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Search results for: D-DIMER
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Crystal structures of aminotransferases Aro8 and Aro9 from Candida albicans and structural insights into their properties
PublicationAminotransferases catalyze reversibly the transamination reaction by a ping-pong bi-bi mechanism with pyridoxal 5′-phosphate (PLP) as a cofactor. Various aminotransferases acting on a range of substrates have been reported. Aromatic transaminases are able to catalyze the transamination reaction with both aromatic and acidic substrates. Two aminotransferases from C. albicans, Aro8p and Aro9p, have been identified recently, exhibiting...
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Diphosphinoboranes as Intramolecular Frustrated Lewis Pairs: P–B–P Bond Systems for the Activation of Dihydrogen, Carbon Dioxide, and Phenyl Isocyanate
PublicationHerein, we present the first example of the activation of small molecules by P-B-P bond systems. The reactivity study involves reactions of two selected diphosphinoboranes, (tBu2P)2BPh (1’) and (Cy2P)2BNiPr2 (2), that differ in terms of their structural and electronic properties for the activation of dihydrogen, carbon dioxide, and phenyl isocyanate. Diphosphinoborane 1’ activates H2 under very mild conditions in the absence of...
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The structurally similar TRFH domain of TRF1 and TRF2 dimers shows distinct behaviour towards TIN2
PublicationThe telomere repeat binding-factor 1 and 2 (TRF1 and TRF2) proteins of the shelterin complex bind to duplex telomeric DNA as homodimers, and the homodimerization is mediated by their TRFH (TRF-homology) domains. We performed molecular dynamic (MD) simulations of the dimer forms of TRF1TRFH and TRF2TRFH in the presence/absence of the TIN2TBM (TIN2, TRF-interacting nuclear protein 2, TBM, TRF-binding motif) peptide. The MD results...
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Organic solvents aggregating and shaping structural folding of protein, a case study of the protease enzyme
PublicationLow solubility of reactants or products in aqueous solutions can result in the enzymatic catalytic reactions that can occur in non-aqueous solutions. In current study we investigated aqueous solutions containing different organic solvents / deep eutectic solvents (DESs) that can influence the protease enzyme's activity, structural, and thermal stabilities. Retroviral aspartic protease enzyme is responsible for the cleavage of the...
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Synthesis, physicochemical and theoretical studies on new rhodium and ruthenium dimers. Relationship between structure and cytotoxic activity
PublicationTwo dimeric compounds of the general formulae (Et3NH)2[Rh2(μ2-L)4Cl2] (1) (where L = thiophene-2-carboxylate) and [((η6-p-cymene)Ru)2(μ-Cl)3]PF6 (2) have been synthesized using a new method. The unique anionic complex 1 (space group P bca) has octahedral coordination in which the equatorial positions are occupied by the oxygen atoms of four thiophene-2-carboxylates in a paddle wheel fashion. In complex 2 (space group ), each Ru(II)...
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Structural, spectral and magnetic properties of Ni(II), Co(II) and Cd(II) compounds with imidazole derivatives and silanethiolate ligands
PublicationA series of new metal heteroleptic complexes have been obtained in simple reactions of 1-(3-aminopropyl)-imidazole (api) and 1,4-bis(imidazol-1-yl)-butane (bbi) ligands with metal silanethiolates or acetylacetonates. The obtained complexes are the coordination polymers [Ni{SSi(tBuO)3}2(μ-api)]n1, [Co{SSi(tBuO)3}2(μ-api)]n2, [Cd{SSi(tBuO)3}2(μ-api)·2CH3OH]n3, [Cd{SSi(tBuO)3}2(μ-bbi)·CHCl3]n4 and the dimer [Co{SSi(tBuO)3}2(μ-bbi)·3CH3OH]25....
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Molecular basis and quantitative assessment of TRF1 and TRF2 protein interactions with TIN2 and Apollo peptides
PublicationShelterin is a six-protein complex (TRF1, TRF2, POT1, RAP1, TIN2, and TPP1) that also functions in smaller subsets in regulation and protection of human telomeres. Two closely related proteins, TRF1 and TRF2, make high-affinity contact directly with double-stranded telomeric DNA and serve as a molecular platform. Protein TIN2 binds to TRF1 and TRF2 dimer-forming domains, whereas Apollo makes interaction only with TRF2. To elucidate...
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Mutually polarizable QM/MM model with in situ optimized localized basis functions
PublicationWe extend our recently developed quantum-mechanical/molecular mechanics (QM/MM) approach [Dziedzic et al., J. Chem. Phys. 145, 124106 (2016)] to enable in situ optimization of the localized orbitals. The quantum subsystem is described with ONETEP linear-scaling density functional theory and the classical subsystem – with the AMOEBA polarizable force field. The two subsystems interact via multipolar electrostatics and are fully...
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Non-toxic fluorine-doped TiO2 nanocrystals from TiOF2 for facet-dependent naproxen degradation
PublicationIn the present study, the photocatalytic degradation of naproxen (NPX), which is a nonsteroidal anti-inflammatory drug (NSAID), frequently detected in drinking water, was investigated. The F-doped TiO2 with defined morphology was successfully obtained from TiOF2 and applied for photocatalytic degradation under UV-vis and visible light. All samples were characterised by X-ray diffraction, scanning electron microscopy, X-ray photoelectron...
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Performance of the AMOEBA Water Model in the Vicinity of QM Solutes: A Diagnosis Using Energy Decomposition Analysis
PublicationThe importance of incorporating solvent polarization effects into the modeling of solvation processes has been well-recognized, and therefore a new generation of hybrid quantum mechanics/molecular mechanics (QM/MM) approaches that accounts for this effect is desirable. We present a fully self-consistent, mutually polarizable QM/MM scheme using the AMOEBA force field, in which the total energy of the system is variationally minimized...
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Structural features responsible for control of the eukaryotic GlcN-6-P synthase activity
PublicationGlucosamine-6-phosphate (GlcN-6-P) synthase is responsible for catalysis of the first and practically irreversible step in hexosamine metabolism. As UDP-GlcNAc, the final product of the hexosamine path, constitutes one of the essential substrates for assembly of bacterial and fungal cell walls, the enzyme is an interesting target for antimicrobial therapy.The structure of E. coli enzyme, known since 2001, forms a dimer of two identical...