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.)

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.

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.