Distorted metal coordination geometry after relaxation (SetupMetalMover was used, fold tree and constraints were set manually)

[Anonymous]

 

Hello,

I am trying to relax Zn containing peptides like zinc fingers, but always got distorted geometries of the coordination site and much higher scores after the relax. Still, the rest of the peptide looks nice.

To detect the Zn coordination the SetupMetalsMover() was used. Because the fold tree still contains a jump between the first residue and the metal (in the documentation of Rosetta it was said that the function should set up the fold tree correctly by itself), the fold tree was set manually to connect the Zn with one coordinating residue. Also, the distance and angle constraints were set with a cst-file. FastRelax() was used with the standard ref2015 score function for relaxing. An ensemble of ten outputs was created and stored in pdb-files. The files (the cst file was uploaded as txt) and the used code are attached.

All ten runs lead to similar results (therefore only one pdb output file is attached). It seems like that Rosetta tried to maximize the distances between the His and the Zn. Then I also changed the radius of the Zn from 1.09 to 0.5 in the atom_properties.txt and the mm_atom_properties.txt in the pyrosettadatabasechemicals folder or set the charge to 0 in the ZN.params file, hoping to minimize the maybe detected clash between the Zn and the N of His, but the results stayed identical. I surely have overlooked something important and would like to ask, if someone can help.

Thank you in advance!

#Start

from pyrosetta import *

init()





#Metal detection

from pyrosetta.rosetta.protocols.simple_moves import SetupMetalsMover

metaldetector = SetupMetalsMover()





#Fold Tree

ft = FoldTree()

ft.add_edge(1,30,-1)

ft.add_edge(5,31,1)





#Scorefunction

from pyrosetta.teaching import get_fa_scorefxn

scorefxn = get_fa_scorefxn()





#Constraints

from pyrosetta.rosetta.protocols.constraint_movers import ConstraintSetMover

constraints = ConstraintSetMover()

constraints.constraint_file('constr_ZnF.cst')

constraints.add_constraints(True)





#Relax function

from rosetta.protocols.relax import FastRelax

relax = FastRelax()

relax.set_scorefxn(scorefxn)

relax.constrain_relax_to_start_coords(True)

relax.constrain_coords(True)



#Generation of ensemble

E_relax=[]

for i in range(1,11):



#Create the pose from PDB-File

ZnF_Pose = pose_from_pdb('5znf.clean.pdb')



#Using the SetupMetalMover

metaldetector.apply(ZnF_Pose)



#Set the correct fold tree

ZnF_Pose.fold_tree(ft)



#Set constraints

constraints.apply(ZnF_Pose)



#Relax

relax.apply(ZnF_Pose)



#Calculate score of relaxed pose and store it the list E_relax

E_relax.append(scorefxn(ZnF_Pose))



#Create PDB-File from relaxed pose

ZnF_Pose.dump_pdb('ZnF_Pose_relax_{}.pdb'.format(i))









#Mean Score, standard deviation and standard error



mean_E_rel = sum(E_relax)/len(E_relax)



A = []

for i in range(0,10):

a = (E_relax-mean_E_rel)**2

A.append(a)



std_E_rel = (sum(A) / (len(E_relax)-1))**(0.5)

SEM_E_rel = std_E_rel/((len(E_relax))**(0.5))







#Score of the starting structure



ZnF_Pose_start = pose_from_pdb('5znf.clean.pdb')

metaldetector.apply(ZnF_Pose_start)

ZnF_Pose_start.fold_tree(ft)

constraints.apply(ZnF_Pose_start)

start_E = scorefxn(ZnF_Pose_start)

ZnF_Pose_start.dump_pdb('ZnF_pose_start.pdb')





#Outputfile with score of starting structure, mean score of ensemble and score of each relaxed structure



txtfile = 'ZnF_FastRelax_score.txt'



myfile = open(txtfile, 'w')



myfile.write('start_E = {}nmean_E_rel = {} ; Std = {} ; SEM = {}nnE_reln'.format(start_E, mean_E_rel, std_E_rel, SEM_E_rel))



for i in range(0,len(E_relax)):

myfile.write('{}n'.format(E_relax))





myfile.close()

 

[Anonymous]

You need to do your relaxation with a scorefunction that has the metalbinding_constraint scoreterm turned on (given a nonzero weight).  Reweight this scoreterm to, say, 1.0 in the scorefxn object with scorefxn.set_weight( core.scoring.metalbinding_constraint, 1.0 ).

[Anonymous]

Thank you very much, it helped a lot! (Sorry for my delayed answer)

I used scorefxn.set_weight(pyrosetta.rosetta.core.scoring.ScoreType.metalbinding_constraint, 1.0) and now the coordination geometry is normal again.

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