Interaction of tryptophan analogs with POPC lipid bilayers investigated by molecular dynamics calculations

Alan Grossfield, Thomas B Woolf

Research output: Contribution to journalArticle

Abstract

Several experimental structures of integral membrane proteins have demonstrated that tryptophan side chains are found preferentially within the membrane interface, but no clear physical explanation for this preference has been demonstrated. The present work contains a series of molecular dynamics simulations designed to provide insight into this phenomenon. Specifically, we performed conventional unbiased simulations, as well as biased molecular dynamics of indole and N-methylindole within palmitoyloleoyl phosphatidylcholine (POPC) bilayers. The unbiased calculations examined the behavior of the indoles in three environments-the membrane center, the headgroup region, and the water outside the membrane. The biased calculations were performed using a new dynamic windowing procedure, which efficiently moved the indoles through the bilayer. These calculations allowed us to explore the orientation, hydrogen bonding, and energetics of the indole, as a function of its location along the membrane normal. Furthermore, free energy profiles were constructed from the biased simulations, facilitating comparison to experiment and a possible explanation of indole's partitioning behavior.

Original languageEnglish (US)
Pages (from-to)198-210
Number of pages13
JournalLangmuir
Volume18
Issue number1
DOIs
StatePublished - Jan 8 2002

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Lipid bilayers
tryptophan
indoles
Phosphatidylcholines
Tryptophan
lipids
Molecular dynamics
analogs
molecular dynamics
membranes
Membranes
Indoles
interactions
simulation
Free energy
Hydrogen bonds
Membrane Proteins
free energy
Water
Computer simulation

ASJC Scopus subject areas

  • Colloid and Surface Chemistry
  • Physical and Theoretical Chemistry

Cite this

Interaction of tryptophan analogs with POPC lipid bilayers investigated by molecular dynamics calculations. / Grossfield, Alan; Woolf, Thomas B.

In: Langmuir, Vol. 18, No. 1, 08.01.2002, p. 198-210.

Research output: Contribution to journalArticle

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