Dear all,
I'm trying to determine the binding energy of a membrane protein to the
membrane. Ultimately I need to compare the binding energy of the same
protein to two similar types of lipid, the hypothesis being that there
should be a slight difference.
I considered two options: alchemical
On 5/8/14, 3:38 PM, Victor Sojo wrote:
Dear all,
I'm trying to determine the binding energy of a membrane protein to the
membrane. Ultimately I need to compare the binding energy of the same
protein to two similar types of lipid, the hypothesis being that there
should be a slight difference.
Thanks so much, Justin!
Your comments and paper are very helpful indeed. With by eye I meant I
just need to know whether one is bigger than the other, but you're complete
right: no need to speak in qualitative terms when I can quantitatively
determine DeltaDeltaG.
Thanks again!
Victor Sojo
On 2/23/14, 10:36 AM, sojovictor wrote:
Dear all,
I would like to find the difference in the energy of binding or insertion of
a protein into two different types of phospholipid membranes (plus water and
ions). i.e., my hypothesis is that the energy should be lower with one type
of membrane
Thanks, Justin! That's really helpful indeed.
You are correct, I want to know what's the energy change in replacing one
lipid with the other, hypothesising that going to the wrong lipid will
imply an energetic cost.
Via umbrella sampling, I would thus:
1) Set up a full system with protein,
On 2/23/14, 11:54 AM, sojovictor wrote:
Thanks, Justin! That's really helpful indeed.
You are correct, I want to know what's the energy change in replacing one
lipid with the other, hypothesising that going to the wrong lipid will
imply an energetic cost.
Via umbrella sampling, I would thus:
