Influence of the environment in the conformation of α-helices studied by protein database search and molecular dynamics simulations

Mireia Olivella, Xavier Deupi, Cedric Govaerts, Leonardo Pardo

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30 Citations (Scopus)

Abstract

The influence of the solvent on the main-chain conformation (φ and ψ dihedral angles) of α-helices has been studied by complementary approaches. A first approach consisted in surveying crystal structures of both soluble and membrane proteins. The residues of analysis were further classified as exposed to either the water (polar solvent) or the lipid (apolar solvent) environment or buried to the core of the protein (intermediate polarity). The statistical results show that the more polar the environment, the lower the value of φi and the higher the value of ψi are. The intrahelical hydrogen bond distance increases in water-exposed residues due to the additional hydrogen bond between the peptide carbonyl oxygen and the aqueous environment. A second approach involved nanosecond molecular dynamics simulations of poly-Ala α-helices in environments of different polarity: water to mimic hydrophilic environments that can form hydrogen bonds with the peptide carbonyl oxygen and methane to mimic hydrophobic environments without this hydrogen bond capabilities. These simulations reproduce similar effects in φand ψ angles and intrahelical hydrogen bond distance and angle as observed in the protein survey analysis. The magnitude of the intrahelical hydrogen bond in the methane environment is stronger than in the water environment, suggesting that α-helices in membrane-embedded proteins are less flexible than in soluble proteins. There is a remarkable coincidence between the φ and ψ angles obtained in the analysis of residues exposed to the lipid in membrane proteins and the results from computer simulations in methane, which suggests that this simulation protocol properly mimic the lipidic cell membrane and reproduce several structural characteristics of membrane-embedded proteins. Finally, we have compared the φ and ψ torsional angles of Pro kinks in membrane protein crystal structures and in computer simulations.
Original languageEnglish
Pages (from-to)3207-3213
JournalBiophysical Journal
Volume82
Issue number6
DOIs
Publication statusPublished - 1 Jan 2002

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