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Modified residues

Non-natural amino-acids


This example was provided by Hélène Déméné and Gaetan Bellot, from Centre de Biochimie Structurale (Montpellier, France). The full example is described in the Tutorials folder, and only the data related to the chemical modifications are presented in this page.

The example presents the study of a cyclic peptide interacting with G protein-coupled receptors (GPCRs), and more details about the corresponding research can be found on the page of Hélène Déméne.

In order to run a calculation on a polypeptide including modified amino-acids, several files have to be modified, in the CNS set of files provided with ARIA as well as in the ARIA python files. See the page Non-standard residue definitions for more details.

The peptide sequence, shown below, contains 4 modified amino-acids: GLX (chiral D Glutamine), NLE (Norleucine), GLI (Glycine before cyclisation) and CYC (cyclisated Cysteine).

GLI GLX
 VAL
 LEU
 ILE
 PHE
 ARG
 GLU
 ILE HIS
 ALA
 SER
 LEU
 VAL
 PRO
 GLY
 PRO
 SER
 GLU
 ALA
GLY ARG ARG
 ARG ARG GLY ARG ARG THR GLY SER PRO SER GLU GLY ALA HIS VAL SER ALA
ALA NLE ALA
 LYS THR VAL ARG NLE THR CYC










The archive of the examples can be downloaded from the site:


The project directory tree is the same than those already described in the corresponding page.

The project xml file cooresponding to the run with unatural amino-acids is given below. A modification of the simulated annealing protocol is that the high temperatures were divided by two, in order to avoid unstabilities due to the cyclization restraint. 


