Computational protocol: Reprogramming of leukemic cell metabolism through the naphthoquinonic compound Quambalarine B

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Protocol publication

[…] MaxQuant 1.5.3.8 peak picking software and Andromeda search engine were used in label-free experiments. Followed parameters were set during measurement: enzyme specificity considered- Trypsin/P, number of missed cleavages permitted – 2, fixed modification(s) – S-Methyl-L-cysteine sulphoxide (C), variable modification – Oxidation (M), Acetyl (Protein N-term), mass tolerance for precursor ions – 4. 5 ppm and mass tolerance for fragment ions – 0. 5 Da. False discovery rate (FDR) was set as follows: peptide spectrum match FDR – 1%, Protein FDR – 1% and min. score for modified peptides – 40. Human protein database downloaded from uniprot.org on 9/15/2015 with 147 933 entries was used for individual proteins annotation. The “match between runs” feature of MaxQuant was used to transfer identifications to other LC-MS/MS runs based on their masses and retention time (maximum deviation 0.7 min). This setup was also used in quantification experiments. Quantifications were performed with the label-free algorithms described recently []. All MS experiments were done in biological triplicates and measured in technical duplicates. [...] Crystal structures of yeast mitochondrial complex I (CI) from Yarrowia lipolytica (PDB ID 4wz7) and porcine mitochondrial complex II (CII) (PDB ID 1zoy) were used for modeling. The program 3V was used to identify internal cavities connecting the iron-sulfur clusters with the predicted ubiquinone binding cavity in the CI crystal structure []. The geometry of ubiquinone and QB was optimized using DFT-D method with TPSS functional and TZVP basis set [, ]. The effect of water solvation was treated implicitly using COSMO with ε = 78.4. All the optimizations were performed in the TurboMole suite of programs. The Python Molecular Viewer (PMV 1.5.6 rc3) was used to set the docking parameters []. AutoDock Vina version 1.1.2 was used for ubiquinone and QB docking to CI and CII structures []. For the CI structure, the ligands were allowed to sample docking poses in a 60 × 60 × 60 Å box centered around the predicted ubiquinone binding cavity, covering large portion of the lower part of the peripheral arm (Q module) and the transmembrane PP module of the membrane arm. For the CII structure the ligands sampled a box of 30 × 30 × 30 Å around the known crystal position of the ubiquinone moiety. […]

Pipeline specifications

Software tools PMV, AutoDock Vina
Applications Drug design, Protein interaction analysis
Diseases Leukemia, Neoplasms, Leukemia, B-Cell, Precursor T-Cell Lymphoblastic Leukemia-Lymphoma
Chemicals Amino Acids, Ampicillin, Aspartic Acid, Folic Acid, Glycine, Pyruvic Acid, Lactic Acid