TIFR
Department of Chemical Sciences
School of Natural Sciences

Calender

November 2, 2015 at 4.00 pm in AG-69

Title :

EPR and the Binding of Molecules to Cytochrome P450 Enzymes

Abstract :

The cytochromes P450 are a large enzymes superfamily found in every branch of life. Some isoforms help synthesize essential compounds and  are attractive targets for antibiotics. Other isoforms metabolize many pharmaceutical drugs and are one source of drug interactions. Many drugs directly bind heme in the active site but our pulsed EPR studies show a new binding mode with a water as a bridge between heme and drug, sometimes retaining enzymatic activity

October 28, 2015 at 2.30 pm in AG-80

Title :

Seeing enzymes in action

Single-molecule studies of electron-transfer  between copper centers of small laccase (SLAC) from S. coelicolor

Abstract :

Single molecule enzymology provides an unprecedented level of detail about aspects of enzyme mechanisms which have been difficult to probe in bulk. One such aspect is intramolecular electron transfer (ET) which is a recurring theme in the research on oxidoreductases. Recently, we introduced a technique to study ET in enzymes at single molecule level by means of confocal fluorescence microscopy (PNAS. 2008, 105, 3250).

 

I will present recent results on an enzyme, small laccase (SLAC), from S. coelicolor which converts O2 to H2O with concomitant oxidation of organic substrate(s). SLAC is unique, among commonly studied multicopper oxidases (MCO), in its structure (being a homo-trimer of two-domain monomers) and function where it employs a so-called type 1 (T1) Cu site, a trinuclear Cu centre (TNC) and a tyrosine residue (Y108) to catalyze this process which has a high activation barrier. I have measured, for the first time, intramolecular ET rates between the T1 and TNC of SLAC during turnover, one molecule at a time. The distribution across many molecules shows an average ET rate ~450 s-1 independent of substrate concentration, consistent with the proposed enzyme mechanism and with the results of transient kinetics experiments. The activation energy for ET amounts to 350 meV and varies from molecule to molecule with a spread of ±25 meV. Experiments are underway to measure other microscopic rate constants in the enzymatic cycle which have never been measured in bulk. The method is suitable to study ET in a wide range of redox active enzymes in-vitro as well as in-vivo.

October 27, 2015 at 2.30 pm in AG-80

Title :

Cells’ Armour to Prevent Oxidative Stress

How redox non-innocent residues influence enzyme catalysis and protect cells from oxidative damage?

Abstract :

For a long time, amino acid residues have been thought to provide backbone which holds the protein active site in place and directs substrates/products in specific orientations to catalyze chemical reactions. However, ample evidence has appeared in recent literature which signifies the role of redox-active amino acid residues like tyrosine or tryptophan in enzyme catalysis (Chem. Rev. 1998, 98, 705). Such new information has greatly improved our understanding of reaction rates and enzyme catalysis in modern biochemistry.

 

I will present recent results on two different classes of enzymes: heme containing Rice-α-oxygenase (RαO) from Oryza sativa and Cu-containing small laccase (SLAC) from Streptomyces coelicolor which form tyrosyl radicals during turnover. RαO catalyzes the α-oxidation of long chain fatty acids whereas laccases catalyzes the oxidation of phenols, aromatic amines, etc. I have made use of a variety of spectroscopic methods and enzyme kinetics to study the mechanism of operation of these two enzymes. For RαO, I have demonstrated reversible Habstraction of the substrate by a Y379that is formed during enzyme turnover. A very large, weekly temperature dependent kinetic isotope effect (~50) has been observed which is consistent with nuclear tunneling. For SLAC, I have shown that Y108 residue, which resides close to the trinuclear Cu cluster, gets oxidized when there is a shortage of reducing equivalents in the milieu. It is proposed that such reversible oxidation of key protein residues is (one of) the defense mechanisms of cells to prevent oxidative damage of critical machinery by the reactive oxygen species generated during O2 metabolism by the enzymes.

