[gmx-users] sn1 and sn2 chains of popc

[Justin A. Lemkul]

minnale wrote:
> Thanks Justin for your reply
> you mean to say that C32 of glycerol involves in the palimotyl chain 
> formation so call as sn1 chain similarly C12,C13 of glycerol involves in 
> the oleyl chain formation so call as sn2.
> Am I correct?

More or less, let's just get a few things straight.  Numbering like C32, C12, 
C13, etc. is a scheme devised to give sensible atomic numbering to all atoms in 
a 50 (or more)-atom lipid, but is not the same numbering scheme applied in 
conventional lipid numbering from Biochemistry lessons.  To me, "C32" has 
absolutely no bearing on "sn-1."

Look at the structure of glycerol:

	CH2OH
	|
     HO--C--H
	|
	CH2OH

The second carbon is a chiral center, and (as I was taught in Biochemistry), 
that is where we derive the "sn" nomenclature: sn-2 = "stereospecific number 2."

The other carbons are given the obvious numbers of 1 and 3.  By convention, the 
phosphate headgroup is assigned to carbon 3.  Therefore, chain 1 is on the 
"sn-1" carbon, and chain 2 is on "sn-2."

-Justin

> Thanks in advance.
> 
> On Mon, 08 Sep 2008 Justin A.Lemkul wrote :
>  >
>  >
>  >minnale wrote:
>  >>  Hi all,
>  >>may be this is very basic query
>  >>I want to calculate order parameters of popc. I have found in 
> archives that make sn1.ndx(pamitoyl) and sn2.ndx(oleyl) of popc then 
> feed these files to g_order command. Can anyone tell me that why 
> pamitoyl call as sn1 and oleyl call as sn2?
>  >
>  >It derives from the numbering of the carbons on the glycerol backbone.
>  >
>  >-Justin
>  >
>  >>Thanks for your help.
>  >>
>  >>
>  >>
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>  >-- ========================================
>  >
>  >Justin A. Lemkul
>  >Graduate Research Assistant
>  >Department of Biochemistry
>  >Virginia Tech
>  >Blacksburg, VA
>  >jalemkul[at]vt.edu | (540) 231-9080
>  >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>  >
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================