Data on molecular docking simulations of quaternary complexes 'Bst exo- polymerase-DNA-dCTP-metal cations'.
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ABSTRACT:
SUBMITTER: Garafutdinov RR
PROVIDER: S-EPMC7704292 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description: Not available
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Project description:This article reports experimental data related to the research article entitled "Prevention of DNA multimerization using phosphoryl guanidine primers during isothermal amplification with Bst exo- DNA polymerase" (R.R. Garafutdinov, A.R. Sakhabutdinova, M.S. Kupryushkin, D.V. Pyshnyi, 2020) [1]. Here, multimerization efficiency in terms of Tt (time-to-threshold) values obtained for artificial DNA templates with the different nucleotide sequences during isothermal amplification with Bst exo- DNA polymerase is given. Data on the influence of phosphoryl guanidine primers (PGO) on multimerization for the LTc template which has shown high efficiency of multimerization are presented as well.
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Project description:Ternary complexes of wild type or mutant form of human DNA polymerase beta (pol beta) bound to DNA and dCTP substrates were studied by molecular dynamics (MD) simulations. The occurrences of contact configurations (CC) of structurally important atom pairs were sampled along the MD trajectories, and converted into free-energy differences, DeltaG(CC). DeltaG(CC) values were correlated with the experimental binding and catalytic free energies for the wild type pol beta and its Arg183Ala, Tyr271Ala, Asp276Val, Lys280Gly, Arg283Ala, and Glu295Ala mutants. The correlation coefficients show that the strength of the H-bond between dCTP and Asn279 is a strong predictor of the mutation-induced changes in the catalytic efficiency of pol beta. This finding is consistent with the view that enzyme preorganization plays a major role in controlling DNA polymerase specific activity.
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Project description:Imidazole and tetrazole derivatives are widely used as clinical drugs since they possess a variety of pharmaceutical function. Zinc and iron are essential trace elements of the human body, with less toxicity and good biocompatibility. In this paper, two new essential metal mononuclear complexes [M(H2tmidc)2(H2O)2]·2H2O (M = Zn (1), Fe (2)) were synthesized through the reaction of 2-((1H-tetrazol-1-yl)methylene)-1H-imidazole-4,5-dicarboxylic acid (H3tmidc) and ZnSO4·7H2O or FeSO4·7H2O. The crystal structures were determined by means of the X-ray single crystal diffraction technique. Results from fluorescence investigations show that both complexes could interact with BSA as well as HSA through the static quenching mechanism. van der Waals forces and hydrogen bonds play important roles in the interaction of complexes and BSA/HSA since both ΔH and ΔS values are negative. The results of molecular docking are consistent with those in experimental studies. Furthermore, the anticancer activity of H3tmidc and both complexes against Eca-109 were preliminarily evaluated and the results show that both complexes have better anticancer activity than the corresponding ligand H3tmidc.
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Project description:The charge states of proteins can greatly influence their stabilities and interactions with substrates, and the addition of multiple charges (supercharging) has been shown to be a successful approach for engineering protein stability and function. The addition of a fast-folding fusion domain to the Bacillus stearothermophilus DNA polymerase improved its functionality in isothermal amplification assays, and further charge engineering of this domain has increased both protein stability and diagnostics performance. When combined with mutations that stabilize the core of the protein, the charge-engineered fusion domain leads to the ability to carry out loop-mediated isothermal amplification (LAMP) at temperatures up to 74° C or in the presence of high concentrations of urea, with detection times under 10 min. Adding both positive and negative charges to the fusion domain led to changes in the relative reverse transcriptase and DNA polymerase activities of the polymerase. Overall, the development of a modular fusion domain whose charged surface can be modified at will should prove to be of use in the engineering of other polymerases and, in general, may prove useful for protein stabilization.
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Project description:Alkali-stable quaternary phosphonium (QP) is a type of cationic group for hydroxide exchange membranes (HEMs). To elucidate the relationship between structure and alkaline stability, we investigated the kinetics and degradation mechanism of a series of QP cations by both experiment and computation, and established a semi-empirical formula based on the Taft equation to directly estimate alkaline stability of QP cations from the 31P NMR chemical shift δ and the steric substituent constant E s, facilitating the search for QP cations with improved alkaline stability.
