DFT calculation of the Activation of Peroxidase Enzymes

 

In order to understand a activation of peroxidase enzymes we can use two types of analysis.

1.     Potential energy surface for hydrogen bonds.

2.     Mulliken or Hirshfeld charge on the iron and bound peroxide oxygen atoms.

 

Calculating a Potential Energy Surface

To setup up a potential energy surface calculation you will use the hbvec (hydrogen bond vector) program for hydrogen bonds or the fragvec (fragment vector) program for the interaction energy between groups.  Each of these programs specifies a vector and moves one or more atoms along that vector to generate a series of structures.  A single-point energy calculation is carried out for each of the structures and the result is plotted to generate a potential energy surface.  Comparison of different environments permits an understanding of the specific effects of hydrogen bond relay and other group interactions on the activation of molecules at the enzyme active site.

For hbvec good set of displacements is 0.8 Å for the starting position and displacements of 0.05 Å.  A good number is 30.  For fragvec it depends on the bonding you wish to study.  For peroxidases there are two key bonds.  The Fe-O bond and the O-O bond of bound peroxide.  It is interesting to compare different protonation states bound peroxide in order to understand how O-O scission occurs.

Once you have run hbvec or fragvec, copy an input file and name it root1.input where root is the four-letter root name for your hydrogen bonding files.  A script is also generated by hbvec or fragvec that automatically copies this input file to input files for all of the other car files.  The script has the name root.job.  Before you execute root.job you will want to edit the input file to make sure that all of the options you specify are set.  In the present case, because an odd number of electrons are specified it is advisable to specify the Thermal option under the Occupation keyword.  This will give a much higher probability that the self-consistent field (SCF) calculation will converge for all of the structures you have generated in hbvec or fragvec.

          There are number of possible structures in the activation of peroxidases.  Keep in mind that the oxidation state of the iron in the resting state is Fe(III).  Since the porphine ring has a charge of -2, there is one unpaired electron in this system.  Thus, the overall charge is +1 and the spin is 1 (note that the DMol3 input file uses the number of unpaired spins as the input).Using the vi editor you can search for the word Charge in the input file by typing /Charge in vi.  Using the i command to enter text you can add a charge of -1.  You can delete the charge of 0 (the default) using the x (delete) command.  You can change the Spin keyword by searching on Spin and then changing the 0 (default) to a 1.

Activate the script generated by hbvec or fragvec using the following UNIX syntax:

 

Ø     chmod +x [script_name]

 

Then run the script and it will automatically copy the input file giving the appropriate names for the various displaced geometries.

 

Once the job is completed you can extract the energies using pesgen_thermal.  Type the word ‘none’ when prompted for the second set of outmol files (since you only have one).  The file you will obtain in this case is the root.energy file.  The first column is the displacement.  The second column is the uncorrected energy (in kJ/mol).  The third column is a correction term for finite temperature.  The fourth column is the corrected data (in kJ/mol).  A subtracted energy file ready for plotting is stored in the with a kj extension.

 

          There are many possible interesting systems for study in this module.  These are listed below.  These structures follow the Poulos-Kraut mechanism for peroxidase activation.

Bound peroxide (no distal imidazole)

Bound peroxide (including distal imidazole)

Deprotonated peroxide (including distal imidazole)

Reprotonated peroxide (including distal imidazole)

 

For comparison there are also structures of possible electronic intermediates

Bound peroxy intermediate (no distal imidazole, Charge = 0, Spin = 0)

Bound oxy intermediate (no distal imidazole, Charge = 0, Spin = 0)

Bound oxo intermediate (no distal imidazole, Charge = 0, Spin = 0)

 

Calculating the Charge Distribution

Change the commenting on the Mulliken_Charge keyword in the input file.  TO do this you can use the vi editor.  Search for Mulliken_Charge using the command "/Mul".  If the commenting appears as below both the Mulliken and Hirshfeld charges will appear in the outmol file when the job is completed.

 

# -----   Properties Keywords

 

#Bond_Order              on

 

Mulliken_Analysis       charge

#Mulliken_Analysis       population

#Mulliken_Analysis       full

 

Hirshfeld_Analysis      charge

#Hirshfeld_Analysis      dipole

#Hirshfeld_Analysis      quadrupole

 

 

The analysis of Mulliken charge is discussed in the serine protease module.  You may follow the protocol there to extract the Mulliken charge for interesting atoms.  These include the porphine iron (Fe), the oxygen atoms of bound peroxide and possibly the nitrogen atoms of the distal histidine and proximal (iron-bound) histidine that are represented by imidazole.