Protein are linear chains molecules made up of units called amino acids. Approxoimately twenty different amino acids make up a protein chain. They are called polypeptide chains as they often contain a few to several hundred amino acids linked with each other by peptide bonds. Several polypeptide chains form subunits for a large protein. For example the haemoglobin consists of four subunits (Two alpha and two beta chains) each harbouring haeme, an iron containing molecule. The peptide bond between amino acids is fairly flexible. As a result, oligopeptide and polypeptide chains fold to a convoluted shapes. Every protein folds in a particular way to form a distinctive configuration for its specific function. The protein configuration is made primarily by the amino acids side chains. Some amino acid side chains are electrically charged (positive or negative). Others called polar molecules or neutral and strongly attract the electrons. A third group of amino acids are said to have non-polar or hydrophobic side chains. Thus proteins fold up in such a way that non-polar-hydrophobic groups remain buried inside the molecule and the polar and charged groups remain outside.
The sequential and linear arrangement of amino acids in a polypeptide represents its primary structure. The folding of protein chain to form recognizable modules such as alpha helix and beta sheets represents its secondary structure . The three dimensional shape of a polypeptide is called its tertiary structure.Alpha helices and beta sheets provide further stability to protein structure.
The proteins synthesized inside a cell undergo the above mentioned configurational changes to attain stable structures. Otherwise, they will be digested or destroyed by the cellular proteolytic enzymes. The proteins take up different profiles as structuraland functional proteins such as enzymes and hormones etc.
In proteomics, the amino acid sequences are read by automated sequenators and stored in computers as internationally available databases. The information regarding three-dimensional structure of protein is stored in another computerized database called Protein Data Bank. Only three dimensional forms are used to define protein structure.
In proteomics, to delineate information about a protein at atomic and molecular levels, models are constructed. X-ray crystallography can give a skeleton model of a protein from its results on its atomic details. With atomic data, computers nowadays generate graphic images of the molecules on high-resolution screen. Computer modeling of protein began as early as 1970. The computer-generated models depict not only the properties of amino acids in a protein but also help to understand the protein function. One of the computer graphic models is the 'Glowing coal' model.
1.Protein structure helps in understanding biomolecular arrangement in tissue or cellular architecture.
2. Protein structures, protein models and computer aided graphic models help to understand biological reactions mediated by enzymes (proteins).
3. Graphic models provided by computers are valuable to predict which fragments of a medically important protein can be used to design drugs and vaccines.
4. Proteomics also helps in chemical industries to manufacture drugs, various chemical compounds and enzymes.