Use of the program Module to analyse RDC.

The on-line manual is available for use of Module.

1. Example of single domain module. Two files are provided -

sample1.pdb

sample1.dat

The former contains the three dimensional co-ordinates of the molecule of interest (a

thioredoxin in this case). The second file contains RDC's from the molecule. The aim is to

determine the alignment tensor using Module (just to get used to the program).

2. Example of single domain molecule whose overall fold is known but imprecise:

Two files are provided -

sample5.pdb

sample5.dat

The former contains the three dimensional co-ordinates of the molecule of interest (again

thioredoxin). The second file contains RDC's from the molecule. Fit the alignment tensor

using the secondary structural elements. This should allow you to identify regions which have

a different conformation than in the model (check the local 2).

The aim is then to align the different regions (helices and beta-sheets) of the molecule to

define a fold which is in better agreement with the RDC's than the initial model.

3. Example of an extended two-domain molecule. Two files are provided -

sample2.pdb

sample2.dat

The former contains the three dimensional co-ordinates of the extended molecule in a non-

native relative conformation. The second file contains RDC's from the whole molecule in the

correct relative conformation of the two domains. Fit the alignment tensor using the whole

molecule, then different modules separately. You should be able to construct at least one

model, which is in agreement with the RDC's and the covalence of the primary sequence.

4. Example of intermolecular complex. Three files are provided -

sample4.pdb

sample4.dat

sample4.rstrnt

The former contains the three dimensional co-ordinates of the two domains of the molecular

complex in their isolated form. The second file contains RDC's from the two domains in the

complex. The third file contains inter-domain distances (from, for example, inter-nuclear nOe,

or maybe chemical shift mapping) which can be read by the program Module and applied to

the oriented domains. The aim is to find a conformation, which is in agreement with the

RDC's and the distances.

5. Example of an RNA superstructure

sample3.pdb

sample3.dat
The former contains the three dimensional co-ordinates of the hammerhead ribozyme with the

secondary structural elements intact, but the overall fold unwound. The second contains

RDC's from each secondary structural element in the native conformation. The object is to

find this conformation using Module.

6. The final example was again shown in the course, this time we have built the 7 residue peptide

using the Meccano approach, and the aim is to dock this on to the scaffold structure. A pdb file

is provided, containing the peptide conformation, in an arbitrary orientation, and the protein structure

in the absence of this peptide. Experimental RDC data from two alignment media from the whole

molecule should allow the correct orientation and position to be defined.

sample6.pdb

sample6a.dat (data from alcohol phase alignment)

sample6b.dat (data from phage alignment)