Abstract
Adenosine diphosphate ribosylation factor-1 (ARF1) is activated by cell membrane binding of a self-folding N-terminal domain. We have previously presented four possible conformations of the membrane bound, human ARF1 N-terminal peptide in planar lipid bilayers of DOPC and DOPG (7:3 molar ratio), determined from lamellar neutron diffraction and circular dichroism data. In this paper we analyse the four possible conformations by molecular dynamics simulations. The aim of these simulations was to use MD to distinguish which of the four possible membrane bound structures was the most likely. The most likely conformation was determined according to the following criteria: (a) location of label positions on the peptide in relation to the bilayer, (b) lowest mean square displacement from the initial structure, (c) lowest system energy, (d) most peptide-lipid headgroup hydrogen bonding, (e) analysis of phi/psi angles of the peptide. These findings demonstrate the application of molecular dynamics simulations to explore neutron diffraction data.
| Original language | English |
|---|---|
| Pages (from-to) | 379-388 |
| Number of pages | 10 |
| Journal | Molecular Membrane Biology |
| Volume | 22 |
| Issue number | 5 |
| DOIs | |
| Publication status | Published - 1 Sep 2005 |
Keywords
- Adenosine diphosphate ribosylation factor
- Molecular dynamics simulation
- Neutron diffraction
- Phospholipid bilayers
ASJC Scopus subject areas
- Molecular Biology
- Cell Biology
Cite this
Membrane-bound ARF1 peptide : Interpretation of neutron diffraction data by molecular dynamics simulation methods. / Balali-Mood, K.; Harroun, T. A.; Bradshaw, J. P.
In: Molecular Membrane Biology, Vol. 22, No. 5, 01.09.2005, p. 379-388.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Membrane-bound ARF1 peptide
T2 - Interpretation of neutron diffraction data by molecular dynamics simulation methods
AU - Balali-Mood, K.
AU - Harroun, T. A.
AU - Bradshaw, J. P.
PY - 2005/9/1
Y1 - 2005/9/1
N2 - Adenosine diphosphate ribosylation factor-1 (ARF1) is activated by cell membrane binding of a self-folding N-terminal domain. We have previously presented four possible conformations of the membrane bound, human ARF1 N-terminal peptide in planar lipid bilayers of DOPC and DOPG (7:3 molar ratio), determined from lamellar neutron diffraction and circular dichroism data. In this paper we analyse the four possible conformations by molecular dynamics simulations. The aim of these simulations was to use MD to distinguish which of the four possible membrane bound structures was the most likely. The most likely conformation was determined according to the following criteria: (a) location of label positions on the peptide in relation to the bilayer, (b) lowest mean square displacement from the initial structure, (c) lowest system energy, (d) most peptide-lipid headgroup hydrogen bonding, (e) analysis of phi/psi angles of the peptide. These findings demonstrate the application of molecular dynamics simulations to explore neutron diffraction data.
AB - Adenosine diphosphate ribosylation factor-1 (ARF1) is activated by cell membrane binding of a self-folding N-terminal domain. We have previously presented four possible conformations of the membrane bound, human ARF1 N-terminal peptide in planar lipid bilayers of DOPC and DOPG (7:3 molar ratio), determined from lamellar neutron diffraction and circular dichroism data. In this paper we analyse the four possible conformations by molecular dynamics simulations. The aim of these simulations was to use MD to distinguish which of the four possible membrane bound structures was the most likely. The most likely conformation was determined according to the following criteria: (a) location of label positions on the peptide in relation to the bilayer, (b) lowest mean square displacement from the initial structure, (c) lowest system energy, (d) most peptide-lipid headgroup hydrogen bonding, (e) analysis of phi/psi angles of the peptide. These findings demonstrate the application of molecular dynamics simulations to explore neutron diffraction data.
KW - Adenosine diphosphate ribosylation factor
KW - Molecular dynamics simulation
KW - Neutron diffraction
KW - Phospholipid bilayers
UR - http://www.scopus.com/inward/record.url?scp=28544451097&partnerID=8YFLogxK
U2 - 10.1080/09687860500220148
DO - 10.1080/09687860500220148
M3 - Article
C2 - 16308272
AN - SCOPUS:28544451097
VL - 22
SP - 379
EP - 388
JO - Molecular Membrane Biology
JF - Molecular Membrane Biology
SN - 0968-7688
IS - 5
ER -