HINT 2.30 Manual: Chapter 6I

LESSON 7: Optimizing the Position and Orientation of a Small Ligand


This lesson shows how you may be able to use HINT to improve molecular models that include small ligands such as water. In this case we will analyze a single water molecule that was located crystallographically at the active site of the HIV-1 protease/A74704 complex. This water has already been protonated and optimized via molecular mechanics methods, so we will look at the optimization two ways, first by optimizing the water as it is, and second, by removing the hydrogens, adding them back (randomly) and optimizing the resulting water molecule. It would be best for this lesson if there were no molecules from previous lessons currently active in insightII. If you are entering the HINT Tutorial at this point, follow the instructions in Step 1 of Lesson 1.

  1. Prepare the HIV-1 Protease and Ligand

    Get the HIV-1 Protease molecule (hiv1.car) and ligand (a74704.car) models. (Be sure to turn the "Reference" on when reading the second molecule.) Partition each as before (Lesson 3, step 3 and Lesson 5, step 3.)

  2. Identifying and Characterizing Crystallographic Water(s)

    Many crystal structures are reported with the positions of a number of water molecules. Some of these water molecules can be clearly identified as significant contributors to the overall structure of the biomolecule as they, for example, bridge between two subunits, mediate interactions between an enzyme and its inhibitor, or are present in a functionally important location in the biomolecule. Other water molecules are less important, as they are just benignly interacting at the surface of a protein, or interacting only with other waters.

    No universal rule has been developed to quickly ascertain the function of a water molecule, other than visual inspection. However, that is a difficult task before the hydrogens have been added and optimized for interaction. However, simple distance relationships such as water molecules within 4 Angstroms of both subunits are potentially bridging, etc. can be proposed. We are putting forward this new function of HINT to facilitate in understanding water.

  3. Setup to Optimize a Single Water Molecule

    If you examine the structure for the HIV-1 Protease/A74704 complex you will note a single water molecule (opposite of the functional -OH of the inhibitor) that has been read in as part of the inhibitor. To optimize this water, do the following: From the Setup pulldown, select the HINT_DistFunct command and set the default Distance Function for interactions as described previously (i.e., exponential, n = 1, Steric Term on, Scaler = 50).

    Next, select the Optimize_Ligand command from Setupto activate the Optimize_Ligand Setup panel. Review the Lig. Partition Opts. In particular make sure that the Partition-Method is Calculate, Hydrogen-Treatment is Polar_Only, and Polar-Proximity is VIa_Bonds.

    Finally, the Optimization Optns should be set. First, the Cut-Off Radius is a much more important choice here than previously as it determines which "site" atoms are to be used for the calculations. This will significantly impact the speed of the optimization calculations. Generally use around 6 for Cut-Off Radius. Use Van der Waals limit of 1.0 as usual. The Translation Limit is the distance we are allowing the ligand to move in its search for an optimum location. As this water is pretty well locked in, enter 0.2 as the Translation Limit. The Convergence is the how tightly we wish to determine the water's location. Use 0.02 as the Convergence. Finally, Speed is a loosely defined parameter related to how fast the optimization engine finds a solution. Low speeds in the HINT 2.30 version of this function are very slow, so choose 0.6 (which correponds to the integer parameter of 4) for Speed.

  4. Choose Molecules for Water Molecule Optimization

    Pull down the HintTable menu to select the Ligand_Optimization command. We will use Ligand Center as Picked Atom. The first step is to select the ligand molecule. Do that in this case by first picking the Oxygen of the water (part of the A74704 model). You should see A74704:401:OH2 in the Atom in Ligand Parameter if you have picked the proper atom.

    The Site Definition portion of the setup is to identify what molecules (which have already been Partitioned, see step 1 above) are to be included in the "site" definition. In this case both the HIV1 and A74704 models are part of the site. Choose these by selecting the first two Site Object on/off boxes and selecting HIV1 and A74704 from the associated Lists. There is no need to write a HintTable here. Now Press Execute. The calculation may take as long as 12-15 minutes and the following will appear in the insightII Textport:

    Initial Ligand Score: -645.085693
    
    Iteration 1, TestScore = -603.846436
    Iteration 2, TestScore = -603.846436
    Iteration 3, TestScore = -603.846680
    Iteration 4, TestScore = -603.846680
    Iteration 5, TestScore = -600.989380
    Iteration 6, TestScore = -600.989380
    
    Final Search of Ligand Rotation...
    
    Final Ligand Score: -599.026123
    

    Then, the new coordinates for the water will be transferred to insightII and its position will be modified on the screen.

  5. Optimize a Poorly Oriented Water Molecule

    Reload the original A74704 molecule into insightII. (It will be named A747041). Now, with the Builder module and the Mol Builder Parameter Block active, select with the left mouse button the two hydrogens on the water of A747041 and press the Delete button on the Mol Builder. Now we have to Re-Add the hydrogens. (It may be easier to "Blank" A74704 (the older, already optimized ligand using Object Blank before proceeding.) Press the "Big H" icon on Mol Builder; select the oxygen of the water and press Add on the Hybridization Parameter Block. Now, partition the A747041 model. Re-run the Small Ligand Optimization command as before. (You should not have to change the Setup Parameters, just use the HintTable Ligand_Optimization command. You will need to: 1) pick the water Oxygen (of A747041) as the center of the small ligand, and 2) select HIV1 and A747041 as the Site Objects.

    Press Execute.

    Initial Ligand Score: -14985.978516
    
    Iteration 1, TestScore = -713.971558
    Iteration 2, TestScore = -628.637329
    Iteration 3, TestScore = -666.259277
    Iteration 4, TestScore = -666.259277
    Iteration 5, TestScore = -663.368408
    
    Final Search of Ligand Rotation...
    
    Final Ligand Score: -573.689087
    

    This result is not identical to the one obtained by starting with the previously optimized water molecule, but visual inspection indicates they are very similar. If you allow a second cycle, you can increase the score to -535.8, with even better overlap with the A74704 water. NOTE: You must re-partition A747041 before the second (or any suceeding) cycles. The algorithm used to determine the members of the "site" will not function properly otherwise. Also note that one of the reasons that A74704 and A747041 do not match more exactly is that A747041 has a generic H-O-H angle, about 7o different from that of A74704.