Authors: 3. B. Buchmuller, J. Dröden, H. Singh, S. Palei, M. Drescher, R. Linser, D. SummererVol: 144 Pages: 2987?2993Journal: J. Am. Chem. Soc. Year: 2022 Posted: 12 Aug 2024
5-Methylcytosine (mC) and 5-hydroxymethylcytosine (hmC), the two main epigenetic modifications of mammalian DNA, exist in symmetric and asymmetric combinations in the two strands of CpG dyads. However, revealing such combinations in single DNA duplexes is a significant challenge. Here, we evolve methyl-CpG-binding domains (MBDs) derived from MeCP2 by bacterial cell surface display, resulting in the first affinity probes for hmC\/mC CpGs. One mutant has low nanomolar affinity for a single hmC\/mC CpG, discriminates against all 14 other modified CpG dyads, and rivals the selectivity of wild-type MeCP2. Structural studies indicate that this protein has a conserved scaffold and recognizes hmC and mC with two dedicated sets of residues. The mutant allows us to selectively address and enrich hmC\/mC-containing DNA fragments from genomic DNA backgrounds. We anticipate that this novel probe will be a versatile tool to unravel the function of hmC\/mC marks in diverse aspects of chromatin biology.<\/p>")">
Authors: T-C Lin, S. Palei, D. SummererVol: 17 Pages: 1844-1852Journal: ACS Chem. Bio. Year: 2022 Posted: 12 Aug 2024
Methyl-CpG binding domain (MBD) proteins and ten-eleven-translocation (TET) dioxygenases are the readers and erasers of 5-methylcytosine (5mC), the central epigenetic mark of mammalian DNA. We employ light-activatable human TET1 controlled by a genetically encoded photocaged serine to enable in vivo kinetic studies of their interplay at the common substrate methylated cytosine–guanine (mCpG). We identify the multidomain reader MBD1 to negatively regulate TET1-catalyzed 5mC oxidation kinetics via its mCpG-binding MBD domain. However, we also identify the third Cys-x-x-Cys (CXXC3) domain of MBD1 to promote oxidation kinetics by TET1, dependent on its ability to bind nonmethylated CpG, the final product of TET-mediated mCpG oxidation and active demethylation. In contrast, we do not observe differences in TET1 regulation for MBD1 variants with or without the transcriptional repressor domain. Our approach reveals a complex, domain-dependent interplay of these readers and erasers of 5mC with different domain-specific contributions of MBD1 to the overall kinetics of TET1-catalyzed global 5mC oxidation kinetics that contribute to a better understanding of dynamic methylome shaping.<\/p>")">
Authors: 1. S. Palei*, J. Weisner*, M. Vogt, R. Gontala, B. Buchmuller, C. Ehrt, T. Grabe, S. Kleinbölting, M. Müller, G. H. Clever, D. Rauh, D. SummererVol: 13 Pages: 1540–1548Journal: RSC Med. Chem. Year: 2022 Posted: 12 Aug 2024
Ten-eleven translocation dioxygenases (TETs) are the erasers of 5-methylcytosine (mC), the central epigenetic regulator of mammalian DNA. TETs convert mC to three oxidized derivatives with unique physicochemical properties and inherent regulatory potential, and it initializes active demethylation by the base excision repair pathway. Potent small molecule inhibitors would be useful tools to study TET functions by conditional control. To facilitate the discovery of such tools, we here report a high-throughput screening pipeline and its application to screen and validate 31.5k compounds for inhibition of TET2. Using a homogenous fluorescence assay, we discover a novel quinoline-based scaffold that we further validate with an orthogonal semi-high throughput MALDI-MS assay for direct monitoring of substrate turnover. Structure–activity relationship (SAR) studies involving >20 derivatives of this scaffold led to the identification of optimized inhibitors, and together with computational studies suggested a plausible model for its mode of action.<\/p>")">
Modulation of the Photophysics of Nucleotide-Functionalized Copper Nanoclusters Using Aqueous Binary Mixtures
Authors: Journal: The Journal of Physical Chemistry C Year: 2022 Posted: 07 Jul 2023
Deciphering Dual Modes of Parkinsonian Biomolecules Derived Fluorescent Nanoparticles: Protein Specificity and White Light Generation
Authors: Journal: The Journal of Physical Chemistry Letters Year: 2022 Posted: 07 Jul 2023
Cover ART @Inorganic Chemistry
Authors: Manisha Shaw , Dipanjan Samanta, Sharmita Bera, Madhusudan Kr Mahto, Md Abdus Salam Shaik, Suraj Konar, Imran Mondal, Dibakar Dhara, and Amita Pathak*Journal: Inorganic Chemistry Year: 2022 Posted: 04 May 2023
Authors: Manisha Shaw1, Dipanjan Samanta1, Md Abdus Salam Shaik, Angana Bhattacharya, Rajarshi Basu, Imran Mondal, Amita PathakVol: 61 Pages: 14568–14581Journal: Inorganic Chemistry Year: 2022 Posted: 11 Mar 2023
