HfAIM: A reliable bioinformatics approach for in silico genome-wide identification of autophagy-associated Atg8-interacting motifs in various organisms.

ABSTRACT: Most of the proteins that are specifically turned over by selective autophagy are recognized by the presence of short Atg8 interacting motifs (AIMs) that facilitate their association with the autophagy apparatus. Such AIMs can be identified by bioinformatics methods based on their defined degenerate consensus F/W/Y-X-X-L/I/V sequences in which X represents any amino acid. Achieving reliability and/or fidelity of the prediction of such AIMs on a genome-wide scale represents a major challenge. Here, we present a bioinformatics approach, high fidelity AIM (hfAIM), which uses additional sequence requirements-the presence of acidic amino acids and the absence of positively charged amino acids in certain positions-to reliably identify AIMs in proteins. We demonstrate that the use of the hfAIM me

SUBMITTER: Xie Q 

PROVIDER: S-EPMC4854547 | biostudies-literature | 2016 May

REPOSITORIES: biostudies-literature