Computational and theoretical approaches for studies of a lipid recognition protein on biological membranes

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4 Citations (Scopus)

Abstract

Many cellular functions, including cell signaling and related events, are regulated by the association of peripheral membrane proteins (PMPs) with biological membranes containing anionic lipids, e.g., phosphatidylinositol phosphate (PIP). This association is often mediated by lipid recognition modules present in many PMPs. Here, I summarize computational and theoretical approaches to investigate the molecular details of the interactions and dynamics of a lipid recognition module, the pleckstrin homology (PH) domain, on biological membranes. Multi-scale molecular dynamics simulations using combinations of atomistic and coarse-grained models yielded results comparable to those of actual experiments and could be used to elucidate the molecular mechanisms of the formation of protein/lipid complexes on membrane surfaces, which are often difficult to obtain using experimental techniques. Simulations revealed some modes of membrane localization and interactions of PH domains with membranes in addition to the canonical binding mode. In the last part of this review, I address the dynamics of PH domains on the membrane surface. Local PIP clusters formed around the proteins exhibit anomalous fluctua-tions. This dynamic change in protein-lipid interactions cause temporally fluctuating diffusivity of proteins, i.e., the short-term diffusivity of the bound protein changes substantially with time, and may in turn contribute to the formation/dissolution of protein complexes in mem-branes.

Original languageEnglish
Pages (from-to)153-160
Number of pages8
JournalBiophysics and physicobiology
Volume14
DOIs
Publication statusPublished - 2017

Keywords

  • molecular dynamics simulation
  • Peripheral membrane protein
  • phosphatidylinositol phosphate
  • pleckstrin homology domain
  • protein-lipid interaction

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Molecular Biology
  • Physiology
  • Biochemistry, Genetics and Molecular Biology (miscellaneous)

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