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Are proteins flexible around kinked TMs?
- michaelvlevine
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7 years 2 months ago #7080
by michaelvlevine
Are proteins flexible around kinked TMs? was created by michaelvlevine
Hi all,
I am thinking about running a CG simulation of a membrane protein that I study. The protein has a kinked TM and flexibility around the kink is known to be important. Will the TM be flexible around the kink using the MARTINI forcefield? Or will the kink be constrained to fluctuate around the crystallographic angle?
Thanks!
I am thinking about running a CG simulation of a membrane protein that I study. The protein has a kinked TM and flexibility around the kink is known to be important. Will the TM be flexible around the kink using the MARTINI forcefield? Or will the kink be constrained to fluctuate around the crystallographic angle?
Thanks!
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- bart
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7 years 2 months ago #7081
by bart
Replied by bart on topic Are proteins flexible around kinked TMs?
Hi Michael,
The CG Martini force field works rather well for membrane proteins. However, as you state, the structure is usually maintained by an elastic network. Therefore the protein will not be able to deviate much from its initial structure. In you case it seems you know quite well where the hinge is in your protein and by removing the elastic network around the hinge domain movement is free again. This could be a good approach, but requires careful control of the elastic network. For protein I usually use the ELNEDYN network, but I heard that martini without elastic network can work for membrane proteins. Therefore I would advice to also see if you protein maintains is structural integrity if you apply no elastic network at all.
The CG Martini force field works rather well for membrane proteins. However, as you state, the structure is usually maintained by an elastic network. Therefore the protein will not be able to deviate much from its initial structure. In you case it seems you know quite well where the hinge is in your protein and by removing the elastic network around the hinge domain movement is free again. This could be a good approach, but requires careful control of the elastic network. For protein I usually use the ELNEDYN network, but I heard that martini without elastic network can work for membrane proteins. Therefore I would advice to also see if you protein maintains is structural integrity if you apply no elastic network at all.
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- mnmelo
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7 years 2 months ago #7085
by mnmelo
Replied by mnmelo on topic Are proteins flexible around kinked TMs?
Also, depending on the secondary structure, you may be able to get away by just restraining the babckbone bonded parameters, in which case the hinges will have more freedom. See, for instance, the case of the
MscL CG simulations
, which did not require an elastic network.
Typically, an elastic network will be required if you have beta sheets. Structures with helix-only domains should be fairly stable using only the bonded restraints.
Good luck,
Manel
Typically, an elastic network will be required if you have beta sheets. Structures with helix-only domains should be fairly stable using only the bonded restraints.
Good luck,
Manel
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