Summary: Phospholipid 3d structure and forces
- From: mwd :
at : alamos.cray.com (Mark Dalton)
- Subject: Summary: Phospholipid 3d structure and forces
- Date: Thu, 8 Dec 1994 11:44:37 -0700 (MST)
Hi! Here is what I have heard/found about Phospholipids 3d structures
and forces/characteristics (which I need find values for each characteristic
of membrance components). The idea is to model a Cell (to be freely
available for non-profit research).
(Also I am working on writing a Virtual Cell Bio. Course that will be
available via WWW/Mosaic - I need images still, clickable biology).
I hope this can be of help to others also.
Thanks!
Mark
Original Post:
Subject: CCL:Phospholipid 3d structure and forces
Date: Tue, 29 Nov 1994 17:19:16 -0600 (CST)
Hi! I was wondering if anyone has suggestions or know of places where I
could get 3D structures (PDB format) of (cell membrane) phospholipids,
also if there are any formulas/information on strengths and rate of
decrease of the hydrophilic/phobic interactions, pH and ionic strength
of various phospholipids, proteins.
Basically, I am looking for good, accurate and complete information
of characteristics/properties of the various parts of cell membranes.
Does anyone have good references?
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Just so it is clear, I am doing this on my own time, i.e. it is not
part of my job. So Cray is not responsible for my actions,comments,
or ideas.
Of course the Biochem. and Cell Bio. textbooks.
Here is what I have found (in the Cray Channels Volume 16, Number 1):
Terry Stouch's work:
1. Stouch, Terry R., "Lipid Membrane Structure and Dynamics Studied by
All-Atom Molecular Dynamics Simulations of Hydrated Phospholipid
Bilayers" Molecular Simulations, Vol. 10, No 2-3. pp. 317-345.
2. Stouch, Terry R., Howard E. Alper and Donna Bassolino,
"Supercomputing
Studies of Biomembranes" International Journal of Supercomputer
Appllications, 1993.
3. Alper, Howard E., Donna Bassolino, and Terry R. Stouch, "Computer
Simulations of a Phospholipid Monolayer-Water System: The influence
of Long Range Forces on Water Structure and Dynamics" Journal of
Chemical Physics, Vol 98, No. 12, pp. 9798-98-7, 1993.
4. Alper, Howard E., Donna Bassolino, and Terry R. Stouch, "The
Limiting
Behavior of Water Hydrating a Phospholipid Monolayer: A Computer
Simulation Study," Journal of Chemical Physics, Vol. 99, No. 7,
pp. 5547-5559, 1993.
5. Stouch, Terry R., Keith B. Ward, Amanda Altieri, Arnold T. Hagler,
"Simulation of Lipid Crystals: Characterization of Potential Energy
Functions and Parameters for Lecithin Molecules," Journal of
Computational Chemistry, Vol. 12, No. 8, pp. 1033-1046, 1991.
6. Stouch, Terry R. and Donald E. Williams, "On the Conformational
Derived Charges: Studies of the Fitting Procedure," Journal of
Computational Chemistry, Vol. 14, No. 7, pp. 858-866, 1993.
7. Liang, Congxin, Carl S. Ewig, Terry R. Stouch, and Arnold T. Hagler,
"Ab Initio Studies of Lipid Model Species. 1. Dimethylphosphate and
Methylpropylphosphate Anions," Journal of American Chemical Society,
Vol. 115, No. 4, pp. 1537-1545, 1993.
8. Stouch, Terry R. and Donald E. Williams, "Conformational Dependence
of Electrostatic Potential Derived Charges of a Lipid Headgroup:
Glycerylphosporylcholine," Journal of Computational Chemistry, Vol. 13,
No. 5, pp. 622-632, 1992.
9. Williams, Donald E. and Terry R. Stouch, "Characterization of Force
Fields for Lipid Molecules: Applications to Crystal Structures,"
Journal of Computational Chemistry, Vol. 14, No. 8, 1993.
