Conserved tertiary interactions and alpha-helical interaction motifs in protein structure.

摘要

In the past five years, both the number of protein structures in the protein data bank (PDB) and the number of publicly available protein sequences have more than doubled. Therefore, if a structural or sequence motif is identified in a particular protein, it is now possible to search for other instances of that motif in the PDB or sequence databases thus finding if a motif represents a general biological pattern. Here I provide two instances of this procedure. Using the protein structure of BPI as a model system, four conserved tertiary interactions were found in the homologous domains of BPI. Using the PDB, additional examples of conserved tertiary interactions were found, providing additional evidence that conserved tertiary interactions are important for stabilizing the folds of proteins. As a second example, the sequence motif GXXXG was found to be important for stabilizing the quaternary structure of the enzyme pyruvate dehydrogenase. Using both the PDB and available genomic sequence data, additional examples of proteins utilizing the GXXXG motif for stability were found. Therefore, structural research need not be limited to the analysis of only one particular example of a structural motif, but involves both finding the motif and characterization of its general importance.