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 fulfill 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/trafficking 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 artificial neural networks analysis of sorting signal recognition data.
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Acknowledgments
We are indebted to Arpita Sen (UC Berkeley) and members of the Aguilar lab for critical reading of the manuscript. The Aguilar lab is supported by the Center for the Science of Information, an NSF Science and Technology Center, under grant agreement CCF-0939370, by the National Institutes of Health and by the National Science Foundation under Grants No. 5 R21 CA151961-02 and 1021377, respectively.
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Aguilar, R.C. (2015). Introduction to the Analysis of the Intracellular Sorting Information in Protein Sequences: From Molecular Biology to Artificial Neural Networks. In: Cartwright, H. (eds) Artificial Neural Networks. Methods in Molecular Biology, vol 1260. Springer, New York, NY. https://doi.org/10.1007/978-1-4939-2239-0_1
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DOI: https://doi.org/10.1007/978-1-4939-2239-0_1
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