On 8/22/12 9:54 AM, Albert wrote:
hello Justin:
thanks for reply.
I've checked this residue, it is close to protein but I am still curious for
the value with 3.88. Even we also observe something 11, 13 which are the same
weired to me. here is the screen shot for this residue.
https://dl.dropbox.com/u/56271062/1.jpg
I can't tell anything from this angle. Lipids will sample configurations that
lead to their expansion and contraction within the bilayer plane over time. An
individual lipid in a single snapshot simply represents one possible value
within a distribution of values that might be observed. Other lipids and
molecules near the interface will affect its individual APL.
-Justin
thanks again for comments
Albert
On 08/22/2012 03:16 PM, Justin Lemkul wrote:
On 8/22/12 9:12 AM, Albert wrote:
hello Justin:
thanks for reply.
I've read both the paper and manual script. As indicated from the output, I
found the following line:
368 4.295 3.8840018217
I just wondering how could it possible fro residue 368 with a value of 3.88?
My guess would be that this particular lipid is probably bound very tightly to
some protein residue, which leads to the protein and lipid both contributing
to the lateral area in that region. In this case, the protein contributes more
area than the lipid does. You should look at the coordinate file and see what
this residue is doing.
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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