Interactions of Pleckstrin Homology Domains with Membranes: Adding Back the Bilayer via High-Throughput Molecular Dynamics

Eiji Yamamoto, Antreas C. Kalli, Kenji Yasuoka, Mark S.P. Sansom

Research output: Contribution to journalArticle

36 Citations (Scopus)

Abstract

A molecular simulation pipeline for determining the mode of interaction of pleckstrin homology (PH) domains with phosphatidylinositol phosphate (PIP)-containing lipid bilayers is presented. We evaluate our methodology for the GRP1 PH domain via comparison with structural and biophysical data. Coarse-grained simulations yield a 2D density landscape for PH/membrane interactions alongside residue contact profiles. Predictions of the membrane localization and interactions of 13 PH domains reveal canonical, non-canonical, and dual PIP-binding sites on the proteins. Thus, the PH domains associate with the PIP molecules in the membrane via a highly positively charged loop. Some PH domains exhibit modes of interaction with PIP-containing membranes additional to this canonical binding mode. All 13 PH domains cause a degree of local clustering of PIP molecules upon binding to the membrane. This provides a global picture of PH domain interactions with membranes. The high-throughput approach could be extended to other families of peripheral membrane proteins.

Original languageEnglish
Pages (from-to)1421-1431
Number of pages11
JournalStructure
Volume24
Issue number8
DOIs
Publication statusPublished - 2016 Aug 2

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

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