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Snorkeling of lysine side chains in transmembrane helices: how easy can it get?
Author(s) -
Strandberg Erik,
Killian J.Antoinette
Publication year - 2003
Publication title -
febs letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.593
H-Index - 257
eISSN - 1873-3468
pISSN - 0014-5793
DOI - 10.1016/s0014-5793(03)00475-7
Subject(s) - side chain , lysine , transmembrane protein , chemistry , transmembrane domain , lipid bilayer , bilayer , polar , stereochemistry , amino acid , biochemistry , physics , membrane , organic chemistry , polymer , receptor , astronomy
Transmembrane segments of proteins are often flanked by lysine residues. The side chains of these residues may snorkel, i.e. they may bury themselves with their aliphatic part in the hydrophobic region of the lipid bilayer, while positioning the charged amino group in the more polar interface. Here we estimate the free energy cost of snorkeling from thermodynamical calculations based on studies with synthetic transmembrane peptides [Strandberg et al. (2002) Biochemistry 41, 7190–7198]. The value is estimated to be between 0.07 and 0.7 kcal mol −1 for a lysine side chain. This very low value indicates that snorkeling may be a common process, which should be taken into consideration both in experimental and in theoretical studies on protein–lipid interactions.