CSIR - National Chemical Laboratory
CSIR - National Chemical Laboratory
Jha S.K.,University of California at Berkeley |
Marqusee S.,University of California at Berkeley |
Marqusee S.,CSIR - National Chemical Laboratory
Proceedings of the National Academy of Sciences of the United States of America | Year: 2014
Dry molten globular (DMG) intermediates, an expanded form of the native protein with a dry core, have been observed during denaturant-induced unfolding of many proteins. These observations are counterintuitive because traditional models of chemical denaturation rely on changes in solvent-accessible surface area, and there is no notable change in solvent-accessible surface area during the formation of the DMG. Here we show, using multisite fluorescence resonance energy transfer, far-UV CD, and kinetic thiol-labeling experiments, that the guanidinium chloride (GdmCl)-induced unfolding of RNase H also begins with the formation of the DMG. Population of the DMG occurs within the 5-ms dead time of our measurements. We observe that the size and/or population of the DMG is linearly dependent on [GdmCl], although not as strongly as the second and major step of unfolding, which is accompanied by core solvation and global unfolding. This rapid GdmCl-dependent population of the DMG indicates that GdmCl can interact with the protein before disrupting the hydrophobic core. These results imply that the effect of chemical denaturants cannot be interpreted solely as a disruption of the hydrophobic effect and strongly support recent computational studies, which hypothesize that chemical denaturants first interact directly with the protein surface before completely unfolding the protein in the second step (direct interaction mechanism).
Ogale S.B.,CSIR - National Chemical Laboratory |
Ogale S.B.,Indian Institute of Science
Advanced Materials | Year: 2010
Over the past decade intensive research efforts have been carried out by researchers around the globe on exploring the effects of dilute doping of magnetic impurities on the physical properties of functional non-magnetic metal oxides such as TiO 2 and ZnO. This effort is aimed at inducing spin functionality (magnetism, spin polarization) and thereby novel magnetotransport and magneto-optic effects in such oxides. After an early excitement and in spite of some very promising results reported in the literature, this field of diluted magnetic semiconducting oxides (DMSO) has continued to be dogged by concerns regarding uniformity of dopant incorporation, the possibilities of secondary ferromagnetic phases, and contamination issues. The rather sensitive dependence of magnetism of the DMSO systems on growth methods and conditions has led to interesting questions regarding the specific role played by defects in the attendant phenomena. Indeed, it has also led to the rapid re-emergence of the field of defect ferromagnetism. Many theoretical studies have contributed to the analysis of diverse experimental observations in this field and in some cases to the predictions of new systems and scenarios. In this review an attempt is made to capture the scope and spirit of this effort highlighting the successes, concerns, and questions. © 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Kulkarni A.A.,CSIR - National Chemical Laboratory
Beilstein Journal of Organic Chemistry | Year: 2014
This review highlights the state of the art in the field of continuous flow nitration with miniaturized devices. Although nitration has been one of the oldest and most important unit reactions, the advent of miniaturized devices has paved the way for new opportunities to reconsider the conventional approach for exothermic and selectivity sensitive nitration reactions. Four different approaches to flow nitration with microreactors are presented herein and discussed in view of their advantages, limitations and applicability of the information towards scale-up. Selected recent patents that disclose scale-up methodologies for continuous flow nitration are also briefly reviewed. © 2014 Kulkarni; licensee Beilstein-Institut. License and terms: see end of document.
