Evaluating membrane affinity by integrating protein orientations

Fangqiang Zhu, Matthias Clauss

Research output: Contribution to journalArticle

Abstract

Energetic interactions of a protein with lipid bilayers determine its propensity to reside in the membrane. Here we seek to evaluate the membrane interactions for EMAPII, a protein found to be released from the cell by unknown mechanisms, as well as several other proteins. Using a knowledge-based coarse-grained membrane potential, we calculate the free energy profiles for these proteins by integrating out the orientation degrees of freedom. Due to the invariance of energy under in-plane rotations about the membrane normal, the orientation space can be reduced to two dimensions and mapped onto the surface of a unit sphere, thus making visualization, sampling and integration more convenient. The integrated free energy profiles determine the relative probabilities along the membrane normal for the proteins regardless of their orientations, and display distinctive characteristics for membrane proteins and water-soluble proteins. The membrane interactions for EMAPII exhibit typical features of a water-soluble protein, with a high energetic barrier to enter or cross the membrane. Our results thus suggest that similar to the non-classical export of FGF1, the release of EMAPII would involve more complicated mechanisms than simple passive diffusion across the membrane.

Original languageEnglish
Pages (from-to)141-147
Number of pages7
JournalJournal of Molecular Graphics and Modelling
Volume54
DOIs
StatePublished - 2014

Fingerprint

affinity
membranes
proteins
Proteins
Membranes
Membrane Proteins
Free energy
Fibroblast Growth Factor 1
Water
Lipid Bilayers
space orientation
free energy
Membrane Potentials
Lipid bilayers
Invariance
interactions
profiles
water
Visualization
lipids

Keywords

  • Coarse-grained modeling
  • EMAPII
  • FGF1
  • Free energy
  • Non-classical release
  • Protein orientation

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Spectroscopy
  • Computer Graphics and Computer-Aided Design
  • Materials Chemistry
  • Medicine(all)

Cite this

Evaluating membrane affinity by integrating protein orientations. / Zhu, Fangqiang; Clauss, Matthias.

In: Journal of Molecular Graphics and Modelling, Vol. 54, 2014, p. 141-147.

Research output: Contribution to journalArticle

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