When USA budget is back :-\ you may give a try to :
http://webbook.nist.gov/chemistry/
It helped me several times, very intuitive, I use just a formula for a search,
it also accept a wild character for unknown number of atoms.
FF
Dr Felix Frolow
Professor of Structural Biology and Biotechnology, Department of Molecular
Microbiology and Biotechnology
Tel Aviv University 69978, Israel
Acta Crystallographica F, co-editor
e-mail: mbfro...@post.tau.ac.il
Tel: ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608
On Oct 3, 2013, at 16:33 , Andre Luis Berteli Ambrosio
andre.ambro...@lnbio.cnpem.br wrote:
Dear Michael, thank you for the prompt reply.
The host was indeed E. coli.
From what I have been reading I completely agree on the lack of biological
support for such a molecule but still the map seems very convincing of the
presence of cis bonds at such positions… Could such a conformation arise due
to something other than unsaturations?
We are working on isolating the lipid from the purified protein I will sure
follow your suggestions on the additional characterization of this molecule,
especially adding NMR analysis to it. Thanks also for referencing the
literature.
With kind regards,
-Andre.
De: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Em nome de R. M.
Garavito
Enviada em: quinta-feira, 3 de outubro de 2013 10:16
Para: CCP4BB@JISCMAIL.AC.UK
Assunto: Re: [ccp4bb] Identity of a Bacterial lipid
Dear Andre,
It always impressive to see a near atomic resolution structure with a bound
lipid. Congratulations. However, to identify what lipid you have requires a
bit more analysis than just looking in databases. First, what is the
bacterium you are using as the host? If it is E. coli, then the known lipids
are very well characterized. Also, VERY FEW E. coli lipids have sites of
unsaturation, and virtually polyunsaturated fatty acids (PUFAs) have one sp3
carbon in between the double bonds (arising from the mechanisms of
biosynthesis). So your proposed structure doesn't seem right from a
biological sense, which makes looking into databases unproductive.
However, since you solved the structure, do your produce enough protein to
isolate the putative lipid by simple TLC? With the help of a good lipid lab
you should be able to tell what it with greater certainty. Try to get a copy
of Techniques of Lipidology by Morris Kates from Elsevier. Although it is
old school stuff, it will help you isolate enough for mass spec and NMR
analysis.
Good luck,
Michael
R. Michael Garavito, Ph.D.
Professor of Biochemistry Molecular Biology
603 Wilson Rd., Rm. 513
Michigan State University
East Lansing, MI 48824-1319
Office: (517) 355-9724 Lab: (517) 353-9125
FAX: (517) 353-9334Email: rmgarav...@gmail.com
On Oct 3, 2013, at 8:42 AM, Andre Luis Berteli Ambrosio wrote:
Dear colleagues,
We have just determined the crystal structure (at 1.1 A max resolution) of a
recombinant protein that crystallized in complex with a leftover bacterial
lipid, the full identity of which we are currently struggling to identify.
Please see attached (3 views of the molecule).
The map strongly suggests an 18-carbon long polyunsaturated fatty acid, with
5 conjugated unsaturations (at positions 5, 7, 9, 11 and 13, all cis),
covalently bound to some extra chemical group at is polar head. This extra
group seems to be comprised of 4 (5?) atoms, though I am afraid cannot tell
if it extends further into not-so-well-structured atoms.
Myself and a student have spent the last two days searching on the web for
possible matches for this ligand without any success. For instance, we have
generated a SMILES formula for the aliphatic tail comprising the
unsaturations and browsed for similar compounds at PubChem with different
similarity cutoffs, but nothing seemed to resemble the complete molecule.
We would appreciate if you could make any comments on the nature of this
ligand or perhaps suggest your favorite computational tools. We will perform
mass spec on it soon.
Thank you beforehand.
Andre LB Ambrosio, DSc
Laboratório Nacional de Biociências - LNBio
CNPEM, Brazil
FA-density.png