<!DOCTYPE project SYSTEM "project1.0.dtd">
<project name="Bouclei3" version="1.0" author="" date="Tue Mar 28 15:48:04 2006"    
  description="Structure i3cyclique" comment="" references="" 
  working_directory="/RMN2/rmn/bellot/structuri3/structurei3Cycliquei3Short" 
  temp_root="/RMN2/rmn/bellot/structuri3/pathtemp" run="i3cyclique" file_root="i3" cache="no" 
  cleanup="no">
  <data>
    <ccpn_model filename=""/>
    <molecule file="/RMN2/rmn/bellot/structuri3/conversioni3cycl/Seqi3.xml" format="xml" ccpn_id="">
      <linkage_definition name="user_defined"   
        filename="/PROG/LINUX/prog/aria2.0/aria2.0/cns/toppar/topallhdg5.3.pep"/>
      <parameter_definition name="parallhdg5.3.pro" filename=""/>
      <topology_definition name="topallhdg5.3.pro" filename=""/>
    </molecule>
    <spectrum enabled="yes" use_assignments="yes" trust_assigned_peaks="no" structural_rules="no">
      <shifts file="/RMN2/rmn/bellot/structuri3/conversioni3cycl/i3ppm.xml" format="xml" ccpn_id="" 
        default_shift_error="0.01"/>
      <peaks file="/RMN2/rmn/bellot/structuri3/conversioni3cycl/1Hnoesy800.xml" format="xml"     
        ccpn_id="" peak_size="volume" freq_window_proton1="0.04" freq_window_hetero1="0.5" 
        freq_window_proton2="0.02" freq_window_hetero2="0.5">
        <lower_bound_correction value="0.0" enabled="no"/>
        <upper_bound_correction value="6.0" enabled="no"/>
      </peaks>
      <experiment_data molecule_correlation_time="10.0" spectrum_mixing_time="100.0" 
        spectrometer_frequency="800.0"/>
    </spectrum>
    <spectrum enabled="yes" use_assignments="yes" trust_assigned_peaks="no" structural_rules="no">
      <shifts file="/RMN2/rmn/bellot/structuri3/conversioni3cycl/i3ppm2.xml" format="xml" ccpn_id="" 
        default_shift_error="0.01"/>
      <peaks file="/RMN2/rmn/bellot/structuri3/conversioni3cycl/1Hnoesy800NHNH.xml" format="xml" 
        ccpn_id="" peak_size="volume" freq_window_proton1="0.04" freq_window_hetero1="0.5"   
        freq_window_proton2="0.02" freq_window_hetero2="0.5">
        <lower_bound_correction value="0.0" enabled="no"/>
        <upper_bound_correction value="6.0" enabled="no"/>
      </peaks>
      <experiment_data molecule_correlation_time="10.0" spectrum_mixing_time="100.0" 
        spectrometer_frequency="800.0"/>
    </spectrum>
    <spectrum enabled="yes" use_assignments="yes" trust_assigned_peaks="no" structural_rules="no">
      <shifts file="/RMN2/rmn/bellot/structuri3/conversioni3cycl/i3ppm600323.xml" format="xml"    
        ccpn_id="" default_shift_error="0.01"/>
      <peaks file="/RMN2/rmn/bellot/structuri3/conversioni3cycl/1H323noesy600.xml" format="xml" 
        ccpn_id="" peak_size="volume" freq_window_proton1="0.04" freq_window_hetero1="0.5" 
        freq_window_proton2="0.02" freq_window_hetero2="0.5">
        <lower_bound_correction value="0.0" enabled="no"/>
        <upper_bound_correction value="6.0" enabled="no"/>
      </peaks>
      <experiment_data molecule_correlation_time="10.0" spectrum_mixing_time="100.0" 
        spectrometer_frequency="600.0"/>
    </spectrum>
    <spectrum enabled="yes" use_assignments="yes" trust_assigned_peaks="no" structural_rules="no">
      <shifts file="/RMN2/rmn/bellot/structuri3/conversioni3cycl/i3ppm6003232.xml" format="xml" 
        ccpn_id="" default_shift_error="0.01"/>
      <peaks file="/RMN2/rmn/bellot/structuri3/conversioni3cycl/1H323noesyNHNH600.xml" format="xml" 
        ccpn_id="" peak_size="volume" freq_window_proton1="0.04" freq_window_hetero1="0.5" 
        freq_window_proton2="0.02" freq_window_hetero2="0.5">
        <lower_bound_correction value="0.0" enabled="no"/>
        <upper_bound_correction value="6.0" enabled="no"/>
      </peaks>
      <experiment_data molecule_correlation_time="10.0" spectrum_mixing_time="100.0" 
        spectrometer_frequency="600.0"/>
    </spectrum>
    <spectrum enabled="yes" use_assignments="yes" trust_assigned_peaks="no" structural_rules="no">
      <shifts file="/RMN2/rmn/bellot/structuri3/conversioni3cycl+i3short/i3ppm6003233.xml" 
