TIFR
Department of Chemical Sciences
School of Natural Sciences

Calender

March 27, 2017 at 4.00 pm in AG-69

Title :

Mechanistic Origin of Protein Flexibility of Ubiquitin Family Proteins

Abstract :

Here we investigate the mechanistic origins of protein malleability. We develop a methodology using Single-Molecule Force spectroscopy (SMFS), fluorescence spectroscopy and circular dichroism to probe the native and transition states of Ubiquitin and small ubiquitin-related modifier (SUMO2), to get insights into the protein dynamics and mechanical resistance. Both SUMO2 and Ubiquitin have mechanical clamp which serve as a major resistor to force in SMFS experiments. But we show that the core of the protein actually couples to the clamp and determines its overall malleability. And to top it off we look at the interactions which determine the core flexibility in both the proteins.

March 23, 2017 at 4.00 pm in AG-80

Title :

Construct, Deconstruct, Rebuild: Mimicking Nature to Engineer Functional Modules for Bottom-up Synthetic Biology

Abstract :

An ambitious goal posed by synthetic biology is the bottom-up construction of a functional cell. Recently, a droplet-based bilayer platform termed ‘droplet interface bilayer’ was developed. Nanoliter-sized lipid-encased water droplets can be arranged in networks of desired patterns, forming electrical connections between them via membrane pores. The droplets can also be encapsulated in a hydrogel matrix opening new directions for bottom-up protocell / prototissue construction. 

The key to designing functional protocells is understanding the engineering principles of molecular construction at all biological scales (nanometer, nm – millimeter, mm). To this end, I am studying the structural mechanics of protein assemblies, specifically the nuclear lamina, using atomic force microscopy, cryo-electron tomography and in silico approaches. Besides paving the way to rationally design synthetic systems for bio-nanotechnology, the combined approach provides understanding of the structure-function of the macromolecular assembly involved in diseases from a materials science perspective, the underlying goal of ‘materiomics’.

 

March 20, 2017 at 4.00 pm in AG-69

Title :

Membrane-Protein Interaction at the Single Molecule Level

Abstract :

Understanding the interaction between membranes and amyloid protein oligomers  is a key unsolved challenge in the field of antimicrobial peptides and amyloid diseases such as Alzheimer’s and Type II diabetes. While the structure of the membrane-bound monomeric subunit is slowly emerging from bulk studies, we need to know how many monomers make up the oligomer, whether this species subsequently grows to specific sizes, whether specific membrane architectures determine binding, and whether interaction with other membrane proteins substantially alter their statistics. Here we approach this problem by the interaction of amylin and amyloid beta with artificial lipid bilayers. We perform single molecule photobleaching experiment with Total Internal Reflection Fluorescence Microscope to probe the stoichiometry. We also employ an atomic force microscope to probe changes in membrane rheology. Our answers may be significant consequences for the underlying toxic mechanism. 

March 16, 2017 at 2.30 pm in AG-80

Title :

Biological Fingerprints in Molecular Electronics

Abstract :

Electron transfer in and across proteins plays a key role in many biological processes of organisms. Fundamental understanding electron flow within protein structures is not only important for biology, but may also help in the design of bio-electronic devices that directly couple to biological systems. Electrochemistry of redox-active proteins and enzymes is widely used to study electron transfer processes in those systems, while the impact of external voltage-driven electronic transport across bio-molecular junctions has been limited because of limited information that could be obtained from resulting current-voltage characteristics. However, as I will show, protein-based molecular junctions can demonstrate distinct transport efficiencies, i.e. junction-currents, depending on protein orientation, conformation, mutation and especially, the presence of cofactors. Molecular junctions with photoactive membrane proteins and photochromic photoreceptor proteins, which alter their conformation upon light absorption, demonstrate modulation in junction-current with illumination.  Removing or modifying protein cofactors not only shows direct effects on junction currents, but also a transition from tunneling (temperature-independent) to temperature-dependent transport. The high conducting nature of the protein junctions raises questions about the fundamental nature of electron transport across proteins. Finally, I will demonstrate how these biomolecular signatures from molecular electronic transport can be used to map electron transport paths within the protein. Detailed knowledge of nanoscale conduction pathways would enable developing synthetic proteins with higher conductance and different functionalities, which will directly impact the field of bioelectronics.

 

References:

[1] Christopher, B.; Mukhopadhyay, S; Cahen, D; Lederman, D., Towards Bioelectronics with Immobilized Proteins: a review of what we (do not) know. Rep. Prog. Phys. (submitted, arXiv article - 1702.05028)

[2] Mukhopadhyay, S.; Cohen, S. R.; Marchak, D.; Friedman, N.; Pecht, I.; Sheves, M.; Cahen, D. Nanoscale Electron Transport and Photodynamics Enhancement in Lipid-Depleted Bacteriorhodopsin Monomers ACS Nano, 2015, 137, 11226.  

[3] Mukhopadhyay, S.; Dutta, S.; Pecht, I.; Sheves, M.; Cahen, D. Conjugated Cofactor Enables Efficient Temperature-Independent Electronic Transport Across ∼ 6 nm Long Halorhodopsin. J. Am. Chem. Soc. 2014, 8, 7714.

 

March 14, 2017 at 2.30 pm in AG-69

Title :

Soft-oxometalates, Polyoxometalates, Light and Chemistry

Abstract :

Many metal centres, many oxygen atoms and usually charged species can be formally defined as polyoxometalates. They are crystalline and exist in solid state and also as molecular ions in solutions. In our group we explore the formation of unusually large polyoxometalates like that of [Mo132] and it will be discussed. Using light their photocatalytic activities in various organic reactions have also been explored by us and has led to the synthesis of polymeric materials and speciality organic compounds. All such aspects will be discussed and presented. However there exists a liquid like colloidal paradigm based on oxometalates which has been proposed by us to be called soft-oxometalates. Being colloidal they provide a unique opportunity for patterning of polyoxometalates on a microscopic chip using thermo-optic laser tweezers. Such soft states of oxometalates in conjugation with polymeric organic frameworks have been patterned to catalyse simple oxidation reactions and will also be discussed. Finally the use of soft-oxometalates in achieving CO2 reduction coupled with water oxidation will be demonstrated which opens up new possibilities of using these materials for photochemical reduction reactions coupled with oxidation reactions and the reverse.   

March 9, 2017 at 4.00 pm in AG80

Title :

Understanding Amyloid Aggregation in Terms of its Distal Folding Contacts

March 6, 2017 at 4.00 pm in AG-69

Title :

KCC-1 Supported Metal Nanoparticles as Highly Active and Selective Nanocatalysts

March 3, 2017 at 2.30 pm in AG-69

Title :

Development of Cost Effective Organometallic Catalysts for Ccompounds of Industrial Interest

Abstract :

Catalysis is one of the most important branches of chemistry because it enables the production of new molecules and materials that have impact on numerous final applications. Some 75% of all commercially-produced chemical products involve catalysts at some stage in their manufacture, and catalytic processes generate ca. £700Bn in products worldwide annually. Hence, an inexpensive and environmentally benign transition-metal surrogate based catalytic systems, replacing scarce, toxic, and expensive transition metals, is a pressing need. In first part of my talk, I will discuss about the development of earth abundant metal based complexes using pincer ligand scaffold for the (de)hydrogenation reaction(s) of small molecules of industrial importance. This involves synthesis of novel catalytic systems and understanding of the catalytic reactions with a focus on the mechanistic aspect. The second part of my talk consist of development of novel ligand framework based on the cationic phosphine unit, starting from elemental white phosphorous and application in carbon dioxide sequestration chemistry. Additionally, synthesis of metal complexes based on the phosphate back bone relevant for material application will be discussed

March 2, 2017 at 2.30 pm in AG-80

Title :

Organometallic Complexes: Application Spanning from Cataysis to Material Chemistry

Abstract :

Catalysis of organic reactions is one of the most important applications of organometallic chemistry and has been a significant factor in the rapid development of the field as a whole. Organometallic complexes now have numerous applications in the pharmaceuticals, fine chemical, and in material chemistry and are beginning to contribute to the rising topic of energy and green chemistry. The first part of my talk consist of synthesis of unconventional organometallic systems for the hydroamination reaction (addition of amine across C-C multiple bond). The main focus will be on the development of novel bimetallic complexes and their application. The second part of my talk consist of development of metal complexes using phenalenyl (PLY) based ligand systems. PLY is a well-known building block for constructing organic radical based materials for its ability to exist in three redox active states such as cation, neutral radical and anion by accepting sequential electron into its nonbonding molecular orbital (NBMO). The discussion will be utilizing the cationic state of the PLY unit to develop metal complexes for application in catalysis and spintronics.

