DYNAMO NMR Molecular Structure Engine
Reference Guide

What is DYNAMO?

• NOE derived interproton distance restraints.
• NMR derived torsion angle restraints.
• 3J coupling constants.
• Radius of gyration.
• Dipolar couplings.

Some Examples of DYNAMO Applications

• List Backbone or Sidechain Angles in a Given Structure
• Change Backbone or Sidechain Angles in a Given Structure


• NMR Structure Prediction Using Simulated Annealing: ubiquitin


• Compute RMS Between Two Structures
• Compute Average Structure


• Simulate Chemical Shifts Based on Secondary Structure
• Simulate Dipolar Couplings
• Measure Alignment Tensor Parameters via Known Secondary Structure Elements


• Homology Search Based on Chemical Shifts
• Homology Search Base on Dipolar Couplings


• Visualize NMR Parameters

DYNAMO Commands

Using the GMC Editor to Create Sequence Information

DYNAMO v1.0 includes a graphical interface to create GMC files. To create a new GMC file, type the command
gmcEdit
To edit an existing GMC file, type the command
gmcEdit an_existing_gmc_file.gmc

The organization of the interface is straightforward. At the top of the window, there is space for the GMC's filename. Below that is space to specify the atomic masses. Entering a value of 0 for the universal atomic causes DYNAMO to use the standard atomic masses (eg., 12 for C, 1 for H, etc). This is usually not a good idea--the default value of 100 Daltons is appropriate for most dynamics simulations.

Below the dividing line is a section to allow one to add, delete, or edit various structure "segments." A segment is a single protein or nucleic acid chain, or a group of separate small molecules that you wish to think of as a unit (for example, a bunch of water molecules). Clicking on the "new segment" button creates a blank segment. To edit it, select it from the list and click "edit segment." Give each segment a unique name, and assign a starting residue number with the text fields.

Set the segment's type (protein, nucleic acid, or other) with the radio buttons. The sequence can be typed in directly, or entered by pressing the buttons with residue type labels. Each of the valid residue types for each segment type has a corresponding button. Proteins have additional check boxes to end the segment with an amine group on the N terminus or an acid group on the C terminus (these boxes should ordinarily be checked). Nucleic acids have additional check boxes to add phosphates to their 5' or 3' ends. The residue buttons for nucleic acids have one row that create DNA residues (dAde, dCyt, dThy, dGua), and one to create RNA residues (rAde, rCyt, rUri, rGua).

When you're done entering the sequence of a given segment, click the button marked "save changes to this segment".

Since disulfides can connect residues in different segments, they are edited separately in the lower region of the window. As with segments, start by clicking the "new disulfide" button, select the disulfide in the list, and then click "edit disulfide." Each disulfide simply needs to know the segment names and residue numbers of the cysteines to be connected. It doesn't matter which one is designated the "from" residue and which is the "to" residue. As with the segment editor, when you're done entering a disulfide, click the "save changed to this disulfide" button.

Once you've entered all your segments and disulfides, click the "generate GMC" button at the bottom. DYNAMO will first make sure that the information you've entered is valid (eg., that the residues selected for a disulfide are actually cys, that each segment has a unique name, etc). Then it will create the GMC file directory and the tables within it that store the covalent geometry restraints. This process can take a minute or two.

Finally, quit the program with the button marked "quit." (of course)

An Example of Simulated Annealing (ubiquitin)

1. Define the protein sequence of the target molecule ubiquitin. This is done via the graphical editor command:

   
            gmcEdit ubiq
   
   

   In this demo, the sequence has already been created previously. The sequence definition is used to build the DYNAMO "GMC" directory (Generic Molecular Coordinate directory) for the molecule. This directory contains various tables which define the covalent geometry of the target molecule. In addition to the defintions of covalent geometry, the GMC creation process automatically creates a radius of gyration restraint table suitable for a simple globular protein. The creation process also automatically creates a random starting structure.
2. (Optional) create an extended starting structure in PDB format. An example of this is given in the script, which creates the starting structure "ext.pdb" in the GMC directory, using a fast-cooling simulated annealing protocol:

   
              ubiqExt.tcl
   

3. Create the DYNAMO experimental restraint tables from NMR data. The tables have "standard" names, and should be placed in the gmc directory for the target molecule. In this example, input data for NOE, J-coupling, and TALOS-based torsions were used. The source data and conversion scripts can be found in the "orig" directory. The results are stored in files with the following names, which are copied to the GMC directory:

   
              NOE Data: noes.tab
              J Data:   jcoup.tab
              Torsions: torsions.tab
   

4. Run a simulated annealing protocol. An example script for a general slow-cooling protocol is given in:

          ubiqSA.tcl
   

   The output is saved in PDB format, in the GMC directory, with the file name:

          dyn.pdb
   

5. The results of annealing can be reviewed using the tools of DYNAMO. One example is performed by the script: evalSA.tcl This script reads in the refined structure "dyn.pdb", and evaluates the NOE, J, and Torsion restraints. The evaluations are written to tables called: jEval.tab torsionEval.tab noeEval.tab

The DYNAMO Slow Cooling Protcol

The protocol begins with an extended structure that is expected to reside in the GMC directory.

The protocol has three stages. In the first, the structure is brought into the neighborhood of the correct structure using 500 steps of molecular dynamics at 4000K and very tight temperature control. Each dynamics step is 3fs long. No van der Waals interactions are used during this stage.

In the second stage, the coordinates are allowed to cook at 4000K with loose temperature control for 2000 steps of 3fs each. No van der Waals interactions are used during this second stage.

In the final stage, the structure is annealed by slowly reducing the temperature from 4000K to 0K over the space of 12000 molecular dynamics steps. Again, each step is 3fs long. The van der Waals interactions are slowly introduced during cooling. Initally, the atoms are artificially large and very soft. During the course of the cooling, they are made smaller and harder.

The final structure is saved in the GMC directory with the name: dyn.pdb

The backbone RMS can be compared with the X-Ray structure using the command: rms.tcl

or, to compare only the ordered region from residues 2-72: rms.tcl ubiq.gmc/dyn.pdb 2 72

Chemical Shift Homology Search