TIFR
Department of Chemical Sciences
School of Natural Sciences

Calender

May 24, 2018 at 2.30 pm in NMR Seminar Room

Title :

Revisiting the BIM-Trimethylamine and BIM-Ammonia H-Bonded Complexes

May 21, 2018, at 4.00 pm in AG-69

Title :

Comparative study of Native and Hybrid-enzymes: Preparation, Characterization and Reactivity

May 7, 2018 at 4.00 pm in AG-69

Title :

Beyond the Conventional Hybrid Perovskites

May 2, 2018 at 2.30 pm in AG-69

Title :

Viscoelastic response of Liquid at Nanoconfinement

Abstract :

 

Flow properties of confined liquids play crucial roles in a wide range of areas from biology to nanofluidics. Liquids, when confined between two surfaces that are tens of nanometers apart, exhibit unique structural, dynamic, and mechanical properties, which are significantly different from those observed in bulk. In the past, viscosity measurement of confined liquids by different techniques has resulted in contradictory findings. We have developed an experimental scheme, which has two key advantages over  previous techniques used to measure shear-viscosity for liquid films with thickness of few nanometers; (i) the spring measuring the viscous drag has very high stiffness (55000 N/m), and yet force sensitivity of few nN, thus reducing the thermal noise in our measurement. (ii) the force sensing spring stays out of the liquid, and hence has a high resonance frequency and quality factor, allowing us to perform off-resonance measurements with high shear frequency (5-20 kHz) and shear rates (104- 106 s-1). Using this novel shear rheometer, we investigated the role of confinement and substrate wettability on flow properties of polar (water) and non-polar (organic) liquids on several surfaces. We observed reduction in dissipation coefficient under confinement; which is modeled with Carreau-Yasuda model of shear thinning including finite slippage. We found that for purely wetting substrate the nonlinear rheological response solely originates due to nano-confinement, whereas both wettability and confinement play crucial role in case of non-wetting substrates. Finite Element Method (FEM) simulations were performed to understand the behavior of two prongs of our force sensor (tuning fork) at off resonance frequency in air and in liquid medium. Our study helps to separate out the effects of substrate wettability and confinement on shear resistance experienced by liquids at nano-confinement. The rheological response of nano-confined liquids is intriguing and we propose that it is result of criticality with respect to degree of confinement.     

 

 

May1, 2018 at 2.30 pm in AG-80

Title :

Dendritic Fibrous Nanosilica Coated Titanium Dioxide for Morphology Controlled Photocatalysis

April 30, 2018 at 4.00 pm in AG-69

Title :

Identifying key interactions that maintain flexibility of a protein

April 26, 2018 at 2.30 pm in D-406

Title :

Methane transformation to higher oxygenates over nanostructured catalysts

Abstract :

Increasing methane reserves in terms of natural gas, biogas, and shell gas explore its utilization as a solution to future energy security and environment safety. Therefore, methane value addition to higher chemicals get researchers interest in the present scenario.  The direct route is restricted due to low conversion as well low selectivity; hence, indirect route, i.e., via syngas is preferred by industries.

The focus of my talk will be on the effect of various parameters, like noble metal, surface acidity basicity, promotion with another transition metal in a bimetallic system to improve the activity and durability of methane reforming catalyst and the way to regulate ethanol selectivity in CO hydrogenation. 

 

April 25, 2018 at 2.30 pm in AG-80

Title :

Metallic Conductivity in Proteins: A New Paradigm for Biological Electron Transfer and Bioelectronics

Abstract :

Electron transfer is central to all life processes. Every living cell must get rid of a large number of electrons left behind in metabolism when nutrients convert into energy. Aerobic organisms use oxygen to dump these electrons. Electron transfer in proteins occurs through either tunneling or hopping a few nanometers via inorganic cofactors. However, the common soil bacteria Geobacter sulfurreducens transfers electrons over hundreds of micrometers, to insoluble electron acceptors1 or syntrophic partner species2. Electron transfer is using hair-like protein filaments called pili1,2 that function as molecular nanowires and this allows bacteria to survive in environments that lack membrane-permeable electron acceptors such as oxygen. The conductivity of pili exhibits temperature dependence similar to that of disordered metallic polymers1,3. However, metallic conductivity is considered improbable in proteins due to the lack of periodicity in protein structure, thermal fluctuations, and low conductivity values.

I will present our recent electrical, optical and structural studies to identify the structural, molecular and physical mechanism of metallic conductivity in pili. To determine the molecular architecture responsible for conductivity, we are using a suite of complementary experimental and computational methods such as molecular dynamics, x-ray diffraction, circular dichroism, fluorescence microscopy and infrared spectroscopy. Our studies suggest that aromatic amino acids in pili are closely packed from each other        (< 4 Å), forming pi stacking, that can cause in intermolecular electron delocalization, conferring metallic conductivity to pili. Notably, we observe large conformational changes that accelerate electron transfer in pili. Furthermore, we show that improved metallic nature in the pili correlates with the improved pi stacking. These studies defy the current biochemical assumption that all proteins are electronic insulators and need inorganic cofactors for electron transfer. Pili thus represent a new class of electronically functional proteins that can transport electrons at rates and distances unprecedented in biology. I will discuss the implications of these studies for biological electron transfer as well as for bioelectronics.

