Constructing a Model of the Catalytic Triad in Serine Proteases

To construct a model of a serine protease active site you may begin with the file ct.car (ct = catalytic triad). The catalytic triad is Asp-His-Ser (aspartate-histidine-serine). We will use this coordinate file to create a number of input files with different geometries of the hydrogen atoms involved in hydrogen bonding. Hydrogen bonding is a key aspect of the charge relay in the serine protease mechanism. Note that the overall charge of the catalytic triad is -1 in this model.

To construct different hydrogen bond geometries you will need to use the auxilliary program hbvec.f. After downloading hbvec.f run the program using ct.car as the input file. The program will generate a number of car files with displacements of the selected hydrogen atom.

In order to run the program you must select a hydrogen atom, a hydrogen-bond donor and a hydrogen-bond acceptor. For example, if you want to examine the potential energy surface between the serine hydroxyl group (-OH) and the imidazole (N=) in the hydrogen bond (-O…H…N=) you will need to the number (in order of appearance in the car file of the atoms H, O and N, respectively.

If you examine the coordinate (car) file using the vi editor

Ø vi ct.car

you will see that it is difficult to discern. In order to visualize the correct atoms read the car file into insightII.

Ø insightII

Use the Molecule/Get command to read ct.car. Then use the Molecule/Label command to label the atoms. You should see numbers that correspond to the numbers in the car file. The program hbvecm is looking for the order of the atom (i.e. number in the list). Using a separate window and using the vi editor you will need to find the correspondence between these values. Alternatively you may use the program bondchk to find the appropriate atoms based on their distances. There is only one hydrogen atom bonded to an oxygen atom in the structure so there will be only one distance between H and O that is ca. 1 Å. You then need to locate the nitrogen that is about 3 Å from that oxygen and you will have located the appropriate atoms.

The program prompts you for an output file. This file is a script that will copy a template input file to the appropriate number of input files for the coordinate files generated. The script will also contain commands that will create job files.

Note that there are two hydrogen bonds of interest here as shown in the Figure below.

Each of the these hydrogen bonds is affected by the presence of the other. One simple way to compare the effect of each group is to remove the aspartate (acetic acid) and redo the calculation of the potential energy surface. An example is shown below.

The structure above is neutral. Be careful to change the charge in the input file if you copy the input file ct.input.

A further step along these lines would be to remove the histidine and calculate the energy required for deprotonation of the methanol alone.