Dear all, I would to acknowledge everyone that replied to my post, both privately and to the BB, for the very useful comments and suggestions. Here is my conclusion so far: Taking into consideration especially the planarity resulting from the presence of double bonds, it seems that indeed there is only one unsaturation - at position 11 - which suggests the fatty acid identity as the vaccenic acid or (11-cis)-octadecanoic acid, very frequent in E. coli. Cis conformations at positions 5, 7, 9 and 13 remain, but all modeled as single bonds now. Plus, the extra group is well explained by a glycerol molecule. If it is actually a glycerol esterified at more than one position, or even a phospholipid, we cannot tell from the map. I need to read a little more about it to learn what is plausible to propose, especially in regards to an actual function for this protein. Mass spec and NMR are due soon, anyways. Thanks once again and kind regards, -Andre.
De: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Em nome de Uma Katre Enviada em: sexta-feira, 4 de outubro de 2013 18:12 Para: CCP4BB@JISCMAIL.AC.UK Assunto: Re: [ccp4bb] Identity of a Bacterial lipid Perhaps this will help- these people used mass spectrometry to identify the lipid. The expression system was E. coli and the lipid was 18-carbon cis-vaccenic acid. Detection and removal of an artefact fatty acid from the binding site of recombinant Bombyx mori pheromone-binding protein. Oldham NJ<http://www.ncbi.nlm.nih.gov/pubmed?term=Oldham%20NJ%5BAuthor%5D&cauthor=true&cauthor_uid=11418499>, Krieger J<http://www.ncbi.nlm.nih.gov/pubmed?term=Krieger%20J%5BAuthor%5D&cauthor=true&cauthor_uid=11418499>, Breer H<http://www.ncbi.nlm.nih.gov/pubmed?term=Breer%20H%5BAuthor%5D&cauthor=true&cauthor_uid=11418499>, Svatos A<http://www.ncbi.nlm.nih.gov/pubmed?term=Svatos%20A%5BAuthor%5D&cauthor=true&cauthor_uid=11418499>. Chem Senses.<http://www.ncbi.nlm.nih.gov/pubmed/11418499?dopt=Abstract> 2001 Jun;26(5):529-31. Uma. -- Uma Katre Columbus, IN 47201 ________________________________ From: Andre Luis Berteli Ambrosio <andre.ambro...@lnbio.cnpem.br<mailto:andre.ambro...@lnbio.cnpem.br>> To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Sent: Thursday, October 3, 2013 8:42 AM Subject: [ccp4bb] Identity of a Bacterial lipid 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