10. Bassolino, Donna, Howard E. Alper, and Terry R. Stouch, "Solute
Diffusion in Lipid Bilayer Membranes: An Atomic Level Study by
Molecular Dynamics Simulation," Biochemistry, Nov. 30, 1993.
Responses:
1. From mchee : at : oxmol.com Wed Nov 30 08:53:54 1994:
Oxford Molecular has a package called Iditis which validates the PDB files
from BrookHaven and derives additional properties for each protein (from
macromolecular to atom level information). Thus, users will be able to
obtain all sequence and structurel related information about any protein
in the database.
Anyway, in the latest release of the data, which corresponds to the April
1994 release of Brookhaven, there are 4 entries of the same phospholipid
protein - 1AIN (Annexin I from Human), 1ALA (Annexin V from chicken), 1AVH
(Annexin V Hexagonal crystal), 1AVR(Annexin V Rhombohedral crystal). The
last two are from human placenta. All are Ca-binding.
If you are interested in getting more information about Iditis, please
contact the number below.
Regards,
Merk-Na
-------------------------------------
Merk Na Chee, Ph.D.
Applications and Support
Oxford Molecular Inc.
Springfield, VA 22151
E-mail: mchee : at : oxmol.com (Merk Na Chee)
-------------------------------------
2. From DCAMPER : at : elinet1.dowelanco.com Wed Nov 30 06:31:29 1994
Subject: lipids
I don't have any specific reference at hand but I know
Terry Stouch at Bristol Meyers Squib was involved in
extensive modeling of lipid bylayers and I believe molecules
within these lipids. This may be a place to start.
Debby Camper
dcamper : at : dowelanco.com
3. From ccevc16 : at : pinar1.csic.es Wed Nov 30 02:38:08 1994
From: Victor Cruz <ccevc16 : at : pinar1.csic.es>
Subject: Phospholipids
You can find geometrical information at the Cambridge Crystallographic
Database. In particular I am working with DLPE
(dilauroil-phosphatidyl-choline) crystal structure taken from:
Hitchcock,P.B.,et al.,Proc. Nat. Acad Sci. 71:3036(1974).
Cambridge Database can be get from: Dr. Olga Kennard
CCDC,University Chemical Laboratory,Lensfield Road,Cambridge CB2 1EW,U.K.
4. From newhoir : at : duc.auburn.edu Tue Nov 29 18:03:54 1994
From: newhoir : at : duc.auburn.edu (Irene Newhouse)
Subject: Re: CCL:Phospholipid 3d structure and forces
There's a big review on phospholipid structures by Irmin Pascher in
Biochimica et Biophysica Acta that came out at the end of 1992; vol 1113,
pp 339-73.
Irene Newhouse
5. From wchutt : at : alex.monsanto.com Thu Dec 1 15:02:15 1994
From: wchutt : at : alex.monsanto.com (Bill C Hutton)
Subject: phospholipds
The only 3D data I know of is an old X-ray structure. I do not have the
referene here, but I could bring it in. This is a very well known
paper and is used in all of the monographs and reviews of phospholipid
membranes. Some simulation work (computational chemistry) has been done
as well.
Also, I have dozens of non-propriatary NMR NOESY spectra of
phospholpipd vesicles. No one really understands some of the featurews
in this data. Modeling could really help out. This data could go a long
way towards understanding curved bilayer structure and dynamics. I have
not had the time or incentive to carefully evaluate all of the data.
But is is quite interesting. Some early work can be found in J. Amer.
Chem. Soc. 1985, 107 pp 1530-37. There are later papers as well but
again I do not have the references here.
**********************************************************************
W.C. Hutton, Monsanto Company, Corporate Research
wchutt : at : monsanto.com
This message does not necessarily reflect the views of Monsanto Company
or, now that I think of it, anyone else.
**********************************************************************
--
Mark Dalton CH3-S-CH2 H H O H
Cray Research,Inc. | | | \ |
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