On 08/22/2012 03:58 PM, Justin Lemkul wrote:
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
hello Justin:
I think I found similar case which was report in g_membed paper by
GERRIT GROENHOF. This paper was released on J Comput Chem 31: 2169–2174,
2010 titled "g_membed: Efficient Insertion of a Membrane Protein into an
Equilibrated Lipid Bilayer with Minimal Perturbation"
in figure 3 of above paper, Gerrit showed that the ALP of POPC is do
something around 54. here you can find the figure
https://dl.dropbox.com/u/56271062/figure3.jpeg
It is also comment that the software for ALP calculation overestimate
the area of protein so that the value is far from pure lipids ALP. The
author also state that the protein itself may also influence lipids
property.
best
Albert
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