[BioPython] Creating fusion protein like constructs with BioPython

[Mitchell Stanton-Cook]

Hello all.


I am trying to create fusion protein-like model from two separate pdb files.
I introduce a CYS mutant in the target protein, and then wish to form a
disulphide bound between it and a small peptide.

This is pure computational work.


I am using Bio.PDB. As the two structures are in arbitrary frames of
reference I need to rotate and translate to form the "construct".

I wish to have

TargetProtein-CB-SY-SY-CB-SmallPeptide (the peptide is not really added to
the N/C term)

I have tried many different approaches but have failed miserable to get
SmallPeptide rotated relative to TargetProtein at the correct dihedral angle
+/-90deg and bond lengths.

My current approach is (omitting the correct bond length at this time):

 TP-CB-SY     SY-CB-SP
  1    2             3    4

Translate  2 onto 3
Calculate the angle between 1-(23)-4
Calculate the cross product of 1-23 x 23-4
Generate the rotation matrix given the angle and vector
Rotate all SP (SmallPeptide) atoms by this rotation matrix.


This has not worked.

I have had some other ideas and have written code for them. Ideally, I wish
to calculate the rotations about X,Y,Z to place the SP at the correct
dihedral angle followed by translation, but I have no idea how to do this.

1) Can I use Bio.PDB to do this above task or do I need to look at something
else?
2) Does anyone have any ideas on how to complete this goal?

Thanking you for your time.

Mitch