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multidomain protein
- gbalogh
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8 years 7 months ago #4885
by gbalogh
multidomain protein was created by gbalogh
Hello. I would like to study the conformational changes of a large (>700 amino acids) soluble protein using MD simulations. The protein consists of four domains connected with flexible linker regions. The protein can undergo significant conformational changes, but the domains can be considered "rigid". Is MARTINI suitable for studying such a system?
Thanks in advance.
Thanks in advance.
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- helgi
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8 years 5 months ago #5212
by helgi
Replied by helgi on topic multidomain protein
Hello, hello,
It is really hard to say without more information on your system, so very short answer, it depends. In Martini the protein secondary structure is fixed and can not change during your simulation. But if in your case the secondary structure changes are not important but rather rigged protein parts that are moving / re-organizing. Then you can use Martini – probably you would use an elastic network on the rigged protein parts but not on the unstructured linkers between them.
Cheers,
- Helgi
It is really hard to say without more information on your system, so very short answer, it depends. In Martini the protein secondary structure is fixed and can not change during your simulation. But if in your case the secondary structure changes are not important but rather rigged protein parts that are moving / re-organizing. Then you can use Martini – probably you would use an elastic network on the rigged protein parts but not on the unstructured linkers between them.
Cheers,
- Helgi
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