Artificial neural network for the prediction of tyrosine-based sorting signal recognition by adaptor complexes

J Biomed Biotechnol. 2012:2012:498031. doi: 10.1155/2012/498031. Epub 2012 Mar 11.

Abstract

Sorting of transmembrane proteins to various intracellular compartments depends on specific signals present within their cytosolic domains. Among these sorting signals, the tyrosine-based motif (YXXØ) is one of the best characterized and is recognized by μ-subunits of the four clathrin-associated adaptor complexes (AP-1 to AP-4). Despite their overlap in specificity, each μ-subunit has a distinct sequence preference dependent on the nature of the X-residues. Moreover, combinations of these residues exert cooperative or inhibitory effects towards interaction with the various APs. This complexity makes it impossible to predict a priori, the specificity of a given tyrosine-signal for a particular μ-subunit. Here, we describe the results obtained with a computational approach based on the Artificial Neural Network (ANN) paradigm that addresses the issue of tyrosine-signal specificity, enabling the prediction of YXXØ-μ interactions with accuracies over 90%. Therefore, this approach constitutes a powerful tool to help predict mechanisms of intracellular protein sorting.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Adaptor Proteins, Vesicular Transport / chemistry
  • Adaptor Proteins, Vesicular Transport / metabolism*
  • Amino Acid Sequence
  • Computational Biology / methods
  • HeLa Cells
  • Humans
  • Models, Statistical
  • Molecular Sequence Data
  • Neural Networks, Computer*
  • Protein Sorting Signals
  • Protein Subunits
  • Reproducibility of Results
  • Signal Transduction
  • Two-Hybrid System Techniques
  • Tyrosine / chemistry*
  • Tyrosine / metabolism*
  • Yeasts

Substances

  • Adaptor Proteins, Vesicular Transport
  • Protein Sorting Signals
  • Protein Subunits
  • Tyrosine