October 26, 2015 at 4.00 pm in AG-69

Title :

Molecular Probes and Templates for DNA Structures

Abstract :

DNA exists in variety of structural forms supported by canonical (A, B and Z-DNA) and non-canonical [H-DNA, G-quadruplex, i-motif, A-motif etc] hydrogen bonding interactions. Small molecules play key role in the study of DNA structures, biological significance, and to treat diseases related to their structure and function. On the other hand, the unique molecular recognition, persistence length and size of DNA inspire researchers to create novel molecular architectures for numerous applications. In this context, we have been developing mutually templated novel small molecule-ss DNA architectures using canonical and non-canonical hydrogen bonding interactions of nucleobases. In this talk, I shall present our recent results on fluorescence probes and nucleobase conjugates to study canonical and non-canonical hydrogen bonded DNA structures as well as to create hybrid DNA ensembles for applications ranging from biology to materials science.

 

References

 

1.    J. Choi and T. Majima, Chem. Soc. Rev. 2011, 40, 5893; A. Rich, D. R. Davies, F. H. C. Crick and J. D. Watson, J. Mol. Biol., 1961, 3, 71.

2.    N. Narayanaswamy, M. Kumar, R. Sharma, P. K. Samanta, S. K. Pati, S. K. Dhar, T. K. Kundu and T. Govindaraju, Sci. Rep. 2014, 4, 6476.

3.    N. Narayanaswamy, S. Das, P. K. Samanta, K. Banu, S. K. Dhar, S. K. Pati and T. Govindaraju, Nucleic Acids Res. (2015)DOI: 10.1093/nar/gkv875.

4.    N. Narayanaswamy, M. Unnikrishnan, M. Gupta and T. Govinadaraju. Bioorg. Med. Chem. Lett. 2015, 25, 2395.

5.    M. B. Avinash and T. Govindaraju, Nanoscale2014,6, 13348.

6.    N. Narayanaswamy, G. Suresh, U. D. Priyakumar, and T. Govindaraju, Chem. Comm. 2015, 51, 5493-5496.

 

October 12, 2015 at 4.00 pm in AG-69

Title :

Molecular Tools for the Manipulation of Size, Surface Chemistry and Assemblies of Metal Nanoparticles

Abstract :

Nanoscale particles have been envisioned to be the building blocks of a wide variety of future technologies including catalysis, electronic, optical and information technologies.As the nanoparticles have enhanced surface activity a layer of organic molecules are often used as passivating or capping agents. The surface functioanlization assumes significance not just for their stability in diverse solvent media but defines the way nanoparticles interact either with themselves or with the environment/biological systems. For example, water dispersibility is an essential criterion to realize bio-applications of nanoparticles.On the other hand, dispersions in organic media can be utilized to obtain interesting assemblies. In this connection, we have been working on a procedure called “digestive ripening” process in which a colloidal metal suspension in a solvent is refluxed at or above the solvent boiling temperature in the presence of the surface active agent like thiols resulting in the conversion of a highly polydisperse colloid into a monodispersed one (s< 5%). It is hypothesized that the thiols bind and remove reactive surface atoms/clusters from big nanoparticles and redeposit them on smaller nanoparticles.  In this way, large particles become smaller, while small particles become larger and eventually, an equilibrium size is obtained that is specific to each of the digestive ripening agent used. While the original work on digestive ripening has been largely carried out with gold nanocrystals, it has recently been extended to several other nanoparticle systems. Once again, the mechanism of this process is not understood, which is extremely important to generate nanocrystals with controlled and desired size distributions. In this presentation we will review the state of the art in digestive ripening and some of our recent experimental results that we hope will help in developing a mechanistic model for digestive ripening.

 

References:

J. Seth, C. N. Kona, S. S. Das and B. L. V. Prasad, Nanoscale, 2015, 7, 872–876.

P. Sahu and B. L. V. Prasad, Langmuir, Langmuir, 2014, 30, 10143−10150.

P. Sahu and B. L. V. Prasad, Col. Surf A., 2014, 447, 142-147

P. Sahu and B. L. V. Prasad, Nanoscale, 2013, 5, 1768 – 1771

P. Sahu and B. L. V. Prasad, Chem. Phys. Lett. 2012 525–526, 101–104.

D. S. Sidhaye and B. L. V. Prasad, New J. Chem. 2011, 35, 755–763

 

October 5, 2015 at 4.00 pm in AG-69

Title :

Nano-bioconjugation of Mutant Cytochrome P450cam (CYP101) for Biocatalysis

September 10, 2015 at 2.30 pm in AG-66

Title :

Design and Construction of Protein Molecules with Novel Properties

Abstract :

