Subject: Summary: Phospholipid 3d structure and forces

From: [email-masked] (Mark Dalton)
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?

---------------------< End of message >------------------------------
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 [email-masked] 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: [email-masked] (Merk Na Chee)
   -------------------------------------

2. From [email-masked] 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
   [email-masked]

3. From [email-masked] Wed Nov 30 02:38:08 1994
   From: Victor Cruz <[email-masked]>
   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 [email-masked] Tue Nov 29 18:03:54 1994
   From: [email-masked] (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 [email-masked] Thu Dec  1 15:02:15 1994
   From: [email-masked] (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
   [email-masked]
   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
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