Algorithms for Molecular Biology 12.1 Protein Structure Introduction 12.1.1 Background

Proteins are long chains of Amino Acids (AA). There are 20 different AAs that serve as building blocks for proteins. Each AA has a specific chemical structure which contains a carbon backbone similar to all amino acids and a residue which varies between the AAs. The length of a protein chain can range from 50 to 1000-3000 AA (200 on the average). Proteins are known to have many important functions in the cell, such as enzymatic activity, storage and transport of material, signal transduction, antibodies and more. An important property of a protein is the length and composition of the AA chain. The series can be obtained automatically from the gene that encodes for the protein. Another interesting property is the unique folding. The AA composition of a protein will usually uniquely determine (on specific environment conditions) the 3D structure of the protein (e.g., two proteins with the same AA sequence will have the same 3D structure in natural conditions). An experiment conducted by Anfinsen [1] showed that a denaturated protein (unfolded by special chemicals), folded back to its original structure after the removal of the denaturating chemicals. All proteins whose structure is known are stored in the Protein DataBank (PDB) which contains about 20,000 proteins [7]. A protein has multiple levels of structure (see Figure 12.1):