GLYCOSCI STRUCTURE E-FLASH 1
December 23 1994
Barry J. Hardy
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MEETINGS
I just attended the Molecular Graphics Society/British Biophysical
Society meeting on Carbohydrates. It was held in London from Dec 19-20
and co-organized by Steve Homans (St. Andrews, Scotland) and Trevor Howe
(Lilly, U.K.). The meeting received financial support from Glaxo, Lilly,
and Unilever. For those interested in industry events: Peter Grootenhuis
(Organon, NL) announced that patents were pending on their anti-thrombin
III regulators and that he would be reporting further on the details in
Anaheim (April 95). There will be a meeting there organized by Al French
on carbohydrate structure as well as numerous computational chemistry
division meetings. Hope to see you there if you are going.
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RASMUSSEN FORCE FIELD ON THE NET
At the MGS/BBS meeting Kjeld Rasmussen announced Internet availability
of his PEF force field for carbohydrates which he has been working on for
20 years. The access information I noted down is as follows:
for force-field and parameter set code, information and help
use anonymous ftp at
lipida.kla.dth.dk (IP number is 129.142.74.20)
Email queries to cff at lipida.kla.dth.dk
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THE WEB
I have recently been preparing some Web pages and participating
in electronic conferencing. You might enjoy browsing my current pages
to get the feel of these activities. This will give you an idea
of the kind of things you would be doing to participate in the '95
electronic glycoscience conference or in preparing pages that the glycosci
group pages could link to.
I have some pages at http://alcyone.pcl.ox.ac.uk/people/barry.html
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PIMS PARAMETERS FROM ANNE IMBERTY
Anne Imberty of Nantes is forwarding the following structural information
to the group:
Dear colleague,
The present letter is to inform the SYBYL users that the set of carbohydrate
parameters (PIM) that we proposed previously to be used with the TRIPOS force
field has now been revised. If you are interested, please have a look
at the following description
AIM OF THE PIM PARAMETERS
As described previously, the carbohydrate parameters have been developed
mainly to be used for study of protein carbohydrates interactions but they
could also be used for comformational analysis of glycans.
NEW FEATURES
Main improvement of the new release are
1/ Corrections of some errors in the previous set of parameters (kindly
indicated by some users)
2/ Fitting of the energy curve for PHI on the most recent ab initio
study performed by Igor Tvaroska (see ref).
3/ Inclusion of parameters for sialic acid
4/ And on the top, to make life simpler, we provide a small library of
monosaccharides which have already proper atom types and proper charges.
This library now include GlcNAc, Man, Gal, GalNAc, Xyl, Fuc and NeuAc
with the several anomers needed to built complex type glycans.
HOW TO USE THESE PARAMETERS
1/ to build glycans :
- from the library. Just use the JOIN MOLECULES (in OTHER TOOLS in the
BUILD/EDIT menu) on the monosaccharides. Then increase the charge on the
connecting C-X carbon, in the C-1_O-1_C-X sequence, by 0.4)... and check
the resulting sum of charges on the whole molecule.
- from existing structures. First, you have to modify the atom types of
your favorite glycan to the PIM ones (see the published description). Then
derived the charges, either by analogy with charges used in library or by
calculating them with MNDO.
2/ to calculate rigid maps : First remove the hydroxylic hydrogens in your
glycan. Then just use the SYSTEMATIC SEARCH option in Sybyl but do not forget
to lower the proposed 'van der Waals radius scale factors' which are too
high. Also, do not include any electrostatic term in the energy calculations.
3/ to calculate relaxed maps : Keep all the atoms and all the
electrostatic and use the GRID SEARCH options. Use a dielectric constant
quite high (> 10) if you dont want to overestimate intramolecular
hydrogen bonds
4/ to study protein carbohydrate interactions : Use the Pullmann method to
calculate the charges on the protein moiety... once you have added all the
hydrogen atoms and use the distance dielectric function in the energy
calculations.
HOW TO GET THE PIM PARAMETERS
The parameters (and library)can be obtained (at no cost !) by sending a
Email or a letter to the adress given at the bottom of this message. I will
send you a binary file (pim.tpd), the ascii equivalents (in case you need
them) and the library of monosaccharides. What I will need to do that is
-either an anonymous account (please provide the TCPIP number)
-or a regular account with a password (also with the number).
If you do not have access to internet, just send your favorite transfer media
(DC6150 Cartridge, 4mm tape or even disquette) and I will mail it back to
you with the parameters.
FUTURE IMPROVEMENTS
As you may have heard in the recent Symposium on Conformational Analysis of
Carbohydrates (ValMorin, 1994) we are working on the parametrization of
sulfate group. A preliminary set of parameters already exist but we
are working on some better ones. If you are interested, please keep in touch.
REFERENCES
- For the new parameters :
Perez S., Meyer C. & Imberty A. (1995) Practical tools for molecular modeling
of complex carbohydrates and their interactions with proteins. In 'Modelling
of Biomolecular Structures and Mechanisms', A. Pullman, J.Jortner & B.
Pullman (eds.) Kluwer Academic Press, Dordrecht, pp 425-444.
- For the old parameters and for charges, atom types and docking procedures :
Imberty A., Hardman K.D., Carver J.P. & Perez S. (1991) Molecular modelling
of protein/carbohydrate interactions. Docking of monosaccharides in the
binding site of Concanavalin A. Glycobiology 1, 456-484
- For the ab-initio energy curve of 2-methoxytetrahydropyran :
Tvaroska I. & Carver J.P. (1994) Ab initio molecular orbital calculation
of carbohydrate model compounds. 2. Conformational analysis of axial and
equatorial 2-methoxytetrahydropyrans. J. Phys. Chem. 98, 9477-9485.
- For some examples of how we used these parameters :
Imberty A., Perez S., Hricovini M., Shah R.n., & Carver J.P. (1993)
Flexibility in a tetrasaccharide fragment from the high mannose type of
N-linked oligosaccharides. Int. J. Biol. Macromol. 15, 17-23
Bara J., Imberty A., Perez S., Imai K., Yachi A & Oriol R. (1993)
A fucose residue can mask the muc-1 epitopes in normal and cancerous
gastric mucosae. Int. J. Cancer 54, 607-613
Imberty A. & Perez S. (1994) Molecular modelling of protein/carbohydrate
interactions. Understanding the specificities of two legume lectins
towards oliogosaccharides. Glycobiology 4, 351-366
Imberty A., Casset F., Gegg C.V., Etzler M.E. & Perez S. (1994)
Molecular modelling of the Dolichos biflorus seed lectin and its specific
interactions with carbohydrates: a-D-N-acetyl-galactosamine, Forssman
disaccharide and blood group A trisaccharide. Glycoconj. J. 11, 400-413
- For some recent reviews of our group about conformations of glycans :
Imberty A., Bourne Y., Cambillau C., Rouge P. & Perez S. (1993)
Oligosaccharide conformation in protein/carbohydrate complexes. Adv.
Biophys. Chem. 3, 71-117.
Perez S., Imberty A. & Carver J.P. (1994) Molecular modeling : An essential
component in the structure determination of oligosaccharides and
polysaccharides. Adv. Comput. Biol. 1, 147-202.
ADDRESS
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* Dr Anne Imberty * *
* Ingenierie Moleculaire * Tel : (33) 40-67-50-98 *
* INRA * Fax : (33) 40-67-50-92 *
* BP 527 * *
* 44026 Nantes cedex 03 * Email : imberty at nantes.inra.fr *
* FRANCE * *
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That's all for '94 folks. See you next year!
Barry J. Hardy
http://alcyone.pcl.ox.ac.uk/people/barry.html
