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GeneralizedKIC side chain closure.

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GeneralizedKIC side chain closure.

Hi all,

I want to generate cyclic peptides in a binding site employing the anchor design approach similar to and I need to do the closure by amidation between two side chains (K/E) or side chain/C-terminal.

I am using an XML script from the first paper and adapting it for my problem. Below is a section of the script where I define the atoms for the closure:

        <!--selecting the chains-->
        <Chain name="receptor" chains="A"/>
        <Chain name="peptide" chains="B"/>

	<!--selecting the peptide anchor-->
	<Index name="anchor" resnums="320-324"/>
	<And name="peptide_anchor" selectors="peptide,anchor"/>
	<!--selecting the anchor residue and the peptide extensions -->
	<Index name="peptide_extension" resnums="325-328"/>
	<!--selecting the new cyclic peptide -->
	<Index name="cyclic_peptide" resnums="320-328"/>

        <!--select interface of chainB close within 8.0 A of chainA-->
        <Neighborhood name="interface_chA" selector="peptide" distance="8.0"/>
        <Neighborhood name="interface_chB" selector="receptor" distance="8.0"/>
        <And name="AB_interface" selectors="interface_chA,interface_chB"/>


        <!--Extending the stub. Adding residues to the anchor-->
        <PeptideStubMover name="peptide_extension" reset="0">
			<!--Append resname="ORN" repeat="1"/-->
			<Append resname="GLY" repeat="1"/>
			<Append resname="GLY" repeat="1"/>
			<Append resname="GLY" repeat="1"/>
			<Append resname="PRO" repeat="1"/> # This is a residue to play with: PRO,DPRO

        <!--Setting Torsions of newly generated residues to omega 180-->
        <SetTorsion name="set_torsion" foldtree_root="4">
            <Torsion residue="326,327,328" torsion_name="omega" angle="180"/>
        <!--Adds the required constraints to bond introduced to keep it close-->
        <PeptideCyclizeMover name="cyclize" residue_selector="peptide_extension"/>
        <!--Parsed protocol that can be used for pre_selection in the genKIC-->
        <!--Currently number of hydrogen bonds and score-->
        <ParsedProtocol name="preselection_pp">
            <Add filter="total_hbonds"/>
            <Add filter="score_low"/>
        <!--Relax pre KIC-->
        <FastRelax name="relax" scorefxn="beta_cst" repeats="3" ramp_down_constraints="false">
            <MoveMap name="no_relax_peptide_anchor">
            <Chain number="1" chi="0" bb="0"/> # Stop the minimization. Takes too long
                <Span begin="326" end="328" chi="0" bb="0"/>

        <!--GenKIC. Added the custom rama table so that it doesn't bias the pose to just L-aas as we saw the presence of Ds enhance foldability. The preselection mover is basically a count of h-bonds to backbone at this stage (no-designs yet) to increase rigidity and chance of folding-->
        <GeneralizedKIC name="genkic" closure_attempts="10" stop_when_n_solutions_found="1" selector="lowest_energy_selector" selector_scorefunction="high_hbond" pre_selection_mover="preselection_pp">
            <AddResidue res_index="325"/>
            <AddResidue res_index="326"/>
            <AddResidue res_index="327"/>
            <AddResidue res_index="328"/>
            <CloseBond res1="328" atom1="C" res2="324" atom2="NE" bondlength="1.32" angle1="114" angle2="123" torsion="180"/>
            <SetPivots res1="325" res2="326" res3="327" atom1="CA" atom2="CA" atom3="CA"/>
            <AddPerturber effect="randomize_alpha_backbone_by_rama" custom_rama_table="flat_symm_dl_aa_ramatable">
                <AddResidue index="325"/>
                <AddResidue index="326"/>
                <AddResidue index="327"/>
                <AddResidue index="328"/>
            <AddFilter type="loop_bump_check"/>


The closure bond is defined by:

<CloseBond res1="328" atom1="C" res2="324" atom2="NE" bondlength="1.32" angle1="114" angle2="123" torsion="180"/>

However, I get this error with the Anchors:

File: src/protocols/generalized_kinematic_closure/
[ ERROR ] UtilityExitException
ERROR: Unable to auto-assign a lower anchor for the loop to be closed.  Check that the first residue is connected to something that isn't in the loop to be closed and isn't a tail residue.

The command line is:

rosetta_scripts.linuxgccrelease -parser:protocol KIC.xml -in:file:s relax_receptor-peptide-anchor.pdb -nstruct 10 -out:file:silent test.silent -jd2:failed_job_exception false -chemical:include_patches LYS:SidechainConjugation -extra_res_fa sidechain_conjugation/LYX.params

Any help will be much appreciated.


Post Situation: 
Mon, 2022-09-19 06:13