One of the most important challenges in chemical biology is to understand the molecular basis of protein function. Developing new methodologies using chemistry and the ability to apply those methodologies to proteins plays a crucial role in addressing this challenge. I propose to direct my future research program towards applying chemistry to design and engineer novel protein molecules, and to systematically develop a new class of therapeutics with controlled biochemical properties. Part of my research will be focused on the design and total chemical synthesis of medicinally relevant protein molecules with complex polypeptide backbone topologies that are rare or do not occur in natural proteins. I will develop a novel technology, using virtual structure-based screening of peptide fragment libraries from protein data bank, to identify small protein molecules of opposite handedness that will be used as candidate therapeutics. A significant portion of my research will be dedicated to develop and apply chemistry tools to enhance the conformational rigidity, introduced by the incorporation of fixed elements of secondary structures that will improve the stability and receptorbinding affinity of the small protein drug candidates. I will also explore and extend racemic and quasi-racemic crystallography to unravel complex biological questions. All these research projects will be pursued with the goal of addressing a wide range of questions having implications in fundamental as well as in
applied research.

September 9, 2015 at 2.30 pm in AG-66

Title :

A Mirror Image Protein Antagonist of VEGF-A: Total Chemical Synthesis and Racemic Crystallography of A Heterochiral Protein Complex

Abstract :

Using a unique combination of total chemical protein synthesis and mirror image phage display, we have systematically developed a D-protein antagonist of VEGF-A function. The bottleneck in mirror-image phage display is the preparation of the D-protein form of the target molecule, which can only be achieved by chemical synthesis. We prepared the mirror-image form of VEGF-A, i.e. D-VEGF-A, from three unprotected synthetic peptide segments stitched together by one-pot native chemical ligations. Phage displayed libraries of a novel L-protein scaffold were then screened against the D-VEGF-A to identify high affinity binders. The mirror-image form of the selected L-protein binder, i.e. the corresponding D-protein binder, was then chemically synthesized and was shown to specifically bind to native VEGF165 and to inhibit receptor binding. As expected, the D-protein antagonist was found to be non-immunogenic and had a longer half-life in vivo in mice. The binding mode of the D-protein antagonist was determined by high-resolution racemic X-ray crystallography of the {VEGF–A plus D-protein antagonist} heterochiral protein complex. The detailed structural information obtained from this crystal structure will enable the development of improved D-protein antagonists of VEGF-A.

September 7, 2015 at 4.00 pm in AG-69

Title :

Ultrafast 2D and 3D electronic spectroscopy and its applications to the study of Photosynthetic Light Harvesting Complexes

Abstract :

Recently, there has been much interest in the application of ultrafast multi-dimensional electronic spectroscopy in studying various chemical, physical and biological systems. We will review the basic principles of multi-dimensional electronic spectroscopy.  We report on our development and applications of ultrafast coherent 3rd order two-dimensional (2D) and 5ththree-dimensional (3D) spectroscopiesbased on a pulse shaper assisted pump-probe setup [1,2].In 5th order 3D optical spectroscopy, we obtain purely absorptive 3D spectra using five ultrashort optical pulses. For the first time, we also directly observe multistep excitation energy transfer (EET) processes in LHCII using the newly developed ultrafast fifth-order three-dimensional electronic spectroscopy (3DES) [3]. Ultrafast 3rd order two-dimensional electronic spectroscopy (2DES) is an important tool to study EET processes in photosynthetic complexes. However, the multistep EET processes can only be indirectly inferred by correlating different cross peaks from a series of 2DES spectra. Here we observe cross peaks in room temperature 3DES spectra of LHCII that directly indicate energy transfer from excitons in the chlorophyll b (Chl b) manifold to the low-energy level chlorophyll a (Chl a) via mid-level Chla energy states. This new spectroscopic technique will allow scientists to move a step towards mapping the complete complex EET processes in photosynthetic systems.

 

References :

1.    1.  Z. Zhang, K.L. Wells, and H.-S. Tan. "Purely absorptive fifth-order three-dimensional electronic spectroscopy" Opt. Lett. 37, 5058-5060 (2012).

2.      2.  K.L. Wells, P.H. Lambrev, Z. Zhang, G. Garab and H.-S. Tan. "Pathways of energy transfer in LHCII revealed by room-temperature 2D electronic spectroscopy" Phys. Chem. Chem. Phys. 16, 11640-11646 (2014).

3.    3.   Z. Zhang, P.H. Lambrev, K.L. Wells, G. Garab, H.-S. Tan. "Direct observation of multistep energy transfer in LHCII with fifth-order 3D electronic spectroscopy" Nat. Comm. 6, 7194 (2015).

