[gmx-users] sn1 and sn2 chains of popc

[minnale]

Thanks alot Justin for your detailed explanation.
On Mon, 08 Sep 2008 Justin A.Lemkul wrote :
>
>
>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
>
>========================================
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