Protein conformational analysis and online sequence searching: an application to drug research

Protein structure is generally described at a primary or three-dimensional level. The primary structure is the amino acid sequence of the protein, the order that the constituent amino acids occur in a chain. The amino acid sequence of a protein is determined precisely by genes and is the key to understanding the biochemistry of these macromolecules. The three-dimensional structure or the conformation of proteins is determined variously by hydrophobic interactions among the amino acids and other intramolecular forces, such as van der Waals interactions. These interactions affect the secondary, tertiary, and quaternary structure. The pattern of folding of a peptide chain into α helix or β-sheet is referred to as the secondary structure. This is determined by the interaction of closely grouped amino acids. Further folding, which involves interactions between groups distant in the protein, determines the tertiary structure. Finally, the aggregation of monomelic protein subunits into oligomers yields the quaternary structure.