Copper-Catalyzed Protoboration of 1,3-Diynes as a Platform for Iterative Functionalization
Authors: Ghosh, S.; Chakrabortty, R.; Kumar, S.; Das, A.; Ganesh, V.*Journal: ACS Catal. 12, 11660-11666 Year: 2022 Posted: 01 Dec 2022
Fluorescent N, S co-doped Carbon Dots for Tartrazine Sensing and Mechanistic Perception of their Radical Scavenging Activity
Authors: Md Abdus SalamShaik, DipanjanSamanta, ManishaShaw, ImranMondal, RajarshiBasu, AmitaPathakJournal: Sensors and Actuators Reports Year: 2022 Posted: 05 Nov 2022
Palladium-Catalyzed Dual Catalytic Synthesis of Heterocycles
Authors: Tamal Ballav, Rajesh Chakrabortty, Aniruddha Das, Suman Ghosh, Dr. Venkataraman GaneshJournal: Eur. J. Org. Chem. 10.1002/ejoc.202200553 Year: 2022 Posted: 29 Oct 2022
Insights into the Multifunctional Applications of Strategical Co doped MoS2 Nanoflakes
Authors: Rosy Rahman , S. Chaudhuri, Dipanjan Samanta , A. Pathak and T. K. NathJournal: Materials Advances Year: 2022 Posted: 12 Oct 2022
The effects of metal cofactors on the reactivity of quercetin 2,4-dioxygenase: synthetic model studies with M(II)-complexes (M = Mn, Co, Ni, Cu, Zn) and assessment of the regulatory factors in catalytic efficacy
Authors: (21) Nirmalya Podder and Sukanta Mandal*Vol: 51 Pages: 17064–17080Journal: Dalton Trans., 51, 17064–17080 Year: 2022 Posted: 09 Oct 2022
One Order Enhancement of Charge Carrier Relaxation Rate by Tuning Structural and Optical Properties in Annealed Cobalt Doped MoS2 Nanosheets
Authors: Rosy Rahman, Manobina Karmakar, Dipanjan Samanta, Amita Pathak,* Prasanta Kumar Datta* and Tapan Kumar Nath*Journal: New Journal of Chemistry Year: 2022 Posted: 05 Sep 2022
Phosphate based New Organic Polymer Networks for Efficient Dye Sorption and Catalyst Loading for Chemo-selective Reactivity
Authors: Shabari Dutta, Suman Kalyan Samanta* and Santanu Bhattacharya*Journal: Chem. Commun., 2022, 58, 9405–9408 Year: 2022 Posted: 25 Aug 2022
Self-Assembling Behaviour of Perylene, Perylene Diimide, and Thionated Perylene Diimide Deciphered through Non-Covalent Interactions
Authors: S. Parida, S.K. Patra and S. MishraVol: (In Press) Pages: Journal: ChemPhysChem Year: 2022 Posted: 24 Aug 2022
Authors: Sourav Nandi, Anurup Mukhopadhyay, Pratyush Kiran Nandi, Nanigopal Bera, Ritwik Hazra, Jyotirmoy Chatterjee, and Nilmoni Sarkar*Journal: Langmuir Year: 2022 Posted: 30 Jun 2022
The incorrect metabolic breakdown of the nonaromatic amino acid methionine (Met) leads to the disorder called hypermethioninemia via an unknown mechanism. To understand the molecular level pathogenesis of this disorder, we prepared a DMPC lipid membrane, the mimicking setup of the cell membrane, and explored the effect of the millimolar level of Met on it. We found that Met forms toxic fibrillar aggregates that disrupt the rigidity of the membrane bilayer, and increases the dynamic response of water molecules surrounding the membrane as well as the heterogeneity of the membrane. Such aggregates strongly deform red blood cells. This opens the requirement to consider therapeutic antagonists either to resist or to inhibit the toxic amyloid aggregates against hypermethioninemia. Moreover, such disrupting effect on membrane bilayer and cytotoxicity along with deformation effect on RBC by the cross amyloids of Met and Phenylalanine (Phe) was found to be most virulent. This exclusive observation of the enhanced virulent effect of the cross amyloids is expected to be an informative asset to explain the coexistence of two amyloid disorders.<\/p>")">
Authors: S. Mandal, R. Samajdar, S. Parida, S. Mishra, A. BhattacharyyaJournal: ACS Appl. Mater. Interfaces Year: 2022 Posted: 10 Jun 2022
Redox mediation is an innovative strategy for ensuring efficient energy harvesting from metal–oxygen systems. This work presents a systematic exploratory analysis of first-row transition-metal phthalocyanines as solution-state redox mediators for lithium–oxygen batteries. Our findings, based on experiment and theory, convincingly demonstrate that d5 (Mn), d7 (Co), and d8 (Ni) configurations function better compared to d6 (Fe) and d9 (Cu) in redox mediation of the discharge step. The d10 configuration (Zn) and non-d analogues (Mg) do not show any redox mediation because of the inability of binding with oxygen. The solution-state discharge product, transition-metal bound Li2O2, undergoes dissociation and oxidation in the charging step of the battery, thus confirming a bifunctional redox mediation. Apart from the reaction pathways predicted based on thermodynamic considerations, density functional theory calculations also reveal interesting effects of electrochemical perturbation on the redox mediation mechanisms and the role of the transition-metal center.<\/p>")">
