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Topology of membrane proteins - predictions, limitations and variations
Stockholm University, Science for Life Laboratory (SciLifeLab). Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
Stockholm University, Science for Life Laboratory (SciLifeLab). Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
Stockholm University, Science for Life Laboratory (SciLifeLab). Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. NITECH, Japan.
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Number of Authors: 72018 (English)In: Current opinion in structural biology, ISSN 0959-440X, E-ISSN 1879-033X, Vol. 50, p. 9-17Article in journal (Refereed) Published
Abstract [en]

Transmembrane proteins perform a variety of important biological functions necessary for the survival and growth of the cells. Membrane proteins are built up by transmembrane segments that span the lipid bilayer. The segments can either be in the form of hydrophobic alpha-helices or beta-sheets which create a barrel. A fundamental aspect of the structure of transmembrane proteins is the membrane topology, that is, the number of transmembrane segments, their position in the protein sequence and their orientation in the membrane. Along these lines, many predictive algorithms for the prediction of the topology of alpha-helical and beta-barrel transmembrane proteins exist. The newest algorithms obtain an accuracy close to 80% both for alpha-helical and beta-barrel transmembrane proteins. However, lately it has been shown that the simplified picture presented when describing a protein family by its topology is limited. To demonstrate this, we highlight examples where the topology is either not conserved in a protein superfamily or where the structure cannot be described solely by the topology of a protein. The prediction of these nonstandard features from sequence alone was not successful until the recent revolutionary progress in 3D-structure prediction of proteins.

Place, publisher, year, edition, pages
2018. Vol. 50, p. 9-17
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:su:diva-160275DOI: 10.1016/j.sbi.2017.10.003ISI: 000443661300004PubMedID: 29100082OAI: oai:DiVA.org:su-160275DiVA, id: diva2:1249260
Available from: 2018-09-18 Created: 2018-09-18 Last updated: 2019-08-23Bibliographically approved

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Govindarajan, SudhaBassot, ClaudioVästermark, ÅkeLamb, JohnShu, NanjiangElofsson, Arne
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Science for Life Laboratory (SciLifeLab)Department of Biochemistry and Biophysics
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