Photoinduced Electron Transfer in DNA Repair: A Computational Study
UV radiation (200-400 nm) causes damage of DNA, mostly producing the cyclobutane
pyrimidine and (6-4)-pyrimidine-pyrimidone (PP) photodimers. (6-4) photolyase is a DNA repair enzyme that selectively repairs (6-4)PP photodimer, using visible light. This repairprocess is a complex photocycle comprising of several electron transfer (ET) steps possibly coupled to proton transfer, controlled by the protein. The key repair steps are the forward electron transfer (FET) and the back electron transfer (BET) which involve the FADH−chromophore and the (6-4)PP. Experimentally, the ET rates of these steps have been estimated, but the overall repair mechanism remains elusive.
We wish to predict the ET rates with in the photolyase repair site and evaluate the roles of various factors that may influence these ET rates. Towards this, we have set up a multiscale computational apparatus based on a combination of QM, hybrid QM/MM and MD methodologies. With this approach, we have computed the energies of the FADH− - (6-4) PP (Donor-Acceptor) complex in different electronic states, formally describing the electron transfer reaction. We then evaluate the effects of the protonation state of key residues, the solvent and DNA counterions on these states and also account for the effect of the protein dynamics. Using these complex energy estimates, we predict the FET and BET rates employing the semi classical Marcus formalism and compare them against the experimental observations.
Biophysics of RNA
Characterization of the Non-Covalent Interactions of Propofol Using Mass Resolved Spectroscopy
Propofol is probably the most widely used anaesthetic and became sadly famous several years ago as the cause of dead of the pop star Michael Jackson. The molecule exerts its action by docking on the GABAA receptors in the central nervous system. But why does it like to interact with the receptor, and how is its trip until it reaches the active site? Using a combination of laser spectroscopy and quantum mechanical calculations, under a reductionist approach, we will try to shed light on the forces that govern such odyssey.
Semiconductor Materials for Solar Hydrogen Production Using Water and Abundant Sulfur Compounds
As a clean non-fossil fuel, hydrogen generation by the combination of solar light and semiconductors have drawn great attention as ideal “green” processes for solving global energy and environmental issues. Herein, the recent results of our studies directed to developing semiconducting materials for solar hydrogen production via photodecomposition of water and hydrogen sulfide are presented. Efficient conversion of solar energy to hydrogen via water splitting on photoelectrochemical (PEC) cell is a promising approach. We have developed morphologically modified WO3, doped FeVO4as well as composite CdS/CdSe/ZnS quantum dots decorated titanium dioxide nanotube arrays as photoanode materials, which show significantly improved performances in applications for solar hydrogen generation. The enhancement of photoelectrochemical performances can be attributed to improved electrical conductivities, efficient separation of photoexcited charges and superior charge carrier transport properties of the developed materials. In this talk, hydrogen production from decomposition of H2S using CuAlGaO4as stable and efficient low band gap (1.87 eV) photocatalyst is also presented. Apart from water, H2S which is a toxic gas and produced in large quantities in petroleum refineries has all possibilities for being an alternative source of hydrogen production for both energy and environmental requirements.
n-pi* Interaction: Too Weak But Can Compete With Strong Hydrogen Bonding Interaction
The Role of CH and SH Groups as Hydrogen Bond Donors in Stabilizing Molecular Complexes
Detecting Reaction Intermediates in Solution and Guiding Cancer Surgery Using Mass Spectrometry
I wish to describe two recent developments in my laboratory using ambient ionization mass spectrometry, a mass spectrometric technique in which the sample of interest is in open air at room temperature. The first concerns detection and identification of solution-phase reaction intermediates, the second concerns mass spectrometric imaging.
Palladium complexes catalyze a variety of oxidation reactions, including the Wacker oxidation, the oxidation of alcohols, and oxidative C-C bond-forming reactions. Simple Pd(II) salts react sluggishly with oxygen, but in the presence of suitable ligands or solvents, Pd complexes are capable of aerobic oxidation reactions. A key step in these reactions is the oxidation of Pd(0) by O2 to regenerate a Pd(II) intermediate. We have employed a battery of mass spectroscopic techniques such as desorption electrospray ionization mass spectrometry (DESI-MS, millisecond reaction times), electrospray ionization mass spectrometry (ESI-MS, minutes reaction times), and nano-electrospray ionization mass spectrometry (nanospray-MS, minutes reaction times) to search for reaction intermediates formed during the aerobic oxidation of 1,2-diols. By monitoring active reactions with mass spectrometry operating at various timescales, we have directly detected and identified a number of novel intermediates generated in solution during the fast alcohol oxidation and slow aerobic re-oxidation of (neocuproine)Pd(0). These studies reveal the formation of a novel trinuclear palladium complex, [(neocuproinePd(II))3(m3-O)2]2+. The identification of this previously unreported species provides new insights on the mechanism of aerobic oxidation mediated by Pd complexes.
