Computational protocol: Critical lysine residues within the overlooked N-terminal domain of human APE1 regulate its biological functions

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Protocol publication

[…] Biophysical parameters of different APE1 peptides (molecular weight and pI) were calculated by the computing algorithms available at the Swiss Institute of Bioinformatics (http://www.expasy.ch/tools/pi_tool.html).For phylogenetic analysis, a total of 17 APE1 orthologous metazoan sequences (Homo sapiens, Pan troglodytes, Macaca mulatta, Equus caballus, Sus scrofa, Bos taurus, Canis lupus familiaris, Mus musculus, Rattus norvegicus, Ornithorhyncus anatinus, Xenopus laevis, Xenopus tropicalis, Salmo salar, Danio rerio, Gasterosteus aculeatus, Caenorhabditis elegans and Strongylocentrotus purpuratus) were retrieved from databases using the BLAST algorithm (). Out-group sequences were not included because of the almost complete lack of the N-terminal domain in other organisms. Alignment of the amino acid residues 1–60 and of the cDNA nucleotide 1–180 was made with the MAFFT program (v6.531b) () with default parameters, and evolutionary trees were inferred using the software MEGA version 4 (). The minimum evolution tree-building method was used to reconstruct the phylogenetic tree (); dendrograms’ topologies were checked by the bootstrap method with 1000 replicates. […]

Pipeline specifications

Software tools APE, MAFFT, MEGA
Databases ExPASy
Application Phylogenetics
Organisms Homo sapiens