CCL:Summary of "MD calculation of biological membranes"
Dear CCLers:
Here is the summary of my post a week ago nemed
"MD calculation of biological membranes".
Thanks to all the responses.
Especially I wish to acknowledge useful imformation from
Dr. C. Nick Hodge (The DuPont Merck Pharmaceutical Company),
Dr. Liisa Laakkonen (City University of New York) and
Dr. Aguinaldo Robinsoni (University of Califronia).
My message is:
> I would like to simulate this interaction and to calculate the
>trajectories of the lipophilic molecules or amphiphilic molecules in
>the membrane mimetic system, using the molecular dynamics (MD)
>calculation.
> Please inform me about the papers related to molecular
> dynamics simulation of the membrane mimetic system.
I have attached the abstarcts to the original informations.
If you have comments on these references, please send a message
to CCL. I plane to take a summer vacation on 8/11 - 8/16 at Kyoto
in Japan. I will read these references, seeing the old temple's garden
at Kyoto. After the vacation, I would like to send a great (?)
message to CCL.
The helpful references are as follows:
ref.1
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Authors
Richard M. Venable, Yuhong Zhang, Barry J. Hardy,
Richard W. Pastor
Tittle
Molecular Dynamics Simulations of a Lipid Bilayer
and of Hexadecane:An investigation od Membrane Fluidity
Source
Science, 262 (8 October), 223-226 (1993)
Abstract
Molecular dynamics simulation of a fluid-phase dipalmitoyl
phosphatidylcholine lipid bilayers in water and of near hexadecane
are reported and compared with nuclear magnetic resonance
spin-lattice relaxation and quasi-elastic neutron scattering data.
On the 100-picosecond time scale of the present simulations,
there is effectively no difference in the reorientational
dynamics of the carbons in the membrane interior and inpure
hexadecane.
Given that the calculated fast reorientational correlation times
and the "microscopic" lateral diffusion of the lipids show
excellent agreement with the experimental results, it is
concluded that the aaparently high viscosity of the membrane
is more closely related to molecular interactions on the surface
rather than in the interior.
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ref.2
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Authors
Woolf TB. Roux B.
Title
MOLECULAR DYNAMICS SIMULATION OF THE GRAMICIDIN CHANNEL IN
A PHOSPHOLIPID BILAYER
Source
Proceedings of the National Academy of Sciences of the United States of
America. 91(24):11631-11635, 1994 Nov 22.
KeyWords Plus
Nuclear-magnetic-resonance. Lipid bilayer. Transbilayer helices. Chain
conformation. Crystal-structures. Ion channel. Membranes. Model.
Resolution. Raman.
Abstract
A molecular dynamics simulation of the gramicidin A channel in an explicit
dimyristoyl phosphatidylcholine bilayer was generated to study the details
of lipid-protein interactions at the microscopic level. Solid state NMR
properties of the channel averaged over the 500-psec trajectory are in
excellent agreement with available experimental data. In contrast with the
assumptions of macroscopic models, the membrane/solution interface region
is found to be at least 12 Angstrom thick. The tryptophan side chains,
located within the interface, are found to form hydrogen bonds with the
ester carbonyl groups of the lipids and with water, suggesting their
important contribution to the stability of membrane proteins. Individual
lipid-protein interactions are seen to vary from near 0 to -50 kcal/mol.
The most strongly interacting conformations are short-lived and have a
nearly equal contribution from both van der Waals and electrostatic
energies. This approach for performing molecular dynamics simulations of
membrane pro teins in explicit phospholipid bilayers should help in
studying the structure, dynamics, and energetics of lipid-protein
interactions. [References: 33]
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ref.3
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Authors
Bassolinoklimas D. Alper HE. Stouch TR.
Title
MECHANISM OF SOLUTE DIFFUSION THROUGH LIPID BILAYER MEMBRANES
BY MOLECULAR DYNAMICS SIMULATION
Source
Journal of the American Chemical Society. 117(14):4118-4129,
1995 Apr 12.
KeyWords Plus
Phospholipid monolayer. Computer-simulation. Water. Lecithin.
Polymers. Behavior. Permeability. Coefficients. Interphases.
Transport.