 

August 31, 2015 at 4.00 pm in AG-69

Title :

Rational Design of Functional Materials: A Chemist's Approach

Abstract :

 

Functional materials have assumed prominent position in several high tech areas. Such materials are not classified on the basis of their origin, nature of bonding or processing techniques but are classified on the basis of functions which they can perform.  The synthesis of such materials has been a challenge and also opportunity to chemists. New functional materials can be designed by interplay of synthesis and crystallographic structure. Other approaches for design of these materials are defects engineering and concepts of hybrids. Unconventional synthetic routes play an important role in this direction as many of these new materials are metastable and hence it is not possible to prepare them by conventional solid state synthesis.  We have prepared [1-18] a number of new functional materials guided by crystallographic approach coupled with novel synthesis protocols. Some typical materials which will be discussed in this talk are La1-xCexCrO3 (materials with tunable band gap and magnetic properties), CeScO3 (with unusual reversible conversion to fluorite lattice), Gd1-xYxInO3, GdSc1-xInxO3, YIn1-xFexO3 (tunable dielectrics) and several lead free relaxor materials. Perovskite and fluorite-type materials with trivalent Ce3+ were successfully prepared from suitable precursor powders by a controlled heating under low pO2. Several interesting pyrochlore based oxygen storage materials, viz. Ce2Zr2O7+x (x = 0.0 to 1.0), Gd2-xCexZr2O7 andGd2-xCexZr2-xAlxO7 (x = 0.0 to 2.0) have been prepared, which have shown interesting redox catalysis. The simple concepts like rA/rB ratio of A2B2O7 pyrochlores could be used to tailor the functional properties. The major focus of this talk will be on the role of synthesis, novel properties exhibited by these functional materials, and their crystallographic correlation.

 

 

 

Our recent publications in the field functional materials

 

[1]  Chem. Mater. 21 (2009) 125

[2]  J. Phys. Chem. C 113 (2009) 12663

[3]  Inorg. Chem. 48 (2009) 11691

 

[4]  Inorg. Chem. 49 (2010) 10415

 

[5]  Inorg. Chem 49 (2010) 1152

 

[6]  Chem.- A Eur. J.17 (2011) 12310

 

[7]  Chem. Mater. 24 (2012) 2186

 

[8]  Analysts 137 (2012) 760

 

 [9]   Nano Letters 12 (2012) 3025

 

 [10]      J. Phys. Chem C 117 (2013) 10929

 

[11]  J. Phys. Chem. C  117 (2013) 2382

 

[12]  Inorg. Chem. 52 (2013) 7873

 

[13]  Inorg. Chem. 52  (2013) 13179

 

[14]  J. Mater. Chem. C, 1 (2013) 3710

 

[15]  J. Phys. Chem. C 118 (2014) 20819

 

[16]  Inorg. Chem. 53 (2014) 10101

 

[17]  Dalton Transaction 44 (2015) 10628

 

August 25. 2015 at 2.30 pm in AG-69

Title :

Teaching Sponges New Tricks: Redox Reactivity and Charge Transport in Microporous Metal-Organic Frameworks

Abstract :

Traditional applications of metal-organic frameworks (MOFs) are focused on gas storage and separation, which take advantage of the inherent porosity and high surface area of these materials. The MOFs’ use in technologies that require charge transport have lagged behind, however, because MOFs are poor conductors of electricity. We show that design principles honed from decades of previous research in molecular conductors can be employed to produce MOFs with remarkable charge mobility and conductivity values that rival or surpass those of common organic semiconductors and even graphite. We expect that such high surface area, ordered, and crystalline conductors will be used for a variety of applications in thermoelectrics, energy storage, electrocatalysis, electrochromics, or new types of photovoltaics. Another virtually untapped area of MOF chemistry is related to their potential to mediate redox reactivity through their metal nodes. We show that MOFs can be thought of as unique macromolecular ligands that give rise to unusual molecular clusters where small molecules can react in a matrix-like environment, akin to the metal binding pockets of metalloproteins. By employing a mild, highly modular synthetic method and a suite of spectroscopic techniques, we show that redox reactivity at MOF nodes can lead to the isolation and characterization of highly unstable intermediates relevant to biological and industrial catalysis, and to unusual reactivity patterns for small molecules.