CORAL/SASREF Dist Restraints Ambiguity with Symmetry

Interactive modelling (MASSHA, SASpy) and global minimization programs (SASREF, BUNCH, CORAL, GLOBSYMM)
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mawhite
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CORAL/SASREF Dist Restraints Ambiguity with Symmetry

#1 Post by mawhite » 2018.02.01 01:24

Hello,

I am having a problem with the ambiguity of distance restraints when applied to symmetry related molecules. I am defining an interface on the symmetry axis with a distance restraint. With a single molecule and P2 symmetry this is unambiguous. If the interface is through residue 308 of the chain then the restraints are as follows (Using CORAL chain identifier notation).

A Simple Dimer

Code: Select all

P2_A.con
NTER 6
A.pdb
CTER 5

P2_A.cnd
distance 8.0
1  308 308     1  308 308
In this case as there is only one other chain, the P2 symmetry molecule, CORAL has no problem assigning this restraint.

A Heterotetramer
Now lets look at a more difficult situation. Lets assume that we have two molecules A & B in the au, with their P2 symmetry related molecules A' and B'. This is a simple hetero-tetramer, or dimer of heterodimers.

Code: Select all

P2_AB.con
NTER 6
A.pdb
CTER 5
NTER 6
B.pdb
CTER 5

P2_AB.cnd
distance 8.0
1  308 308     2  308 308
Now the distance restraint can be applied to either the symmetry related molecules A-B' & B-A', or to the A-B plus the A'-B' molecules. The restraint assignment is ambiguous.

A Stacked Pentameric Ring
Now my situation is slightly more complex. I have a pseudo P52 assembly with two domains per chain. The P2 symmetry is sen crystallographically, but the P5 pentameric-ring is deformed from perfect symmetry. Now I have five molecules ABCDE and their P2 related symmetry equivalents A'B'C'D'E'. Applying the P2 symmetry to the ABCD pentameric ring yields the following restraints.

Code: Select all

P2_ABCDE.cnd
distance 8.0
1   308 308     1  308 308
distance 8.0
2   308 308     5  308 308
distance 8.0
3   308 308    4  308 308
Note that the first restraint can only be assigned to a symmetry related molecule, but that the two other restraints are ambiguous and can apply either inter- or intra-ring. This ambiguity prevents CORAL or SASREF from correctly interpreting this as the interface between two pentameric rings.

I have tried adding several other distance restraints to limit the possibilities, but this ambiguity is preventing the formation of the pseudo P52 assembly.

PS. Attempting to fix the inter-domain interfaces also fails

Does anyone have any ideas as how to restraint this symmetry interface.

Best regards,
Mark

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