Structure-based statistical analysis of transmembrane helices.

European Biophysics Journal : EBJ
Carlos Baeza-DelgadoIsmael Mingarro

Abstract

Recent advances in determination of the high-resolution structure of membrane proteins now enable analysis of the main features of amino acids in transmembrane (TM) segments in comparison with amino acids in water-soluble helices. In this work, we conducted a large-scale analysis of the prevalent locations of amino acids by using a data set of 170 structures of integral membrane proteins obtained from the MPtopo database and 930 structures of water-soluble helical proteins obtained from the protein data bank. Large hydrophobic amino acids (Leu, Val, Ile, and Phe) plus Gly were clearly prevalent in TM helices whereas polar amino acids (Glu, Lys, Asp, Arg, and Gln) were less frequent in this type of helix. The distribution of amino acids along TM helices was also examined. As expected, hydrophobic and slightly polar amino acids are commonly found in the hydrophobic core of the membrane whereas aromatic (Trp and Tyr), Pro, and the hydrophilic amino acids (Asn, His, and Gln) occur more frequently in the interface regions. Charged amino acids are also statistically prevalent outside the hydrophobic core of the membrane, and whereas acidic amino acids are frequently found at both cytoplasmic and extra-cytoplasmic interfaces, basic am...Continue Reading

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Citations

Jan 10, 2013·The Journal of Biological Chemistry·Hai M NguyenK George Chandy
Aug 29, 2013·The FEBS Journal·Daniel C YeeMilton H Saier
Jun 21, 2014·Protein Science : a Publication of the Protein Society·Irina D PogozhevaAndrei L Lomize
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Jul 2, 2015·Viruses·Luis Martinez-Gil, Ismael Mingarro
Sep 1, 2018·The Journal of Biological Chemistry·Matus ValachGertraud Burger
Dec 20, 2018·Bioinformatics·Eduardo MayolMireia Olivella
Aug 16, 2019·PloS One·Alan J Situ, Tobias S Ulmer
Nov 2, 2019·Biochemical Society Transactions·Paul Curnow
Sep 9, 2020·Open Biology·Gerard DuartIsmael Mingarro
Dec 12, 2018·Nature Communications·Manuel Bañó-PoloIsmael Mingarro
Apr 14, 2020·The Journal of Clinical Endocrinology and Metabolism·Peter LaufferDaniëlle C M van der Kaay
Dec 31, 2020·PloS One·Pablo Mier, Miguel A Andrade-Navarro
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Mar 7, 2021·Microorganisms·Mikhail Oliveira LeastroJesús Á Sánchez-Navarro
Mar 28, 2021·Biochimica Et Biophysica Acta. Biomembranes·Gerard DuartIsmael Mingarro
Jan 24, 2015·Langmuir : the ACS Journal of Surfaces and Colloids·Sarah C BernierChristian Salesse
Jun 7, 2014·ACS Chemical Biology·Vicente Andreu-FernándezEnrique Pérez-Payá
Jan 21, 2020·ACS Omega·Manuel Bañó-PoloIsmael Mingarro

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