Introduction to the analysis of the intracellular sorting information in protein sequences: From molecular biology to artifi cial neural networks

Abstract

A precise spatial-temporal organization of cell components is required for basic cellular activities such as proliferation and for complex multicellular processes such as embryo development. Particularly important is the maintenance and control of the cellular distribution of proteins, as these components fulfi ll crucial structural and catalytic functions. Membrane protein localization within the cell is determined and maintained by intracellular elements known as adaptors that interpret sorting information encoded in the amino acid sequence of cargoes. Understanding the sorting sequence code of cargo proteins would have a profound impact on many areas of the life sciences. For example, it would shed light onto the molecular mechanisms of several genetic diseases and would eventually allow us to control the fate of proteins. This chapter constitutes a primer on protein-sorting information analysis and localization/traffi cking prediction. We provide the rationale for and a discussion of a simple basic protocol for protein sequence dissection looking for sorting signals, from simple sequence inspection techniques to more sophisticated artifi cial neural networks analysis of sorting signal recognition data.