TIFR
Department of Chemical Sciences
School of Natural Sciences

Calender

April 21, 2016 at 2.30 pm in AG-80

Title :

Novel Protein Targets of Multi Drug Resistant Acinetobacter baumannii

Abstract :

In the current scenario, widespread multidrug resistivity in ESKAPE pathogens demands identification of novel drug targets to keep their infections at bay. For this purpose, we have identified histone acetyltransferase Hpa2 and DNA-repair enzyme TAG of A. baumannii. Correct sequence alignment and construction of 3D monomeric and dimeric models of proteins having optimal structural parameters is a troublesome task. To overcome these problems, we have designed an easy and optimized protocol for homology modeling. Improvement in the structural features of protein is an onerous process and generally achieved by paying time and computational cost. Herein, it is achieved by reconciliation of FoldX commands which takes less time in execution. Evaluations performed to validate structural parameters and stability of models attests to its quality.

Hpa2 and TAG protein genes were cloned and heterologously expressed in bacterial expression system. The expressed protein was purified up to 98% homogeneity by a two-step purification protocol involving affinity purification followed by the size exclusion chromatography step. The biophysical studies (CD, Fluorescence and ITC) were carried out to characterize the structural and substrate/inhibitors binding parameters.The oligomeric state of enzymes determined in presence of various substrates as well as in extreme physiological conditions using analytical size exclusion, native PAGE and glutaraldehyde crosslinking assay. The enzyme activity is checked using simplified HPLC based biochemical assay. The Hpa2 and TAG proteins were put onto crystallization trials using commercial Hampton screens. The outcomes of these studies will be presented.  

April 18, 2016 at 4.00 pm in AG-69

Title :

Design of CO2 Sorbents Using Functionalized Fibrous Nanosilica (KCC-1: Insights into the Effect of the Silica Morphology (KCC-1 vs. MCM-41)

April 11, 2016 at 4.00 pm in AG-69

Title :

TiO2 coated fibrous nanosilica (KCC-1) for photocatalysis: Particle formation and size quantization

April 4, 2016 at 4.00 pm in AG-69

Title :

Visible Light Triggered Organic Photochemistry inside Water-soluble Nanocages

March 28, 2016 at 4.00 pm in AG-69

Title :

Designer ligands for Mn2+  selective chelation and detection

February 29, 2016 at 4.00 pm in AG-69

Title :

Computational Studies of Optical Charge Transfer Transitions in Non-aromatic Amino Acids and Metal-ligand Complex

February 26, 2016 at 2.30 pm in AG-80

Title :

Directed Evolution of Cytochrome P450 : An Approach to Engineer Thermally Stable Enzyme

February 25, 2016 at 2.30 pm in AG-80

Title :

Elephant, Blind Man, Molecule - Surface Scattering and Surface Chemistry

Abstract :

Understanding the mechanism of energy transfer from a molecule to a metal surface is essential for  building an atomic/molecular level description of surface chemistry. In this talk I will describe some general ideas regarding how a molecule exchanges translational, rotational and vibrational energy when it interacts with a metal surface. I will discuss this in the context of some of our recent work based on quantum state resolved inelastic scattering experiments of diatomic molecules such as: CO, NO and HCl scattering from Au(111) surface.

Further, I will also talk about the process of dissociation of a molecule on a metal surface using  some of our recent work on the HCl/Au(111) system as an example. Our study of this process points towards serious limitations in the the currently available state of the art theoretical methods.  These methods, based on 6-D quantum dynamical simulations using density functional theory based potential energy surface, relying on the Born-Oppenheimer and the rigid surface approximation which have worked well in describing previously well studied dissociation process such as H2 on Cu(111) and N2 on Ru(0001), severely overestimate the dissociation probability when compared to our experiments.

February 22, 2016 at 2.30 pm in AG-66

Title :

Temperature Dependent Protein Malleability (stiffness) Probed by Force and Fluorescence

February 16, 2016 at 2.30 pm in AG-80

Title :

Probing Supra-tc Conformational Exchange in proteins: Insight into Molecular Recognition

Abstract :


Internal motions with diverse timescale (ps–ms) play a crucial role to govern protein function. Molecular recognition events are strongly influenced by motions between the globular rotational correlation time (τc ~ 4 ns) and 40 µs1, known as supra-τc  window.2 This previously hidden timescale window came into evidence from RDC-enhanced structural ensembles of Ubiquitin.2 I will present how we have extended the kinetic limit of detection to 2.5 µs by using high power spin-lock in Rrelaxation dispersion (RD) experiments, which enabled us to detect the supra-τc  motion directly and precisely. These experiments showed that side chains of both ubiquitin and the third immunoglobulin binding domain of protein G (gb3) move on the µs timescale through redistribution of the populations of their side-chain rotamers, which interconvert on the ps to ns timescale, making it likely that this “population shuffling” process is a general mechanism.3

 

The high spin-lock power R RD experiments also facilitated the detection of supra-τc motion for the first time in the backbone of GB3 protein, which is routinely being studied by NMR spectroscopists for several years. Backbone dynamics at various temperatures between 262 K and 275 K, in super-cooled conditions, revealed the existence of a global motion in the first β-turn (G9–K13) region of GB3. Lower supra-τc order parameters and enhanced fluctuations in the RDC ensemble also indicate the plasticity of the first β-turn region to one-digit microsecond timescale motion.

 

Interestingly, the same region of the protein takes part in binding during antibody recognition. Energy landscape, obtained via Eyring relationship between the exchange rate and temperature, indicates that the conformational exchange in GB3 involves multiple conformers within ground state.

 

1.  Michielssens, S.; Peters, J. H.; Ban, D.; Pratihar, S.; Seeliger, D.; Sharma, M.; Giller, K.; Sabo, T. M.;

      Becker, S.; Lee, D.; Griesinger, C.; de Groot, B. L., A designed conformational shift to control protein

     binding specificity. Angewandte Chemie 2014, 53 (39), 10367-71.

2.  Lange, O. F.; Lakomek, N. A.; Fares, C.; Schroder, G. F.; Walter, K. F.; Becker, S.; Meiler,

     J.;  Grubmuller, H.; Griesinger, C.; de Groot, B. L., Recognition dynamics up to microseconds

     revealed from an RDC-derived ubiquitin ensemble in solution. Science 2008, 320 (5882), 1471-5.

3.  Smith, C. A.; Ban, D.; Pratihar, S.; Giller, K.; Schwiegk, C.; de Groot, B. L.; Becker, S.; Griesinger, C.;

     Lee, D., Population shuffling of protein conformations. Angewandte Chemie 2015, 54 (1), 207-10.

February 15, 2016 at 4.00 pm in AG-69

Title :

Investigation of Neutral and Cationic States of the N-H...X Hydrogen Bond

February 8, 2016 at 4.00 pm in AG-69

Title :

Synthesis and Application of KCC-1 Supported Ultra-Small Metal Nanocatalysts

January 21, 2016 at 2.30 pm in AG-80

Title :

Regulation of all-trans-lycopene in Photosynthetic Organisms: Role of Light and Redox Equivalents

January 18, 2016 at 4.00 pm in AG-69

Title :

Optical Sensors for Detecting Metal Ions and PH Changes in vivo

January 15, 2016 at 11.00 a.m. in AG-80

Title :

Nanostructured Silica-Titania Hybrid Material using Fibrous Nano-Silica (KCC-1) as Hard Template for Photocatalysis