Hey there!
I'm using gromacs software for ligand binding simulation. I want to investigate structural change of protein after complex formation.
How long the MD should last to reach the most reasonable results? Should I consider the real process lasting? How can I estimate that?
THANKS
Dear Stefan,
Seriously? I thought that it is in the range of nanoseconds? Because that is how much time needed for domain movement is:
http://www.ch.embnet.org/MD_tutorial/pages/MD.Part1.html#Introduction
Here is some article to confirm the time needed for domain movement:
http://www.sciencedirect.com/science/article/pii/S0014579303008664
http://www.sciencedirect.com/science/article/pii/S0006349503747201
Regards,
Radif
Dear Stefan,
Seriously? I thought that it is in the range of nanoseconds? Because that is how much time needed for domain movement is:
http://www.ch.embnet.org/MD_tutorial/pages/MD.Part1.html#Introduction
Here is some article to confirm the time needed for domain movement:
http://www.sciencedirect.com/science/article/pii/S0014579303008664
http://www.sciencedirect.com/science/article/pii/S0006349503747201
Regards,
Radif
it all depends on the protein you are using for structural studies...intially try for 50 or 70 nanosecond to see structural changes.. but if your protein doesn't show any changes during that run...you may need to extend the run upto 100 or may be 150 nanoseconds...
Thanks Mr. Sharma for your answer but my ligand is too small and it may cause no obvious structural change! your instruction may put me in an indecision situation.
Mr. Radifar
In this case the first text you have linked to your answer verified the Stefan answer. I'm looking for secondary structure motions and transition.
Thanks for your help
Rigid Body Motions (1 to 10Å, 10-9 to 1s) --> that's equivalent to 1 ns - 1 s
Homa, there is something I would like to confirm. This protein that you simulate, is it an enzyme or receptor? If it is a receptor then the binding effect could bring change of structure not only in the vicinity of the ligand but also in the effector area (the part of receptor that responsible for the signal transduction).
I asked this because I remembered how the agonist bind GPCR and could change the structure in the effector area. And I thought that this kind of change would require longer time. And I tried to look up the elucidation of GPCR activation to find an excellent article:
http://www.sciencedirect.com/science/article/pii/S0092867413000111
Turns out that such change takes microsecond, so Stefan could be right in some cases, sorry Stefan!
So once again, it depends on your protein type, is it a receptor or an enzyme?
Dear Mr. Radifar
My protein is neither receptor nor enzyme. It is kind of carrier protein and I want to be sure it could interact with its native receptor after ligand binding.
Thanks for your helpful links
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