Molecular dynamics study of the solvation of an alpha-helical transmembrane peptide by DMSO

A.M. Duarte, C.P.M. van Mierlo, M.A. Hemminga

Research output: Contribution to journalArticleAcademicpeer-review

22 Citations (Scopus)

Abstract

10-ns molecular dynamics study of the solvation of a hydrophobic transmembrane helical peptide in dimethyl sulfoxide (DMSO) is presented. The objective is to analyze how this aprotic polar solvent is able to solvate three groups of amino acid residues (i.e., polar, apolar, and charged) that are located in a stable helical region of a transmembrane peptide. The 25-residue peptide (sMTM7) used mimics the cytoplasmic proton hemichannel domain of the seventh transmembrane segment (TM7) from subunit a of H+-V-ATPase from Saccharomyces cerevisiae. The three-dimensional structure of peptide sMTM7 in DMSO has been previously solved by NMR spectroscopy. The radial and spatial distributions of the DMSO molecules surrounding the peptide as well as the number of hydrogen bonds between DMSO and the side chains of the amino acid residues involved are extracted from the molecular dynamics simulations. Analysis of the molecular dynamics trajectories shows that the amino acid side chains are fully embedded in DMSO. Polar and positively charged amino acid side chains have dipole¿dipole interactions with the oxygen atom of DMSO and form hydrogen bonds. Apolar residues become solvated by DMSO through the formation of a hydrophobic pocket in which the methyl groups of DMSO are pointing toward the hydrophobic side chains of the residues involved. The dual solvation properties of DMSO cause it to be a good membrane-mimicking solvent for transmembrane peptides that do not unfold due to the presence of DMSO.
Original languageEnglish
Pages (from-to)8664-8671
JournalThe Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical
Volume112
Issue number29
DOIs
Publication statusPublished - 2008

Keywords

  • proton translocation channel
  • aib-rich peptide
  • yeast v-atpase
  • secondary-structure
  • force-field
  • simulations
  • proteins
  • nmr
  • dimethylsulfoxide
  • conformation

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