Comparison Between The Various Protein Classification Schemes
- Publisher: Journal of Engineering Computers & Applied Sciences
Journal of Engineering Computers & Applied Sciences
(issn: 2319-5606, eissn: 2319-5606)
Applied Sciences; Biochemistry | Domain, folding, family, class, and evolutionary relationships
The structure of proteins refers to the bimolecular arrangement of molecules. Proteins are polymers made up of individual molecules joined together by polypeptide bonds. The molecules making up proteins are referred to as amino acids. Proteins tend to fold into different conformations. Protein folding can be attributed to several non-covalent interactions between molecules. Such interactions include hydrophobic interactions, Van der Waals attraction forces, ionic, and hydrogen bonding. Proteins possess numerous types of structures. Since the establishment of the Protein Data Bank (PDB), protein structures exceeding 8000 have been deposited (Mount 32). Proteins are usually classified based on folds and families. The two properties in proteins are influenced by amino acid sequencing and are important in the identification of proteins which share an evolutionary relationship. Protein structures are often divided into many discrete domains (Bourne and Helge 26). A domain is a folding unit having a distinct structure from the others. A domain also functions independently from the others. Proteins must therefore be separated into the different domains prior to classification. The level of folding within these domains further helps in the classification of proteins into superfamily and later families (Hadley 1106). Several classification methods have been formulated with the aim of comparing different protein structures. Classification according to the folding patterns has lead to the creation of a number of databases within PDP. Among the most popular databases within PDP includes Structural Classification of Proteins (SCOP), Classification by class, architecture, domain topology, and homology (CATH), and protein families (Pfam). Proteins are mainly classified in terms of structure and function (Barton 554).