From mwd@alamos.cray.com Thu Dec 8 14:18:49 1994 Received: from timbuk.cray.com for mwd@alamos.cray.com by www.ccl.net (8.6.9/930601.1506) id NAA13958; Thu, 8 Dec 1994 13:44:47 -0500 Received: from pajarito.cray.com (mwd@pajarito.cray.com [128.162.56.9]) by timbuk.cray.com (8.6.9/8.6.9M) with SMTP id MAA07915 for ; Thu, 8 Dec 1994 12:44:43 -0600 Received: by pajarito.cray.com (5.0/CRI-5.13) id AA02207; Thu, 8 Dec 1994 11:44:39 +0700 From: mwd@alamos.cray.com (Mark Dalton) Message-Id: <9412081844.AA02207@pajarito.cray.com> Subject: Summary: Phospholipid 3d structure and forces To: chemistry@ccl.net Date: Thu, 8 Dec 1994 11:44:37 -0700 (MST) X-Mailer: ELM [version 2.4 PL22] Content-Type: text Content-Length: 7758 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 mchee@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@oxmol.com (Merk Na Chee) ------------------------------------- 2. From DCAMPER@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@dowelanco.com 3. From ccevc16@pinar1.csic.es Wed Nov 30 02:38:08 1994 From: Victor Cruz 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@duc.auburn.edu Tue Nov 29 18:03:54 1994 From: newhoir@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@alex.monsanto.com Thu Dec 1 15:02:15 1994 From: wchutt@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@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. | | | \ | Los Alamos,NM 87544 CH2-C-COOH //\ ---C--CH2-C-COO C-CH2-C-COO mwd@cray.com | | || || | // | NH2 \\/ \ / CH NH3 O NH3 NH URL = http://lenti.med.umn.edu/~mwd/mwd.html