Narlikar L.,CSIR - National Chemical Laboratory
Nucleic Acids Research | Year: 2013
High-throughput chromatin immunoprecipitation has become the method of choice for identifying genomic regions bound by a protein. Such regions are then investigated for overrepresented sequence motifs, the assumption being that they must correspond to the binding specificity of the profiled protein. However this approach often fails: many bound regions do not contain the 'expected' motif. This is because binding DNA directly at its recognition site is not the only way the protein can cause the region to immunoprecipitate. Its binding specificity can change through association with different co-factors, it can bind DNA indirectly, through intermediaries, or even enforce its function through long-range chromosomal interactions. Conventional motif discovery methods, though largely capable of identifying overrepresented motifs from bound regions, lack the ability to characterize such diverse modes of protein-DNA binding and binding specificities. We present a novel Bayesian method that identifies distinct protein-DNA binding mechanisms without relying on any motif database. The method successfully identifies co-factors of proteins that do not bind DNA directly, such as mediator and p300. It also predicts literature-supported enhancer-promoter interactions. Even for well-studied direct-binding proteins, this method provides compelling evidence for previously uncharacterized dependencies within positions of binding sites, long-range chromosomal interactions and dimerization. © 2012 The Author(s). Published by Oxford University Press.
Sen S.S.,CSIR - National Chemical Laboratory
Angewandte Chemie - International Edition | Year: 2014
Mission accomplished: More than 100 years after first attempts at isolating a stable silanone, this task has finally been completed with the isolation of a metallosilanone complex (see Scheme). The elusive bare Si-O bond was made accessible by utilizing the coordination sphere of an electron-rich chromium fragment in combination with a sterically demanding saturated N-heterocyclic carbene (NHC) to protect the reactive site. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Bhojgude S.S.,CSIR - National Chemical Laboratory |
Biju A.T.,CSIR - National Chemical Laboratory
Angewandte Chemie - International Edition | Year: 2012
Let's couple together! The multicomponent reactions involving arynes offer direct access to unusual heterocyclic scaffolds and 1,2-disubstituted arenes. This transition-metal-free, one-pot construction of molecular complexity is likely to play a pivotal role in various carbon-carbon and carbon-heteroatom bond-forming reactions. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Menon V.,CSIR - National Chemical Laboratory |
Rao M.,CSIR - National Chemical Laboratory
Progress in Energy and Combustion Science | Year: 2012
Bioconversion of renewable lignocellulosic biomass to biofuel and value added products are globally gaining significant prominence. Market forces demonstrate a drive towards products benign to natural environment increasing the importance of renewable materials. The development of second generation bioethanol from lignocellulosic biomass serves many advantages from both energy and environmental point of views. Biomass an inexpensive feedstock considered sustainable and renewable, is an option with the potential to replace a wide diversity of fossil based products within the energy sector; heat, power, fuels, materials and chemicals. Lignocellulose is a major structural component of woody and non-woody plants and consists of cellulose, hemicellulose and lignin. The effective utilization of all the three components would play a significant role in the economic viability of cellulosic ethanol. Biomass conversion process involves five major steps, choice of suitable biomass, effective pretreatment, production of saccharolytic enzymes-cellulases and hemicellulases, fermentation of hexoses and pentoses and downstream processing. Within the context of production of fuels from biomass, pretreatment has come to denote processes by which cellulosic biomass is made amenable to the action of hydrolytic enzymes. The limited effectiveness of current enzymatic process on lignocellulose is thought to be due to the relative difficulties in pretreating the feedstocks. The present review is a comprehensive state of the art describing the advancement in recent pretreaments, metabolic engineering approaches with special emphasis on the latest developments in consolidated biomass processing, current global scenario of bioethanol pilot plants and biorefinery concept for the production of biofuels and bioproducts. © 2012 Elsevier Ltd. All rights reserved.
Bhunia A.,CSIR - National Chemical Laboratory |
Yetra S.R.,CSIR - National Chemical Laboratory |
Biju A.T.,CSIR - National Chemical Laboratory
Chemical Society Reviews | Year: 2012
This tutorial review is aimed at highlighting recent developments in transition-metal-free carbon-carbon and carbon-heteroatom bond-forming reactions utilizing a versatile class of reactive intermediates, viz., arynes, which hold the potential for numerous applications in organic synthesis. Key to the success of the resurgence of interest in the rich chemistry of arynes is primarily the mild condition for their generation by the fluoride-induced 1,2-elimination of 2-(trimethylsilyl)aryl triflates. Consequently, arynes have been employed for the construction of multisubstituted arenes with structural diversity and complexity. The versatile transition-metal-free applications of arynes include cycloaddition reactions, insertion reactions and multicomponent reactions. In addition, arynes have found applications in natural product synthesis. Herein, we present a concise account of the major developments that occurred in this field during the past eight years. © 2012 The Royal Society of Chemistry.