        format="xml" ccpn_id="" default_shift_error="0.01"/>
      <peaks file="/RMN2/rmn/bellot/structuri3/conversioni3cycl/1H323noesy600D2O.xml" format="xml" 
        ccpn_id="" peak_size="volume" freq_window_proton1="0.04" freq_window_hetero1="0.5" 
        freq_window_proton2="0.02" freq_window_hetero2="0.5">
        <lower_bound_correction value="0.0" enabled="no"/>
        <upper_bound_correction value="6.0" enabled="no"/>
      </peaks>
      <experiment_data molecule_correlation_time="10.0" spectrum_mixing_time="100.0" 
        spectrometer_frequency="600.0"/>
    </spectrum>
    <spectrum enabled="yes" use_assignments="yes" trust_assigned_peaks="no" structural_rules="no">
      <shifts file="/RMN2/rmn/bellot/structuri3/conversioni3cycl/i3ppm600313.xml" format="xml" 
        ccpn_id="" default_shift_error="0.01"/>
      <peaks file="/RMN2/rmn/bellot/structuri3/conversioni3cycl/1H313noesy600.xml" format="xml" 
        ccpn_id="" peak_size="volume" freq_window_proton1="0.04" freq_window_hetero1="0.5" 
        freq_window_proton2="0.02" freq_window_hetero2="0.5">
        <lower_bound_correction value="0.0" enabled="no"/>
        <upper_bound_correction value="6.0" enabled="no"/>
      </peaks>
      <experiment_data molecule_correlation_time="10.0" spectrum_mixing_time="100.0" 
        spectrometer_frequency="600.0"/>
    </spectrum>
    <spectrum enabled="yes" use_assignments="yes" trust_assigned_peaks="no" structural_rules="no">
      <shifts file="/RMN2/rmn/bellot/structuri3/conversioni3cycl/i3ppm6003132.xml" format="xml" 
        ccpn_id="" default_shift_error="0.01"/>
      <peaks file="/RMN2/rmn/bellot/structuri3/conversioni3cycl/1H313noesyNHNH600.xml" format="xml" 
        ccpn_id="" peak_size="volume" freq_window_proton1="0.04" freq_window_hetero1="0.5" 
        freq_window_proton2="0.02" freq_window_hetero2="0.5">
        <lower_bound_correction value="0.0" enabled="no"/>
        <upper_bound_correction value="6.0" enabled="no"/>
      </peaks>
      <experiment_data molecule_correlation_time="10.0" spectrum_mixing_time="100.0" 
        spectrometer_frequency="600.0"/>
    </spectrum>
    <hbonds file="/RMN2/rmn/bellot/structuri3/data/i3cycHBond1-15-32-50.tbl" format="tbl" ccpn_id="" 
      enabled="yes" data_type="standard"/>
    <initial_structure file="" format="iupac" ccpn_id="" enabled="no"/>
  </data>
  <structure_generation engine="cns">
    <cns local_executable="/PROG/LINUX/prog/CNS/cns_solve_1.1/intel-i686-linux_g77/bin/cns" 
      keep_output="yes" keep_restraint_files="yes" create_psf_file="yes" generate_template="yes" 
      nonbonded_parameters="PROLSQ">
      <annealing_parameters>
        <unambiguous_restraints first_iteration="0" k_hot="10.0" k_cool1_initial="10.0" 
          k_cool1_final="50.0" k_cool2="50.0" averaging="sum"/>
        <ambiguous_restraints first_iteration="0" k_hot="10.0" k_cool1_initial="10.0" 
          k_cool1_final="50.0" k_cool2="50.0" averaging="sum"/>
        <hbond_restraints first_iteration="0" k_hot="10.0" k_cool1_initial="10.0" k_cool1_final="50.0" 
          k_cool2="50.0" averaging="sum"/>
        <dihedral_restraints k_hot="5.0" k_cool1="25.0" k_cool2="200.0"/>
        <karplus_restraints parameter_class="1" a="6.98" b="-1.38" c="1.72" d="-60.0" k_hot="0.0" 
          k_cool1="0.2" k_cool2="1.0"/>
        <karplus_restraints parameter_class="2" a="6.98" b="-1.38" c="1.72" d="-60.0" k_hot="0.0" 
          k_cool1="0.2" k_cool2="1.0"/>
        <karplus_restraints parameter_class="3" a="6.98" b="-1.38" c="1.72" d="-60.0" k_hot="0.0"  
          k_cool1="0.2" k_cool2="1.0"/>
        <karplus_restraints parameter_class="4" a="6.98" b="-1.38" c="1.72" d="-60.0" k_hot="0.0" 
          k_cool1="0.2" k_cool2="1.0"/>
        <karplus_restraints parameter_class="5" a="6.98" b="-1.38" c="1.72" d="-60.0" k_hot="0.0"  
          k_cool1="0.2" k_cool2="1.0"/>
        <rdc_restraints parameter_class="1" method="SANI" first_iteration="0" k_hot="0.0" 
          k_cool1="0.2" k_cool2="1.0" r="0.4" d="8.0" border_hot_initial="0.1" border_hot_final="40.0" 
