| Introduction to Protein Structure |
Although proteins are unique, they share certain common characteristics
(Fig. 1). The primary structure of each protein is determined by the sequence of specific amino acids, encoded by the mRNA, which directs the proper folding of the polypeptide chain into the secondary structure. One type of secondary structure is the alpha helix, a region of the polypeptide that folds into a corkscrew shape. Beta strands are linear structures of polypeptides, bonding together to form a flat beta sheet. Other regions of secondary structure may include turns and random coils. These helices, strands, turns, and coils interact chemically with each other to form the unique three-dimensional shape of the protein, called the tertiary structure. For some proteins, a single polypeptide chain folded in its proper three-dimensional structure creates the final protein. Many proteins, however, have several different polypeptide subunits that make the final active protein. For these proteins, the interactions between the different subunits form the quaternary structure.
Discrete portions of proteins can fold independently from the rest of the protein and have their own function. These are called domains, and serve as one of the building blocks of that protein. Domains are evolutionarily mobile, capable of rearranging as new proteins evolve. There are thousands of structural domains, and many of them have been conserved widely across proteins. New proteins appear to have arisen over evolutionary time by bringing different domains together in a process known as domain shuffling. Domains often contain smaller motifs, consisting of a conserved pattern of amino acids, or of combinations of structural elements formed by the folding of nearby amino acid sequences. An example of a motif is a helix-loop-helix, which binds to DNA. Very similar motifs are found in many proteins that are not related. Scientists have classified conserved domains and motifs in a number of databases so that new proteins can be easily analyzed for the presence of these elements.