Prepping Thrombin to reproduce TIES paper

[AlexW12344]

Hiya,

If I want to prep Thrombin to reproduce the TIES paper what is the best way to include the disulfide bridges? The standard TIES protein prep pipeline with tleap does not add these. How was this protein prepped for the paper? https://pubs.acs.org/doi/abs/10.1021/acs.jctc.0c01179

Cheers, Alex

[apbhati1]

Hey Alex,

In order for tleap to add disulphide bridges, the best way could be to (a) define all of them (SG-SG bonds) in the input PDB after the coordinates (see example provided below for a PDB with three disulphide bridges), and (b) rename all CYS residues involved to CYX. After this, tleap should automatically add disuphide bridges.

"ATOM 3059 O ASN A 446 5.544 47.384 99.520 1.00 46.31 O ATOM 3060 OXT ASN A 446 6.037 45.354 99.711 1.00 0.00 O TER 3061 ASN A 446 CONECT 1251 2851 CONECT 1737 3033 CONECT 2142 2546 CONECT 2546 2142 CONECT 2851 1251 CONECT 3033 1737 END"

Hope this helps!

Cheers, Agastya

[adw62]

Hey Agastya,

I put the CYX as they describe here https://ambermd.org/tutorials/basic/tutorial7/index.php but did not see the bridges at the end. They also discuss using the bond command in LEaP to define which CYX are bound to each other which would need modification to the default tleap script in TIES?

I will try again and leave the connect information in the PDB. I hope with CYX and the connect tleap will add the bridges automatically.

Cheers, Alex

[apbhati1]

hey Alex,

That's right. Using the bond command would require modification to the code base, this is why I prefer the approach I suggested. Please give it a go and let me know if you face issues with that.

Cheers, Agastya

[AlexW12344]

Okay nice thanks for the advice this works well to build the bridges :)