Objective

• To view the active site (where the site of a protein binds to ligand molecule) pockets of the protein

Theory

Protein molecules are the fundamental units of all living cells. These macromolecules have a vital role in various cellular functions. Each protein has specific function in our body. The structure of the protein has a very important role in its function. The binding of a protein with other molecules is very specific to carry out its function properly. For this reason every protein has a particular structure. Proteins are the molecules, with a linear chain of amino acids initially, thus folds into secondary, tertiary and quaternary structures. The tertiary structure of a protein is more important due to the folding of the secondary structures, tertiary structures form the pockets or clefts, where the ligand or potential molecules, or small atoms can bind to the protein molecule, where these sites can be predicted as active sites of the molecule.

The active sites are lined up with the amino acid residues. Molecules with appropriate shape and appropriate groups can bind to the active site of the protein molecule. The mechanism is as simple as lock and key, as the particular lock opens with the only particular key, the molecule or the substrate with perfect shape can only fit into the active site.

PyMol:

PyMOL is Copyrighted © software DeLano Scientific LLC, San Carlos, California, U.S.A. That is Free for all to use, modify, and redistribute.Warren Lyford Delano, developed the interested molecular visualization tool PyMol, which has been regularly used by crystallographers (who find outs the macromolecular structures through the technique crystallography). In many Journal papers (research papers) we can see the structural images are created using PyMol. User can get the high quality images and animations of biological macromolecules like proteins. PyMol can be freely available, since it is an open source visualization tool or software with the python (programming language) interpreter. This visualization software have inbuilt demonstration of what it does (Figure 1).

To see the demo go to the standard menu bar, select the wizard menu, from the submenu select demo with representations.

Figure 1: Demo representation of the molecules in PyMol

PyMol is used to visualize the .pdb files, which are mostly available from the protein databank, contains the structures extracted from techniques like x-ray crystallography, NMR Spectroscopy. With the help of initial experimental data, the structural biologists use these techniques or methods to determine the location of each atom relative to each other in a molecule. The x-ray crystallography has x- ray diffraction pattern data, in NMR spectroscopy the scientist need the information of local conformation and distance between the atoms that are close to one another.

In x-ray crystallography the protein is purified and then crystallized, which is then treated to x-ray beams. These crystallized proteins are analyzed to get the distribution of electrons in proteins, by diffracting the x-ray beams into one or other characteristic pattern of spots. Once we get the distribution of electrons, which gives the map of electron density is interpreted to determine the location of each atom.

In NMR Spectroscopy they use, strong magnetic field to determine the protein structure. The protein is purified and subjected to strong magnetic field which is then probed with the radio waves. Thus we can observe the resonances, which can be analyzed to give the list of atomic nuclei that are close to each other. This list is used to build a model of protein that can show a location of each atom.