Kumar P.,CSIR - National Chemical Laboratory |
Dwivedi N.,CSIR - National Chemical Laboratory
Accounts of Chemical Research | Year: 2013
The search for new and efficient ways to synthesize optically pure compounds is an active area of research in organic synthesis. Asymmetric catalysis provides a practical, cost-effective, and efficient method to create a variety of complex natural products containing multiple stereocenters. In recent years, chemists have become more interested in using small organic molecules to catalyze organic reactions. As a result, organocatalysis has emerged both as a promising strategy and as an alternative to catalysis with expensive proteins or toxic metals.One of the most successful and widely studied secondary amine-based organocatalysts is proline. This small molecule can catalyze numerous reactions such as the aldol, Mannich, Michael addition, Robinson annulation, Diels-Alder, α-functionalization, α-amination, and α-aminoxylation reactions. Catalytic and enantioselective α-oxygenation of carbonyl compounds is an important reaction to access a variety of useful building blocks for bioactive molecules. Proline catalyzed α-aminoxylation using nitrosobenzene as oxygen source, followed by in situ reduction, gives enantiomerically pure 1,2-diol. This molecule can then undergo a variety of organic reactions. In addition, proline organocatalysis provides access to an assortment of biologically active natural products including mevinoline (a cholesterol lowering drug), tetrahydrolipstatin (an antiobesity drug), R(+)-α-lipoic acid, and bovidic acid.In this Account, we present an iterative organocatalytic approach to synthesize both syn- and anti-1,3-polyols, both enantio- and stereoselectively. This method is primarily based on proline-catalyzed sequential α-aminoxylation and Horner-Wadsworth-Emmons (HWE) olefination of aldehyde to give a γ-hydroxy ester. In addition, we briefly illustrate the broad application of our recently developed strategy for 1,3-polyols, which serve as valuable, enantiopure building blocks for polyketides and other structurally diverse and complex natural products. Other research groups have also applied similar strategies to prepare such bioactive molecules as littoralisone, brasoside and (+)-cytotrienin A. Among the various synthetic approaches reported for 1,3-polyols, our organocatalytic iterative approach appears to be very promising and robust. This method combines the merit of organocatalytic reaction with an easy access to both enantiomerically pure forms of proline, mild reaction conditions, and tolerance to both air and moisture. In this Account, we present the latest applications of organocatalysis and how organic chemists can use this new tool for the total synthesis of complex natural products. © 2012 American Chemical Society.
Narlikar L.,CSIR - National Chemical Laboratory
Nucleic acids research | Year: 2014
An important question in biology is how different promoter-architectures contribute to the diversity in regulation of transcription initiation. A step forward has been the production of genome-wide maps of transcription start sites (TSSs) using high-throughput sequencing. However, the subsequent step of characterizing promoters and their functions is still largely done on the basis of previously established promoter-elements like the TATA-box in eukaryotes or the -10 box in bacteria. Unfortunately, a majority of promoters and their activities cannot be explained by these few elements. Traditional motif discovery methods that identify novel elements also fail here, because TSS neighborhoods are often highly heterogeneous containing no overrepresented motif. We present a new, organism-independent method that explicitly models this heterogeneity while unraveling different promoter-architectures. For example, in five bacteria, we detect the presence of a pyrimidine preceding the TSS under very specific circumstances. In tuberculosis, we show for the first time that the spacing between the bacterial 10-motif and TSS is utilized by the pathogen for dynamic gene-regulation. In eukaryotes, we identify several new elements that are important for development. Identified promoter-architectures show differential patterns of evolution, chromatin structure and TSS spread, suggesting distinct regulatory functions. This work highlights the importance of characterizing heterogeneity within high-throughput genomic data rather than analyzing average patterns of nucleotide composition. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.