Methodology - Programs

The starting material for the study of enzymes has been an Internet database, Protein Data Bank (PDB). In these pages, I got the 3D structure of human cytochrome forms determined using single crystal X-ray diffraction.

Next I used the program PyMOL (molecular graphics system designed for medium to large biomolecules such as proteins). The software can generate high-quality illustrations molecular graphics images and animations. Among other things, allow me to adapt the work to remove materials that are unsuitable for searching channel using the plugin MOLE.
MOLE program is a joint work of the National Research Biomolecular Masaryk University in Brno, and Department of Physical Chemistry Palacky University in Olomouc. It is based on Dijkstra's algorithm, which searches the Voronoi diagram and takes into account the distance to the nearest atom. [10] File formats PyMOL can read the PDB contained maps.



Channels found by program MOLE and visualized in PyMOL.
Blue is shown canal PW2f, red and green solvation channel (CYP2D6).



The search results are sorted by channels geometric preferences. Identification of internal residues were carried out a thorough visual inspection. Its advantage lies not only in the correct detection of the presence of amino acid residues, but also in consideration of their spatial orientation. Successive comparison is the expected finding of similar elements and draw the necessary conclusions.

In the table are given human CYP forms, which I am focusing on. Then the identification codes of the PDB database, the presence of ligands with their locations and number of strings forming enzyme.

The first step was to be recorded in the vicinity of residues and the heme cavity, which is shared by all channels. All the space I have called the active site. The overall topography is seen in the attached pictures.

The second step involved comparing the tunnels of the same type and the third point was to re-verify the PyMOL application.

In cases of polymeric enzymes I made the sum of the individual data strings. The sum represents the unification of the channel or volume. their maximum capacity.