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Side chain orientation/dynamics in time
- z.sichaib
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4 years 1 week ago #8488
by z.sichaib
Side chain orientation/dynamics in time was created by z.sichaib
Dear Martini users,
I have research & technical related question:
I have a coarse-grained trajectory with Martini Force Field of a protein (5 transmembrane helices) embedded in a bilayer with 6 types of lipids.
I am interested in lipid-protein interactions.
I would like to characterize the side-chain dynamics/orientation of some key residues in time:
* if their side chains are pointing toward the membrane, ---> in this case, they can interact with the lipids
* or point toward the opposite side (inside of the protein/buried), ---> interaction with the lipids is not possible.
Is there a way to characterize this? a quantity to measure?
Thank you in advance for your help.
Best,
Zeineb
I have research & technical related question:
I have a coarse-grained trajectory with Martini Force Field of a protein (5 transmembrane helices) embedded in a bilayer with 6 types of lipids.
I am interested in lipid-protein interactions.
I would like to characterize the side-chain dynamics/orientation of some key residues in time:
* if their side chains are pointing toward the membrane, ---> in this case, they can interact with the lipids
* or point toward the opposite side (inside of the protein/buried), ---> interaction with the lipids is not possible.
Is there a way to characterize this? a quantity to measure?
Thank you in advance for your help.
Best,
Zeineb
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