 

[1] Malvankar et al. Nature Nanotechnology, 6, 573-579 (2011)

[2] Summers et al. Science, 330, 1413-1415 (2010)

[3] Malvankar et al. Nature Nanotechnology, 9, 1012-1017 (2014)

 

 

Research website: https://malvankarlab.yale.edu

 

April 23, 2018 at 4.00 pm in AG-69

Title :

Optical Charge Transfer Transitions Associated with Charged Amino Acids: Creating a Spectral Basis Set to Interpret ProCharTS

April 20, 2018 at 2.30 pm in AG-66

Title :

Peptide Ligand G Protein-Coupled Receptors are Dynamic Molecules in Lipid Membrane

Abstract :

G protein-coupled receptors (GPCRs) constitute a large group of membrane proteins, known to undergo a set of well-defined structural transitions upon activation and signaling. In our work, we address the molecular dynamics of peptide ligand GPCRs using solution and solid-state NMR. We work with human class A GPCRs that are activated by peptide hormones, such as neuropeptide Y (NPY) or ghrelin. The GPCRs are expressed in prokaryotic systems or by cell-free synthesis. In the talk, results on three research topics will be discussed. (i) Studies on the equilibrium dynamics of GPCRs using static 15N CP NMR, 15N NMR spectra acquired as a function of the CP contact time, and 13C MAS NMR experiments confirm the high molecular dynamics of three peptide ligand GPCRs. Quantitative determination of 1H-13C order parameters through measurement of the 1H-13C dipolar couplings in separated local field NMR experiments revealed axially symmetric motions of the GPCRs and molecular fluctuations of large amplitude [1, 2]. (ii) Data will be reported that led to the development of structural models of NPY bound to the Y1 and the Y2 receptors. Isotope-labeled NPY was used to determine the secondary structure of the receptor bound ligand. Upon receptor binding, the C-terminal α‑helix of NPY, formed in membrane environment in the absence of receptor, is unwound starting at Thr32 to make optimal contact of the C‑terminal residues within the binding pocket. The NMR signals of several hydrophobic residues in the α-helical region of NPY were broadened upon receptor binding. The ligands are tethered to the second extracellular loop by hydrophobic contacts, with the N-terminal part of its helix facing the solvent. The C‑terminal pentapeptide of NPY inserts deeply into the transmembrane bundle, making optimal contacts to the Y2 receptor including a contact NPY’s amidated C‑terminus with Gln3.32 in a polar cluster within helices 2 and 3 of the receptor [3, 4]. (iii) We will report data on the dynamics and ligand binding of the human GHS receptor, which plays a key role in the development of obesity [5].

 

[1]Schmidt et al. Chemistry 2014, 20, 4986.

[2] Thomas et al. J. Biomol. NMR 2015, 61, 347.

[3] Kaiser et al. Angew. Chem. Int. Ed. 2015, 52, 7446.

[4] Yang et al. Nature 2018, DOI: 10.1038/s41586-018-0046-x, in press.

 

[5] Schrottke et al. Sci. Rep. 2017, 7, 46128.

 

April 16, 2018 at 4.00 pm in AG-69

Title :

New approaches for studying the structure of protein oligomers in lipids and in solutions

Abstract :

Understanding the interaction between membranes and amyloid protein oligomers is a key unsolved challenge in the field of biophysics. Here we describe new tools to address this challenge. We show that single molecule photobleaching with a home-built Total Internal Reflection Fluorescence Microscope can measure the relative membrane affinity of each type of oligomers. Also, an Atomic Force Microscope coupled to a home-built Confocal Fluorescence Microscope can probe the membrane phase dependant binding of these oligomers.  Separately, fiber-optic in-probe modulation of pH  during an NMR experiment can potentially probe the evolving oligomeric structure.

April 12, 2018 at 4.00 pm in AG-66

Title :

Mechanistic Insights into the Inhibition of Fibrillation of Alpha-Synuclein by Triphala and Destabilization of Preformed Fibrils

April 9, 2018 at 4.00 pm in AG-69

Title :

Understanding the Effect of Distant Mutation on the Charge Transfer Band of Azurin Using Ultrafast Spectroscopy

April 2, 2018 at 4.00 pm in AG-69

Title :

Mn(II) Sensor Diaries: Stumbling upon a Hg(II) Sensor

March 26, 2018 at 4.00 pm in AG-69

Title :

Seminal Electrode Materials for Battery and Supercapacitor Applications