Objective

• To visualize the secondary structure of a protein. 

Theory

Proteins are important biological macromolecules, usually considered as fundamental units of a cell which play a vitally important role in different cell functions. The function of a protein is very specific and dependent on the molecule to which it binds. The protein structure is classified into primary, secondary, tertiary and quaternary. These molecules, form a linear chain of amino acids initially, and then fold into secondary, tertiary and quaternary structures. The different secondary structures of a protein are alpha helices, beta pleated sheets and loops. During the due course of evolution, some regions of the protein remain conserved which are regarded as motifs, play a key role in determining the function of that particular protein. In simple terms, researchers say that the molecules having similar structure will have a similar function. To understand the structural biology, visualization of complex macromolecular structure is essential. PyMol is an open source, three dimensional visualization tool to view the macromolecular structures like proteins and nucleic acids.

All the proteins are made up of long chain of amino acids that fold into a 3-D shape. Amino acids are organic compounds that contain a hydrogen atom, α carbon, two functional groups and a side chain R group. There are almost 20 amino acids found in human body which vary in their R groups. Amino acids are linked to each other by peptide bond. A peptide bond is formed when the carboxyl group of one amino acid linked to the amino group of another molecule through a covalent bond. 

The primary structure of a protein is made up of a linear sequence of amino acids. It is synthesized during the translation process of DNA to mRNA. DNA (Deoxyribonucleic acid) is the genetic material that contains all the genetic information for the development and maintaining all functions in all living organisms. The information is stored as genetic codes using four types of bases. They are adenine (A), guanine (G), cytosine(C) and thymine (T). RNA is differing from DNA only in 1 base pair i.e. in RNA, it is uracil (U) instead of thymine. mRNA (messenger RNA) is a molecule of RNA which is forming from DNA transcription process. During the transcription process, DNA is transcribed to mRNA i.e. thymine is replaced by Uracil. 

The intermolecular and intra-molecular hydrogen bonding between the amide groups in primary structure of protein form secondary structure. The attraction of hydrogen molecule towards electro negative atom (N, F, O etc) within same molecule is called intra-molecular hydrogen bonding and formed between two different molecules. Alpha helices and beta sheets are two important secondary structures in protein (Figure 1). Alpha helix is a right-handed conformation, beta sheets or strands which may be located parallel or anti parallel to each other (each strand).

 Figure 1: Example for Secondary structure of a protein - Human Alpha- Hemoglobin

 PyMol 

PyMOL is Copyrighted © software DeLano Scientific LLC, San Carlos, California (U.S.A.). It is free for all to use, modify, and redistribute. Warren Lyford Delano, developed the interesting molecular visualization tool PyMol, which has been regularly used by crystallographers (who finds out the macromolecular structures through the technique crystallography). In many journal papers (research papers), we can see the structural images created using PyMol. Users can get high quality images and animations of biological macromolecules like proteins. PyMol is freely available, since it is an open source visualization tool with python (programming language) interpreter. This visualization software have inbuilt demonstration of what it does (Figure 2).

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

 Figure 2: Screenshot to view the demo of representations

PyMol is used to visualize the .pdb files, which are mostly available from the protein databank. It contains 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.