February 28, 2017 at 2.30 pm in AG-69

Title :

Fibrous Nanosilica/TiO2 Hybrids for Photocatalytic H2 Production

February 27, 2017 at 4.00 pm in AG-69

Title :

Structural Insights into the Mechanical Properties of Ubiquitin Family Proteins (using Steered Molecular Dynamics Simulations)

 

February 23, 2017 at 2.30 pm in AG-80

Title :

A Theoretical Model to explain the DNP Induced NMR Signals Using TEMPOL at 3.4 T

Abstract :

Dynamic nuclear polarization (DNP) is one of the most efficient methods to increase the sensitivity of NMR and MRI by transferring polarization from electron spins to nuclear spins.  For radicals in solid solutions the nuclear signal enhancements during microwave irradiation are interpreted either using the thermal mixing (TM) mechanism or a combination of the solid-effect (SE) and cross-effect (CE) mechanisms.  Although the SE and CE based analysis of the lineshape of the enhancement as a function of the MW frequency has been possible, it was only realized recently that these lineshapes are correlated to the electron polarization distribution in the sample. To quantify this correlation a theoretical model was introduced based that describes the electron spectral-diffusion (eSD) mechanism and its contribution to DNP through the new indirect-CE (iCE) mechanism. 

February 21, 2017 at 2.30 pm in AG-69

Title :

Directed Evolution of Thermally Stable Cytochrome P450: An Approach for Alkane Hydroxylation

February 20, 2017 at 4.00 pm in AG-69

Title :

Bi-ion : A new electroactive species for batteries

February 17, 2017 at 2.30 pm in AG-69

Title :

Cryo-electron microscopy (cryo-EM) studies of mammalian mitochondrial and Mycobacterium smegmatis ribosomes

Abstract :

Ribosomes the protein synthesis machinery are large macromolecular complexes. The mammalian mitochondrial ribosomes (mitoribosomes) are responsible for synthesizing 13 membrane proteins that form essential components of the complexes involved in oxidative phosphorylation (or ATP generation) for the eukaryotic cell. The mitoribosome contains significantly smaller rRNAs and a large mass of mitochondrial ribosomal proteins (MRPs), including large mito-specific amino acid extensions and insertions in MRPs that are homologous to bacterial ribosomal proteins and an additional 35 mito-specific MRPs. The cryo-EM structures of the mitoribosome have yielded the architecture of small subunit of the mitoribosome and existence of the previously eluded E-site within the mitoribosome. The mitoribosomes are susceptible to the antibiotics that targets the bacterial ribosomes because the mitoribosomes are believed be of prokaryotic origin. A docking study of antibiotics in to bacterial and mitochondrial ribosomes have provided rational to the differential affinity of these antibiotic. 

 

Mycobacterium smegmatis is widely used as a model organism to study pathogenic mycobacteria, such as Mycobacterium tuberculosis. About one third of M. smegmatis mRNAs are leaderless, lacking a 5’UTR and therefore also lacking a Shine-Dalgarno sequence. How ribosomes initiate protein synthesis from leaderless mRNAs is unknown. We have obtained a 5 Å resolution cryo- EM map of the M. smegmatis 70S ribosome, with some core regions resolved to 4 Å. Our map reveals two unique features of the mycobacterial ribosome: (i) an altered conformation of the previously identified steeple feature on the large (50S) ribosomal subunit (ii) a novel protein density mass is found below the origin of the rim of the small (30S) ribosomal subunit platform that appears to correspond to an α-helical structure of up to ~33 amino acid residues. While we continue to improve the resolution of our cryo-EM map, we are also using mass spectroscopy to identify the α-helical density. I will summarize the results of these studies that I have been involved in, and will outline my future research plan on the protein synthesis in Plasmodium falciparum ribosome that I would like to pursue as an independent investigator.