Transmembrane Protein 3-D Coordinate File Preparation Question?

User discussions
1

Hello I hope you are all doing well.:)

Several transmembrane Pannexin1 3-D coordinate files have been submitted to the PDB, however, I believe all are missing coordinates in some of the Pannexin1 coils and or loops, accordingly I believe it would be best to just ab initio model these portions and then cut and paste these coordinates back into the proper PDB coordinate file before GROMACS simulating would you agree that this would be the best methodology in this case?

Thanks:)
Joel

2

I would model the loops with the rest of the protein there. If you just model the structure of a polypeptide, there is no guarantee that it is compatible with the remainder of the structure.

3

Hello Justin and thank you for your kind update. The problem is that the protein´s most pivotal domains and residues have been Cryo-EM modeled, accordingly would you find it best then to just use the PDB cryo-EM coordinates as is then when simulating i.e. leaving out the residues without coordinates?

Best,
Joel

4

No, I’m suggesting exactly the opposite - use the existing coordinates and build the missing loops into it. Simulating a fragmented protein makes no sense.

5

Hello and thanks a bunch, would you suggest MODELLER for this?

Best,
Joel

6

I’ve used it a bunch for the same purpose, so it’s a good place to start.

7

Hi ok thanks a bunch:)