- Posts: 11
Receptor-ligand interactions
- edroaldo
-
Topic Author
- Offline
- Fresh Boarder
Less
More
11 years 9 months ago #1055
by edroaldo
Receptor-ligand interactions was created by edroaldo
Dear MARTINI users,
I would like to know if MARTINI might be used to study the interaction between a protein and a peptide ligand and how would I approach that systems, for example, using elastic networks ...
Thank you very much.
I would like to know if MARTINI might be used to study the interaction between a protein and a peptide ligand and how would I approach that systems, for example, using elastic networks ...
Thank you very much.
Please Log in or Create an account to join the conversation.
- edroaldo
-
Topic Author
- Offline
- Fresh Boarder
Less
More
- Posts: 11
11 years 9 months ago #1056
by edroaldo
Replied by edroaldo on topic Receptor-ligand interactions
Dear all,
I will provide more details about my problem. I would like to simulate the extracellular domain of a integrin protein and their interactions with the adhesion peptide RGD. I would like to know if it is possible verify the association of the RGD peptide with its high affinity position in the integrin. I know that conformational changes might occur during these interactions and I also reading the JCTC paper "Combining an Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition".
I really appreciate any advice.
Thank you very much!
I will provide more details about my problem. I would like to simulate the extracellular domain of a integrin protein and their interactions with the adhesion peptide RGD. I would like to know if it is possible verify the association of the RGD peptide with its high affinity position in the integrin. I know that conformational changes might occur during these interactions and I also reading the JCTC paper "Combining an Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition".
I really appreciate any advice.
Thank you very much!
Please Log in or Create an account to join the conversation.
- siewert
-
- Offline
- Admin
Less
More
- Posts: 61
11 years 9 months ago #1057
by siewert
Replied by siewert on topic Receptor-ligand interactions
The answer is yes/no/maybe!
Yes, because binding of a peptide to a protein has been simulated before with Martini in case of the transport receptor OppA, see: R.P.A. Berntsson, M.K. Doeven, F. Fusetti, R.H. Duurkens, D. Sengupta, S.J. Marrink, A.M.W.H. Thunnissen, B. Poolman, D.J. Slotboom. The structural basis for peptide selection by the transport receptor OppA. EMBO J., 28:1332-1340, 2009. (open access).
No, because the interaction strength of soluble proteins appears to be overestimated with Martini, i.e. proteins are too sticky and get easily trapped in non-realistic bound states. We are currently working on improving Martini in this respect.
Maybe, it might work better in some cases and the only way to find out is run the simulation ... Consider using polarizable water as well.
Yes, because binding of a peptide to a protein has been simulated before with Martini in case of the transport receptor OppA, see: R.P.A. Berntsson, M.K. Doeven, F. Fusetti, R.H. Duurkens, D. Sengupta, S.J. Marrink, A.M.W.H. Thunnissen, B. Poolman, D.J. Slotboom. The structural basis for peptide selection by the transport receptor OppA. EMBO J., 28:1332-1340, 2009. (open access).
No, because the interaction strength of soluble proteins appears to be overestimated with Martini, i.e. proteins are too sticky and get easily trapped in non-realistic bound states. We are currently working on improving Martini in this respect.
Maybe, it might work better in some cases and the only way to find out is run the simulation ... Consider using polarizable water as well.
Please Log in or Create an account to join the conversation.
- edroaldo
-
Topic Author
- Offline
- Fresh Boarder
Less
More
- Posts: 11
11 years 9 months ago #1058
by edroaldo
Replied by edroaldo on topic Receptor-ligand interactions
Ok. Thank you very much!
Please Log in or Create an account to join the conversation.
Time to create page: 0.099 seconds