function of their size and initiate at different times from random nucleation sites represented by a spatial point process. This can be represented by a marked point process random field model. The mathematical representation of the grain cells, thus formed, is developed. This could be extended to the non-trivial inverse problem of locating a grain nucleation site from the grain centroid and volume data. This is demonstrated on data generated using diffraction Contrast Tomography (DCT).

May 30, 2017 at 2.30 pm in AG-69

Title :

Designing Carbon-Metal Oxide Nanostructures for Energy Applications

Abstract :

The ever increasing world energy needs, the severity of environmental pollution issues, limited fossil fuel resources, have triggered extensive research in pursuit of efficient renewable energy sources and sustainable storage technologies. Electrochemical capacitors (ECs) often called supercapacitors (SCs) are promising clean energy storage solutions for high power management and grid applications. In general, the ultimate performance characteristics of SCs primarily depend on the way constituent electrode materials are engineered and how the electrodes are fabricated. The presentation is aimed at exploring three important aspects of the SC, such as i) simple, continuous and energy-efficient method to synthesize high-quality carbon nanomaterials such as hydrophilic carbon nano-onions (CNOs), ii) enhancing performance of such nanocarbon by various nanocomposites and efficient heteroatoms doping techniques, iii) working on different SC configurations (symmetric & asymmetric) to enhance the specific energy and power density of the device and iv) to evaluate the device performance by using industrially recommended best practices and methods to get reliable performance data using fabricated devices which actually mimic the real supercapacitor in market. The carried out PhD research work essentially establishes an inherent relationship among synthesis-structure-property-application of as-synthesized CNOs, its nanocomposites and doped CNOs at the nanoscale.

May 29, 2017 at 4.00 pm in AG-69

Title :

Elucidating Energy Landscape of β-rich Globular Proteins

May 22, 2017 at 4.00 pm in AG-69

Title :

Dendritic Fibrous Nano-Silica (DFNS) Based Hybrid Materials for Light Harvesting and Energy Storage

May 15, 2017 at 4.00 pm in AG-69

Title :

Designing Ligands for Chelating Redox Active Metal Ions

May 9, 2017 at 3.00 pm in AG-69

Title :

Surface Modified ZnO Nanostructures: Synthesis, Optical Studies and  Applications in Photocatalysis

May 9, 2017 at 2.00 pm in AG-69

Title :

Nanomaterials for Energy Application

May 8, 2017 at 4.00 pm in AG-69

Title :

Photocatalytic sp3 C-H Activation inside Water-soluble Nanocages

May 1, 2017 at 4.00 pm in AG-69

Title :

Amylin and Amyloid beta: Structure, Membrane Interaction and Cellular Entry Mechanisms

Abstract :

Amyloid beta (Aβ) oligomer is thought to be the major toxic species for the Alzheimer’s disease. But it is still unknown whether different regions play specific roles in the multi-step toxicity pathway. Here, we have decoupled the functionality of the core region (residues 18-35) vs the N- terminal (1-9) in terms of affinity towards membrane, entry and spatial distribution within neuronal cells. Using temperature dependence of cell entry, we probe the underlying mechanism of cell entry is active or passive. We also probe the role of membrane potential in mediating membrane affinity, by artificially creating a transmembrane potential in small unilammelar vesicles.

Amylin is another amyloidogenic peptide, which is responsible for type-II diabetes. For amylin too, the smaller oligomeric species is the major toxic species. Here, to understand the relation between structure and function, we have probed the secondary structural changes between the oligomers and fibrils of amylin using Raman and IR spectroscopy. We also perturb the lone di-sulphide linkage in this peptide to understand its role in membrane binding and toxicity. 

 

April 27, 2017 at 2.30 pm in AG-80

Title :

Nanostructured Materials for Photo-catalysis

April 24, 2017 at 4.00 pm in AG-69

Title :

Charge Transfer Transitions Associated with Charged Aminoacids: A Classical Electronic Donor-Bridge-Acceptor Paradigm

April 21, 2017 at 2.30 pm in AG-80

Title :

Leveraging organic chemistry for solving biological problems: Bioconjugation and bacterial signaling as case studies

Abstract :

The underlying philosophy of my research program is to utilize organic chemistry to address questions in both applied and fundamental biological sciences. In this talk, I shall discuss how I propose to employ organic chemistry for: a) developing technologies for protein bioconjugation, and b) studying c-di-GMP signaling in bacteria. In the first half of my talk which will focus on bioconjugation, I shall describe my proposed approach for bridging disulfide bonds of proteins and using this chemistry for fabricating antibody-drug conjugates, for peptide stapling and as disulfide mimics. Additionally, I shall discuss my proposed strategies for performing cysteine-independent protein bioconjugation that we are currently pursuing in my research group. The second half of my talk will focus on the bacterial second messenger, c-di-GMP, a cyclic dinucleotide that plays a major role in biofilm formation.1 Intriguingly, bacteria contain numerous c-di-GMP synthase enzymes (diguanylate cyclases or DGCs) which when individually deleted, engender distinct phenotypes suggesting they have distinct roles despite each being responsible for generating the same product. To elucidate the roles of individual DGCs and to understand why bacteria express so many DGCs, I propose to develop a chemical genetics-based platform that I shall describe in my talk. Additionally, I shall describe a chemoproteomic approach that I seek to develop for discovering the c-di-GMP interacting proteome of bacterial cells. I believe that the insights on c-di-GMP signaling obtained from these studies will significantly contribute towards developing novel antibacterial therapy directed at targeting this fascinating signaling mechanism.

1) D. Kalia et al., Chem. Soc. Rev., 2013, 42, 305–341.

April 20, 2017 at 2.30 pm in AG-80

Title :

Efficacious strategies for cysteine-mediated protein bioconjugation

Abstract :

The development of chemoselective organic reactions that proceed rapidly under physiological conditions to form stable covalent linkages have revolutionized modern biological and clinical research. One such reaction, Michael addition between the thiol functional groups of cysteine residues of proteins and maleimides to form thio-maleimide linkages, is extensively used for labeling proteins with fluorophores, affinity tags, polyethylene glycol moieties and drug molecules for a diverse range of applications. In particular, the tremendous success of antibody-drug conjugates (ADCs) generated by appending drug molecules to antibodies by employing this chemistry has had a transformative impact on cancer therapy. Consequently, recent reports on the susceptibility of these linkages to undergo thiol exchange-mediated breakdown in the physiological milieu1, 2 are extremely alarming. In my talk, I shall describe two approaches that my research group has developed3, 4 to overcome this problem. One of these approaches is based on our discovery that unlike conventional maleimides, exocyclic olefinic maleimides form thiol exchange-resistant conjugates and hence are preferable for thiol bioconjugation.3 In another approach, we have rationally designed a photoactivable maleimide derivative that after bioconjugation can be irradiated with UV light to trigger rapid thio-maleimide ring hydrolysis to form stable conjugates.4 I shall also discuss how we plan to use these new scaffolds for generating stable ADCs.

1) B. Q. Shen et al., Nat. Biotechnol. 2012, 30, 184–189.

2) R. P. Lyon et al., Nat. Biotechnol. 2014, 32, 1059–1062.

3) D. Kalia* et al., Angew. Chem. Int. Ed. 2016, 55, 1432–1435.

4) D. Kalia* et al., Angew. Chem. Int. Ed. 2017, 56, 1885–1889.

April 17, 2017 at 4.00 pm in AG-69

Title

The N-H...N Hydrogen Bond - Structure and Strength