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Project description:In the era of acquired microbial resistance (AMR), resulting in the ineffectiveness of antibiotics is of keen interest for researchers in current scenarios. Ten novel metal complexes of gemifloxacin have been synthesized by reacting it with essential and trace elements in a 2:1 ratio predetermined conducto-metrically. As these metals are either present in the body or co-administered as metallic supplements can alter the level of antibiotics. Therefore, Metal complexes of Gemifloxacin, an important member of the fluoroquinolone family, were synthesized. The possible coordination of gemifloxacin with these metals has been proposed by the electronic and elemental data obtained through molar conductance, elemental analysis, and spectroscopic techniques like ultraviolet-visible (UV-Vis), infrared (IR), and proton-nuclear magnetic resonance (1H NMR) studies. In the light of these studies, the monoanionic bidentate ligand behavior of gemifloxacin in complexation with metals has been revealed. For in-vitro microbial studies, these newly synthesized complexes were tested against eleven different bacteria including Gram + ve and Gram -ve organisms, and one fungal strain. The results were compared with the parent drug by applying ANOVA through SPSS software version 22. Therefore, it has been found that among all synthesized metal complexes, the G-M01 complex exhibits increased activity against B. subtilis, P. mirabilis, E. coli, K. pneumonia, and C. freundii. Complex G-M02, G-M03, G-M04, and G-M10 show more pronounced activity than Gemifloxacin against S. aureus and M. luteus. Moreover, the binding orientations of the synthesized metal complexes into the binding site of the urease enzyme revealed that all the docked metal complexes oriented away from the Ni bi-center, and the inactivation of urease is due to their interaction with entrance flap residues.
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Project description:A series of some novel copper complexes derived from Biginelli condensation of DHPHS. The ligand and its transition metal complexes show more antimicrobial activities which was substantiated by molecular docking studies. Transition metal complexes four possess antioxidant properties supported by the DNA-binding, cleavage, and viscosity measurement (Prasad et al., 2011) [1]. The in Silicon DNA binding reveals copper complex is bound to be Minor groove and other manganese, cobalt, nickel complexes are bound to the Major groove portion of DNA through hydrogen bonds and hence copper (II), manganese (II), cobalt (II), nickel (II) complexes are called Minor groove and Major groove binder respectively. The DNA cleavage studies of metal complexes presented more protruding activity in the attendance of H2O2 associated to that in the absence of H2O2. In continuance of our ongoing research on DNA binding and cleavage happenings of transition metal complexes, in this paper we obtainable the synthesis, characterization and DNA cleavage activities.
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Project description:The goal of this study was to determine the effects of commonly used nuclease treatments and their divalent metal cation cofactors on Pol I occupancy during NET-seq. Other groups have previously used micrococcal nuclease (MNase) + CaCl2 and deoxyribonuclease I (DNase I) + MnCl2 in NET-seq protocols probing for Pol II occupancy. However, the effect of these treatments on polymerase occupancy has not been fully explored. Therefore, we tested the impact of these treatments (CaCl2, CaCl2 + MNase, MnCl2, and MnCl2 + DNase I) on Pol I occupancy in vivo. We found that the exposure of Pol I to either CaCl2 or MnCl2 caused a significant reduction in occupancy on the rDNA template. Nuclease treatment (with either MNase or DNase I) did not cause an additional significant effect on Pol I occupancy in vivo beyond that of either CaCl2 or MnCl2. Finally, we found that MnCl2 treatment caused a more significant reduction in Pol I occupancy as compared to CaCl2, suggesting that perhaps MnCl2 stimulates the intrinsic cleavage activity of Pol I more robustly vs. CaCl2 in vivo. Altogether, these findings indicate that the inclusion of these treatments (especially that of divalent metal cations) in NET-seq protocols for Pol I cause a significant change in the polymerase occupancy.
2022-10-27 | GSE216460 | GEO