          border_cool1_initial="40.0" border_cool1_final="40.0" border_cool2_initial="40.0" 
          border_cool2_final="40.0" center_hot_initial="0.1" center_hot_final="0.1" 
          center_cool1_initial="10.0" center_cool1_final="10.0" center_cool2_initial="10.0" 
          center_cool2_final="10.0"/>
        <rdc_restraints parameter_class="2" method="SANI" first_iteration="0" k_hot="0.0" 
          k_cool1="0.2" k_cool2="1.0" r="0.4" d="8.0" border_hot_initial="0.1" border_hot_final="40.0" 
          border_cool1_initial="40.0" border_cool1_final="40.0" border_cool2_initial="40.0" 
          border_cool2_final="40.0" center_hot_initial="0.1" center_hot_final="0.1" 
          center_cool1_initial="10.0" center_cool1_final="10.0" center_cool2_initial="10.0" 
          center_cool2_final="10.0"/>
        <rdc_restraints parameter_class="3" method="SANI" first_iteration="0" k_hot="0.0" 
          k_cool1="0.2" k_cool2="1.0" r="0.4" d="8.0" border_hot_initial="0.1" border_hot_final="40.0" 
          border_cool1_initial="40.0" border_cool1_final="40.0" border_cool2_initial="40.0" 
          border_cool2_final="40.0" center_hot_initial="0.1" center_hot_final="0.1" 
          center_cool1_initial="10.0" center_cool1_final="10.0" center_cool2_initial="10.0" 
          center_cool2_final="10.0"/>
        <rdc_restraints parameter_class="4" method="SANI" first_iteration="0" k_hot="0.0" 
          k_cool1="0.2" k_cool2="1.0" r="0.4" d="8.0" border_hot_initial="0.1" border_hot_final="40.0" 
          border_cool1_initial="40.0" border_cool1_final="40.0" border_cool2_initial="40.0" 
          border_cool2_final="40.0" center_hot_initial="0.1" center_hot_final="0.1" 
          center_cool1_initial="10.0" center_cool1_final="10.0" center_cool2_initial="10.0" 
          center_cool2_final="10.0"/>
        <rdc_restraints parameter_class="5" method="SANI" first_iteration="0" k_hot="0.0" 
          k_cool1="0.2" k_cool2="1.0" r="0.4" d="8.0" border_hot_initial="0.1" border_hot_final="40.0" 
          border_cool1_initial="40.0" border_cool1_final="40.0" border_cool2_initial="40.0" 
          border_cool2_final="40.0" center_hot_initial="0.1" center_hot_final="0.1" 
          center_cool1_initial="10.0" center_cool1_final="10.0" center_cool2_initial="10.0" 
          center_cool2_final="10.0"/>
        <flat_bottom_harmonic_wall m_rswitch_hot="0.5" m_rswitch_cool1="0.5" m_rswitch_cool2="0.5" 
          rswitch_hot="0.5" rswitch_cool1="0.5" rswitch_cool2="0.5" m_asymptote_hot="-1.0" 
          m_asymptote_cool1="-1.0" m_asymptote_cool2="-0.1" asymptote_hot="1.0" asymptote_cool1="1.0" 
          asymptote_cool2="0.1"/>
        <symmetry_restraints k_packing="1.0" k_ncs="50.0"/>
      </annealing_parameters>
      <md_parameters dynamics="torsion" random_seed="89764455" tad_temp_high="3000.0" 
        tad_timestep_factor="9.0" cartesian_temp_high="800.0" cartesian_first_iteration="0" 
        timestep="0.003" temp_cool1_final="500.0" temp_cool2_final="50.0" steps_high="4000" 
        steps_refine="2000" steps_cool1="2500" steps_cool2="2000"/>
    </cns>
    <job_manager default_command="csh -f"/>
  </structure_generation>
  <protocol floating_assignment="yes">
    <iteration number="0" n_structures="20" sort_criterion="total_energy" n_best_structures="7">
      <assignment/>
      <merging method="standard"/>
      <calibration relaxation_matrix="no" distance_cutoff="6.0" estimator="ratio_of_averages" 
        error_estimator="distance"/>
      <violation_analysis violation_tolerance="1000.0" violation_threshold="0.5"/>
      <partial_assignment weight_threshold="1.0" max_contributions="20"/>
    </iteration>
    <iteration number="1" n_structures="20" sort_criterion="total_energy" n_best_structures="7">
      <assignment/>
      <merging method="standard"/>
      <calibration relaxation_matrix="no" distance_cutoff="6.0" estimator="ratio_of_averages" 
        error_estimator="distance"/>
      <violation_analysis violation_tolerance="5.0" violation_threshold="0.5"/>