Abstract
This study extends previous studies of the mechanism of small molecule
diffusion through lipid membranes. Atomic level molecular dynamics
simulations of over 4 ns of benzene in fully hydrated
dimyristoylphosphatidylcholine (DMPC) bilayers were performed at four
different temperatures above the gel-to-la phase transition temperature.
These studies confirm previous observations that small solutes diffuse at
different rates in different locations in the bilayer. This difference in
diffusion is likely to be due to ''jumps'' (single, large movements)
between voids which are most common in the center of the bilayer. The
benzene molecules appear to favor different regions of the bilayer at
different temperatures. Although at 320 K the solutes show no regional
preference, at 310 K they migrate to the center of the bilayer, while at
340 K they reside mostly near the head group region. This correlates with
the distribution of free volume which concentrates at the bilayer center
at low temperature but becomes more diffuse at higher temperatures. The
mechanism of the diffusional process was found to be complex. Not only
does the rate of diffusion depend on location within the bilayer, but the
characteristics of this process appear to respond to temperature changes
differently in the different regions of the bilayer. Only short time
motions are dependent directly on the temperature. Longer time motions
depend additionally on the size and availability of voids and the rate of
torsional isomerization of the lipid molecules. It was found that an
increase in kinetic energy was not always coincident with a jump; some
jumps may be passive processes. This study provides further evidence that
the interior of lipid bilayer membranes is not a homogeneous system
analogous to pure alkane. Rather it is a structured system with different
properties depending on the distance from the lipid/water interface.
[References: 47]
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ref.4
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Authors
Huang P. Loew GH.
Title
INTERACTION OF AN AMPHIPHILIC PEPTIDE WITH A PHOSPHOLIPID
BILAYER SURFACE BY MOLECULAR DYNAMICS SIMULATION STUDY
Source
Journal of Biomolecular Structure & Dynamics. 12(5):937-956, 1995 Apr.
KeyWords Plus
Corticotropin-releasing-factor. Lipid bilayer. Computer-simulation.
Monte-carlo. Liquid-crystal. Hydrophobic peptides. Secondary
structures. Potential functions. Sodium octanoate. Water.
Abstract
Corticotropin-releasing factor (CRF) is the principal neuroregulator of
adrenocorticotropic hormone (ACTH) secretion, Previous experiments have
demonstrated that CRF binds avidly to the surface of single egg
phosphatidylcholine vesicles and its amphiphilic secondary structure might
play an important role in the function. In this study, the interaction of
the residues 13-41 in human CRF with the surface of a DOPC bilayer was
investigated by molecular dynamics (MD) simulation in order to understand
the role of the membrane surface in the formation of the amphiphilic a
helix as well as to determine the effects of the peptide on the lipid
bilayer. The model used included 60 DOPC molecules, 1 helical peptide
(CRF(13-41)) on the bilayer surface, and explicit waters of solvation in
the lipid polar head group regions, together with constant-volume periodic
boundary conditions in three dimensions. The MD simulation was carried out
for 510 ps. In addition, CRF(13-41), initially in a helical form, was
simulated ill vacuo as a control. The results indicate that while it was
completely unstable in vacuo, the peptide helical form was generally
maintained on the bilayer surface, but with distortions near the terminal
ends. The peptide was confined to the bilayer headgroup/water region,
similar to that reported from neutron diffraction measurement of
tripeptides bound to the phosphatidylcholine bilayer surface (Ref 1). The
amphiphilicity of the peptide marched that of the bilayer headgroup
environment, with the hydrophilic side oriented toward water and the
hydrophobic side making contact with the bilayer hydrocarbon core. These
results support the hypothesis that the amphiphilic environment of a
membrane surface is important in the induction of peptide amphiphilic
alpha-helical secondary structure. Two major effects of the peptide on the
lipids were found: the first CH2 segment in the lipid chains was
significantly disordered and the lipid headgroup distribution was
broadened towards the water region. [References: 69]
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Morio Murakami
Molecular Chemistry Laboratory
Pharmaceutical Research Division
Takeda Chemical Industries, LTD.
2-17-85, Jusohonmachi, Yodogawa-ku, Osaka 532, JAPAN
E-mail. murakami -8 at 8- lab.takeda.co.jp
FAX 81-6-300-6306
TEL 81-6-300-6618
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