Surgical resection is the main curative option for gastrointestinal cancers. The extent of cancer resection is commonly assessed during surgery by pathologic evaluation of (frozen sections) of the tissue at the specimen margin(s). We compare this to an alternative procedure, desorption electrospray ionization mass spectrometric imaging (DESI-MSI), for 62 human cancerous and normal gastric tissue samples. In DESI-MSI, microdroplets strike the tissue sample, the resulting splash enters a mass spectrometer, and a statistical analysis, the Lasso method (multi-class logistic regression with L1 penalty), is applied to classify tissues based on the molecular information obtained directly from DESI-MSI. The results obtained suggest that DESI-MSI/Lasso may be valuable for routinely assessing margins in gastric cancer surgery.
Title : Understanding the Aggregation Properties of Amyloid Beta Through Solid State NMR and Designed Mutations
Zn+2 can alter the aggregation properties and toxicity of Amyloid beta (Aβ) by selectively precipitating out the soluble oligomers. What does it change? Using Solid State NMR on fibrils Aβ40 grown in the presence of Zn+2, we show that the turn region of the peptide is affected. We have found that the fibrils of Aβ40 grown in the presence of equal concentration of Zn+2 has a similar hairpin shape but they differs in the turn region. However what we actually need to look at are the biologically active metastable oligomers, (not the fibrils) and focus on the turn region. Using a technique recently developed in the lab for looking at metastable structures, we find that the oligomers are different only in the turn and the terminal regions. This suggests that the conformational change starts at the two hydrophobic arms of the peptide. We are now trying to selectively disturb the stereospecific interaction in the nucleation centre by selective alternation of some amino acids in to their "dextro" forms, which leaves chemical property of the peptide unchanged.
Title : to be announced
Title : Magic Angle Spinning NMR Studies of M218--60, VDAC, and bR
In the last few years magic angle spinning (MAS) NMR has emerged as an important approach to examine the structure and function of membrane proteins. One of the primary advantages is that it enables studies of structure and function in native or quasi-native lipid environments, thus circumventing the perturbing effect of detergents which are often required for solution NMR experiments and crystallography. In addition, it has become possible to enhance the sensitivity of these experiments using dynamic nuclear polarization (DNP) by factors of ~100, thus facilitating more detailed structural studies. In this presentation we discuss the applications of MAS and DNP to three membrane proteins: M2 from influenza-A, the voltage dependent anion channel (VDAC), and bacteriorhodopsin. Studies of M218-60 indicate that this construct, which is fully functional, assembles as a dimer of dimers, rather a tetramer as seen in solution NMR and crystallographic studies. In addition, the amino-admantanyl drugs bind in the pore rather than on the surface. The structure, determined by a variety of dipole recoupling experiments shows that the His and Trp responsible for the H+ conduction are tightly packed M218-60 and that the transfer is likely an intermolecular process. We study VDAC in 2D crystals of DMPC and show that the protein perturbs the lipid gel®liquid crystalline transition, but that the protein does not change conformation dramatically in traversing this transition. We also delineate the structure of the N-terminal tail and show that it is situated in contact with the face of the β-barrel. Finally, we study the structure of photocycle intermediates of bR with DNP enhanced spectra and obtain evidence that bR could be a inward directed OH- pump rather than an outward directed H+ pump.
Title : To be announced
Title : Phosphorylation of an uv Inducible Protein (UVI31+) of Chlamydomonas reinhardtii
Seminar by Mr. Palas Roy
Title: "Molecular Perspective to Photoinduced Processes in Organic Photovoltaics"
Title: Fibrils, membranes, crystals, sediments: solid-state NMR of large proteins
Solid-state NMR is an increasingly powerful tool to characterize challenging proteins. Notably, it can analyze an astonishing variety of states, as proteins inserted in membranes, crystals and simple sediments. Combined with other biophysical approaches, solid-state NMR thus gives unique insight into protein structure, and ultimately function. We will illustrate this with some recent examples from our laboratories, including the DnaB helicase from Helicobacter pilori, the BmrA ABC transporter, as well as the yeast prion fibrils Ure2p and Sup35p, for which we will show results related to sample preparation, sequential assignments and structural aspects.