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Predicting Structural and Functional Properties of Membrane Proteins from Protein Sequence
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
2011 (English)In: Annual Reports in Computational Chemistry / [ed] Wheeler, R.A., Amsterdam: Elsevier Science BV , 2011, 39-64 p.Chapter in book (Refereed)
Abstract [en]

Integral transmembrane (TM) proteins are essential constituents of biological membranes where they fulfill a variety of important cellular functions. Because of difficulties with determining their structures by experimental techniques, comparably few 3D structures of membrane proteins are known so far. Therefore, computational methods trained on the available structures using only the protein sequence as input have become important tools in this field. In this chapter, we give a short introduction to the topic and then summarize recent bioinformatics tools for the prediction of structural as well as functional properties of alpha-helical and beta-barrel TM proteins. We present methods that allow predicting the locations of alpha-helical and beta-strand TM segments, to determine the exposure status of residues in the TM region to the surrounding lipids, and that allow functional annotations from the protein sequence.

Place, publisher, year, edition, pages
Amsterdam: Elsevier Science BV , 2011. 39-64 p.
, Annual Reports in Computational Chemistry, ISSN 1574-1400 ; 7
Keyword [en]
membrane protein topology, helical bundle, beta barrel, helix kink, reentrant loop, helix interaction, lipid exposure, propensity scale, functional classification, position-specific scoring matrix, amino acid composition
National Category
Biochemistry and Molecular Biology Other Computer and Information Science
URN: urn:nbn:se:su:diva-94443DOI: 10.1016/B978-0-444-53835-2.00002-XISI: 000311387200003ISBN: 978-0-44-454302-8OAI: diva2:653574
Available from: 2013-10-04 Created: 2013-10-04 Last updated: 2013-10-21Bibliographically approved

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