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 language | English |
|---|---|
| Pages (from-to) | 141-147 |
| Number of pages | 7 |
| Journal | Journal of Molecular Graphics and Modelling |
| Volume | 54 |
| DOIs | |
| State | Published - 2014 |
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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 journal › Article
}
TY - JOUR
T1 - Evaluating membrane affinity by integrating protein orientations
AU - Zhu, Fangqiang
AU - Clauss, Matthias
PY - 2014
Y1 - 2014
N2 - 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.
AB - 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.
KW - Coarse-grained modeling
KW - EMAPII
KW - FGF1
KW - Free energy
KW - Non-classical release
KW - Protein orientation
UR - http://www.scopus.com/inward/record.url?scp=84908651622&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84908651622&partnerID=8YFLogxK
U2 - 10.1016/j.jmgm.2014.10.009
DO - 10.1016/j.jmgm.2014.10.009
M3 - Article
C2 - 25459766
AN - SCOPUS:84908651622
VL - 54
SP - 141
EP - 147
JO - Journal of Molecular Graphics and Modelling
JF - Journal of Molecular Graphics and Modelling
SN - 1093-3263
ER -