      <partial_assignment weight_threshold="0.9999" max_contributions="20"/>
    </iteration>
    <iteration number="2" n_structures="20" sort_criterion="total_energy" n_best_structures="7">
      <assignment/>
      <merging method="standard"/>
      <calibration relaxation_matrix="no" distance_cutoff="6.0" estimator="ratio_of_averages" 
        error_estimator="distance"/>
      <violation_analysis violation_tolerance="3.0" violation_threshold="0.5"/>
      <partial_assignment weight_threshold="0.999" max_contributions="20"/>
    </iteration>
    <iteration number="3" n_structures="20" sort_criterion="total_energy" n_best_structures="7">
      <assignment/>
      <merging method="standard"/>
      <calibration relaxation_matrix="no" distance_cutoff="6.0" estimator="ratio_of_averages" 
        error_estimator="distance"/>
      <violation_analysis violation_tolerance="1.0" violation_threshold="0.5"/>
      <partial_assignment weight_threshold="0.99" max_contributions="20"/>
    </iteration>
    <iteration number="4" n_structures="20" sort_criterion="total_energy" n_best_structures="7">
      <assignment/>
      <merging method="standard"/>
      <calibration relaxation_matrix="no" distance_cutoff="6.0" estimator="ratio_of_averages" 
        error_estimator="distance"/>
      <violation_analysis violation_tolerance="1.0" violation_threshold="0.5"/>
      <partial_assignment weight_threshold="0.98" max_contributions="20"/>
    </iteration>
    <iteration number="5" n_structures="20" sort_criterion="total_energy" n_best_structures="7">
      <assignment/>
      <merging method="standard"/>
      <calibration relaxation_matrix="no" distance_cutoff="6.0" estimator="ratio_of_averages" 
        error_estimator="distance"/>
      <violation_analysis violation_tolerance="1.0" violation_threshold="0.5"/>
      <partial_assignment weight_threshold="0.96" max_contributions="20"/>
    </iteration>
    <iteration number="6" n_structures="20" sort_criterion="total_energy" n_best_structures="7">
      <assignment/>
      <merging method="standard"/>
      <calibration relaxation_matrix="no" distance_cutoff="6.0" estimator="ratio_of_averages" 
        error_estimator="distance"/>
      <violation_analysis violation_tolerance="0.1" violation_threshold="0.5"/>
      <partial_assignment weight_threshold="0.93" max_contributions="20"/>
    </iteration>
    <iteration number="7" n_structures="20" sort_criterion="total_energy" n_best_structures="7">
      <assignment/>
      <merging method="standard"/>
      <calibration relaxation_matrix="no" distance_cutoff="6.0" estimator="ratio_of_averages" 
        error_estimator="distance"/>
      <violation_analysis violation_tolerance="0.1" violation_threshold="0.5"/>
      <partial_assignment weight_threshold="0.9" max_contributions="20"/>
    </iteration>
    <iteration number="8" n_structures="20" sort_criterion="total_energy" n_best_structures="7">
      <assignment/>
      <merging method="standard"/>
      <calibration relaxation_matrix="no" distance_cutoff="6.0" estimator="ratio_of_averages" 
        error_estimator="distance"/>
      <violation_analysis violation_tolerance="0.1" violation_threshold="0.5"/>
      <partial_assignment weight_threshold="0.8" max_contributions="20"/>
    </iteration>
    <water_refinement solvent="water" n_structures="10" enabled="no" write_solvent_molecules="no"/>
  </protocol>
  <analysis>
    <structures_analysis enabled="yes"/>
    <procheck executable="/PROG/LINUX/prog/PROCHECK/procheck/procheck.scr" enabled="yes"/>
    <prosa executable="/PROG/LINUX/prog/PROSA/prosa2003.install" enabled="yes"/>
    <whatif executable="/PROG/LINUX/prog/WHATCHECK/whatcheck/whatcheck" enabled="no"/>
  </analysis>
  <report>
    <ccpn export_noe_restraint_list="no" export_structures="yes"/>
    <molmol enabled="yes"/>
    <noe_restraint_list pickle_output="no" text_output="yes" xml_output="yes"/>
    <spectra write_assigned="no" write_assigned_force="no" iteration="last"/>
  </report>
</project>
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