Demo ExperimentDesign

Run it by typing MMMx demo_ExperimentDesign. This example generates logfile demo_ExperimentDesign.log.

Modules used

Only module ExperimentDesign is used.

Source code

% MMMx Demo: Functionality of the ExperimentDesign module
%

# log

!ExperimentDesign

   import 2LZM T4L % load T4 lysozyme crystal structure
   
   import 2ADC RRM % load NMR structure of an RNA recognition motif

   sitescan mtsl T4L T4L_sites % sitescan for T4 Lysozyme, default set CILMSTV of residues 
      
   sitescan mtsl RRM RRM_sites I % sitescan for the protein part of the RRM, only isoleucine  
   
   sitescan iap-4tu RRM SL_sites u 1 0.1 % sitescan (only uracil) for the RNA part
   
   pairlist T4L_sites T4L T4L_pairs 15 80 % a site pair list for T4 lysozyme

   hetpairlist RRM_sites SL_sites RRM RRM_pairs 15 80 

   plot T4L_distributions pdf

   distributions mtsl T4L T4L_distribution
       68   131
       72   131
       75   131
       76   131
       79   131
       86   131
       89   131
      109   131
   .distributions

   plot RRM_distributions pdf
   
   distributions mtsl|iap-4tu RRM RRM_distribution
      RRM_pairs
   .distributions
   
   import 1BUY EPO % import what was once very popular in professional cycling
   
   sitescan mtsl EPO EPO_sites % perform site scan
   
   ENMpairs EPO_sites EPO EPO_enm_pairs 15 80 % score site pairs for elastic network modeling  

.ExperimentDesign

# report

Functionality

The demo imports a T4 Lysozyme structure with PDB identifier 2LZM and stores it with internal identifier T4L. It also imports a RNA recognition motif with bound RNA stemloop with PDB identifier 2ADC and stores it with internal identifier RRM.

The first spin-labelling sitescan is performed with spin label mtsl on entity T4L and stored in file T4L_sites.lst. The extension .lst is appended by default. The demo then performs two spin-labeling sitescans on the RRM/stemloop complex. First, a scan with label mtsl is performed on entity RRM, generating site list RRM_sites. The RRM is scanned only for substituting isoleucine residues by a spin label. Second, a scan with label iodoacetamido-proxyl as a thiouracil label is performed on entity RRM, generating site list SL_sites. Only uracil nucleotides are considered for labeling.

The demo then generates two site pair lists, one from T4L_sites.lst referring to entityt T4L and stores it in file T4L_pairs.lst. Site pairs are included only if the mean distance ranges between 15 and 80 Å. The second list combines labels from RRM_sites.lst with labels from SL_sites.lst, referring to entity RRM. The pair list is stored as RRM_pairs.lst and again site pairs are included only if the mean distance ranges between 15 and 80 Å.

Then, basis file name T4L_distributions is declared for distance distribution output plots and file format pdf is selected for these plots. Distributions are generated with label mtsl for entity T4L and are stored in numerical format with basis file name T4L_distribution. A list of 8 spin pairs is declared. Note that this computation of distance distributions does not require a previous site scan or pair list generation.

After this, a new basis file name RRM_distributions is declared for plots, which are again stored in pdf format. In this case, distributions are genarted for the existing pair list RRM_pairs. An orthogonal spin labelling scheme with labels mtsl and iap-4tu is used.

The final example of this demo imports PDB structure 1BUY of erythropoietin into entity EPO. At sitescan with mtsl is performed to provide list EPO_sites.lst. Site pairs are generated and scored from this list for elastic network modeling of conformation change of EPO. The list is stored as EPO_enm_pairs.lst, considering only pairs with mean distance between 15 and 80 Å.

Outputs

Site and pair list are stored in a self-explaining human-readable format. Figures are stored as vector graphics in PDF format. Distance distributions are stored as comma-separated value (.csv) files with the distance in units of Å as the first column and probability density in units of as the second column.