[phenixbb] Coupling ligand occupancy with helix displacement

John Michael Bruning bruning at stanford.edu
Wed Jun 6 11:06:44 PDT 2018


I have a very flexible covalent adduct that adopts three alternative conformations (A,B,C) in my structure . Conformations A and C are solvent exposed, while conformation B is buried. The buried conformation B displaces a regulatory helix (resseq 589:598) by a few angstrom, while the solvent exposed conformations do not displace this helix. I can't seem to write a occupancy .params file that fulfills:

1.) occ. of ligand conformation B = occ. of displaced helix conformation # coupling of ligand binding with helix displacement

2.) occ. non-displaced helix conformation = (1 - occ. displaced helix conformation)

3.) sum occ. ligand conformations A+B+C = 1 # assuming protein was initially labeled 100%

It seems like #7 from http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=12 is my situation, but I can't quite seem to modify this for my case. For example, something like:

constrained_group {
                selection = chain A and resname CPE and altid B or chain A and resseq 589:598 and altid B}

Captures the concerted conformation aspect (1) (occupancy for ligand conformation B = occupancy for displaced helix) and the sum occupancy of the displaced and non-displaced helix = 1 (2), but the sum of the the alternative conformations A+B+C > 1.0 (w/ A+C = 1.0) (3)

Incidentally, my resolution is 2.4 Ang. Thanks for any help!






John Bruning, Post-Doctoral Scholar

Stanford University, Glenn Lab

CCSR Building, #3110


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