Pipeline publication

[…] b' antibody (OGHis; Medical and Biological Laboratories), anti-HA antibody (3F10; Roche), anti-FIV p24 Capsid antibody (PAK3-2C1; Santa Cruz Biotechnology); anti-alpha-tubulin (TUBA) antibody (DM1A; Sigma), and anti-VSVg antibody (P5DA; Roche). For FIV reporter assays, HEK293T cells were used for the target of infection. Ten microliter of the culture supernatant of transfected cells was inoculated into HEK293T cells in a 96-well plate (Nunc), and the firefly luciferase activity was measured by using the BrillianStar-LT assay system (Toyo-b-net) and the 2030 ARVO X multilabel counter instrument (PerkinElmer) according to the manufacturers\xe2\x80\x99 procedures., Homology modeling was performed using the SWISS-MODEL server [\xe2\x80\x93]. After BLAST searches [] of the bobcat and puma A3Z3 amino acid sequences against protein data bank sequence entries (http://www.rcsb.org/pdb/), the crystal structure of human APOBEC3A (PDB: 5KEG) [] was selected as the best template for homology modeling per the Global Model Quality Estimations, QMEAN statistical parameters, and modeled sequence length. Each generated model was minimized and refined using Discovery Studio (Dassault Syst\xc3\xa8mes BIOVIA, Discovery Studio Modeling Environment, Release 4.1, San Diego: Dassault Syst\xc3\xa8mes, 2007). Mutant models and 3D images were generated with PyMOL (The PyMOL Molecular Graphics System, version 1.8 Schr\xc3\xb6dinger, LLC)., The data are expressed as averages with the standard deviations (SDs), and statistically significant differences were determined using Student\xe2\x80\x99s t test., The A3Z3 sequences of five pumas, two bobcats and two cheetahs were submitted to DDBJ (accession numbers LC376039-LC376042)., , Electronic supplementary material , The online version of this article (10.1186/s12977-018-0414-5) contains supplementary material, which is available to authorized users., KS conceived the study and designed experiments; Y.Konno, S.Nagaoka, IK, KY, Y.Kagawa, RK, HA and TK performed experiments; Y.Konno, S.Nagaoka, IK, KY and HA analyzed data; MT' […]

Pipeline specifications

Software tools SWISS-MODEL, QMEAN, PyMOL
Organisms Lentivirus, Homo sapiens, Puma concolor, Lynx rufus
Chemicals Amino Acids