Subject: CCL:Summary of "MD calculation of biological membranes"

From: [email-masked] (Morio Murakami)
Date: Fri, 11 Aug 1995 18:52:55 +0900

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.   [email-masked]
   FAX         81-6-300-6306
   TEL         81-6-300-6618 
*************************************************