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Nanoinformatics: An Emerging Trend in Cancer Therapeutics
Published in Rajesh Singh Tomar, Anurag Jyoti, Shuchi Kaushik, Nanobiotechnology, 2020
Medha Pandya, Snehal Jani, Vishakha Dave, Rakesh Rawal
Native atomic bonds and interactions to drug binding sites mainly express the mechanisms and effectiveness of therapeutic action. The protein structure prediction is accurately comparable to experimental residues is challenging [55]. The critical assessment of protein structure prediction (CASP) community provides an opportunity to research groups through objectively test their structure prediction methods. It presents an independent evaluation of the cutting- edge protein structure modeling to the research community and software users. The variety of methods generates protein models. Though it is unclear what exactly done, the methods roughly classified the following groups: “Modeler,” “Raptor,” “Zhang” group, “Rosetta,” “Lee” group, and others. The use of physics-based methods in protein structure refinement is highly encouraging. It is highly complementary to knowledge-based methods and allows the future repetitive refinement of protein structures to experimental accuracies. In this study, MD simulations and loop refinements further polished predicted models of fusion proteins [25] in CASP11 recommend that the refinement performs significant dynamics, where the averaged models have very poor MolProbity scores. Molecular dynamics (MD) simulations used in combination with a better-quality selection and averaging protocol. The preliminary 3D model of AF9-MLL fusion protein acquired from homology modeling and further refined by MD simulation to improve the accuracy of the structure.
Green synthesized silver nanoparticles with mushroom extracts of Paxina leucomelas and Rhizopogon luteolus induce ROS-Induced intrinsic apoptotic pathway in cancer cells
Published in Inorganic and Nano-Metal Chemistry, 2022
Nazan Gökşen Tosun, Özlem Kaplan, Rizvan Imamoğlu, İbrahim Türkekul, İsa Gökçe, Aykut Özgür
Western-Blot experiment was performed to analyze protein expression levels of the Bax, Bcl-2, and Casp-9 in treated MCF-7, A549, Saos-2, and HT-29 cells with IC50 values of the PL-AgNPs and RL-AgNPs. Cells were lysed by RIPA lysis buffer, and the protein concentrations of cell lysates were measured using a BCA protein assay kit. 50 µg of total protein was electrophoresed on 12% SDS-PAGE gel, and then proteins were transferred onto a PVDF membrane using a Trans-blot turbo transfer system (Bio-Rad). The membranes were blocked by 5% skimmed milk powder (in TBST) for 1 h at room temperature. Target proteins were detected using primary antibodies for anti-Bax (1:1000), anti-Bcl-2 (1:500), anti-pro-Casp9 (1:500) and anti-Gapdh (1:5000). The blots were incubated with the primary antibodies overnight at 4 °C. Then, the membranes were washed with TBST and incubated with goat anti-rabbit IgG H&L (HRP) secondary antibody (1:10000) for 1 h at room temperature. Protein bands were visualized using the ChemiDoc™ imaging system (Bio-Rad) by enhanced chemiluminescence (ECL) substrate. Gapdh was used as the internal control for the normalization of the data, and protein expression levels were calculated using ImageLab 6.1 software.