The impact of secondary coordination sphere engineering on water oxidation reactivity catalysed by molecular ruthenium complexes: a next-generation approach to develop advanced catalysts
Authors: (20) Ayyan Ghosh, Sreeja Dasgupta, Animesh Kundu and Sukanta Mandal*Vol: Pages: 10320–10337Journal: Dalton Trans.,51, 10320–10337 Year: 2022 Posted: 31 May 2022
Authors: S. Rahman, K. Rajak, S. Mishra, and A. K. DasVol: (In Press) Pages: Journal: J. Mol. Graph. Model. Year: 2022 Posted: 24 May 2022
Staphylococcus aureus causes a wide range of common diseases in both community-acquired and hospital-acquired environments. The treatment becomes challenging due to the emergence of multi-drug resistant strains such as Methicillin-Resistant Staphylococcus aureus (MRSA). This study aims to find some drugs that can be used in repurposing. Virtual screening has been performed against S. aureus FemX using 1,918 FDA-approved drugs, which provides the top 10 drugs with good binding affinity. These drugs are re-docked to understand their interaction patterns with FemX. Docking study shows a high score for three drugs, Lumacaftor, Dihydroergocornine and Olaparib, and they are selected for molecular dynamics and quantum mechanical analysis. Molecular dynamics calculation shows that drug-FemX forms a stable structure compared to apo-FemX. Besides, the free energy landscape reveals that drug-proteins complexes possess a single global minimum indicating their thermodynamic stability. MMGBSA calculations show that Lumacaftor, Dihydroergocornine and Olaparib have the binding free energy of −30.03, −19.22 and −16.54 kcal\/mol, respectively. The analysis of the wavefunctions from quantum chemical calculations reveals the presence of non-covalent interactions between drug and receptor, dominated by aromatic π-π interactions. The drug-receptor interaction energy estimated from quantum mechanical methods suggests an important role of dispersion interactions in stabilising the drug molecules in FemX. The hierarchy of computational methods of increasing accuracy employed in this work finds Lumacaftor to be the most potent inhibitor against FemX.<\/p>")">
Conjugation of RNA via 2’-OH acylation: Mechanisms determining nucleotide reactivity
Authors: B. Jash, E. T. KoolJournal: Chemical Communication 2022, 58, 3693-3696 Year: 2022 Posted: 01 Apr 2022
Spin-Vibronic Coupling in the Quantum Dynamics of a Fe(III) Trigonal Bipyramidal Complex
Authors: K. K. Dakua, K. Rajak, and S. MishraVol: 156 Pages: 134103Journal: J. Chem. Phys. (2022) Year: 2022 Posted: 29 Mar 2022
Modulation of Electrochemical and Spectroscopic Properties in Ru(II)-Terpyridyl End-capped Homobimetallic Organometallic Complexes by Varying pi-Conjugated Organic Spacers
Authors: A. Sil, S. S. Roy, V. K. Mishra, S. N. Islam, S. Mishra, and S. K. PatraVol: (In Press) Pages: Journal: Chemistry Select (2022) Year: 2022 Posted: 29 Mar 2022
Authors: H. Battula, S. Muduli, S. P. Bandi, S. Kapoor, S. Mishra, H. Aggarwal, V. Venuganti, S. JayantyVol: (In Press) Pages: Journal: J. Photochem. Photobiol. A Year: 2022 Posted: 29 Mar 2022
Transbilayer Coupling of Lipids in Cells Investigated by Imaging Fluorescence Correlation Spectroscopy
Authors: N. Bag, E. London, D. A. Holowka, B. A. BairdJournal: Journal of Physical Chemistry B (Accepted) Year: 2022 Posted: 04 Mar 2022
A Palmitoylation Code Controls PI4KIIIalpha Complex Formation and PI(4,5)P2 Homeostasis at the Plasma Membrane
Authors: A. Batrouni,* N. Bag,* H. Phan, B. Baird, J. BaskinJournal: Journal of Cell Science Year: 2022 Posted: 04 Mar 2022
Oxygenolysis of a series of copper(II)-flavonolate adducts varying the electronic factors on supporting ligands as a mimic of quercetin 2,4-dioxygenase-like activity
Authors: (19) Nirmalya Podder, Subhasis Dey, Anakuthil Anoop,* and Sukanta Mandal*Vol: 51 Pages: 4338 - 4353Journal: Dalton Trans., 51, 4338 - 4353 Year: 2022 Posted: 16 Feb 2022
Dangling Carboxylic Group That Participates in O-O Bond Formation Reaction to Promote Water Oxidation Catalyzed by a Ruthenium Complex: Experimental Evidence of an Oxide Relay Pathway
Authors: (18) Animesh Kundu, Suman K. Barman, and Sukanta Mandal*Vol: 61 Pages: 1426-1437Journal: Inorg. Chem. 61, 1426-1437 Year: 2022 Posted: 17 Dec 2021
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