Beginning Perl for Bioinformatics

Chapter 11. Protein Data Bank

The success of the Human Genome Project in decoding the DNA sequence of human genes has captured the public imagination, but another project has been quietly gaining momentum, and it promises equally revolutionary results. This project is an international effort to determine the 3D structure of a comprehensive range of proteins on a genome-wide level using high-throughput analytical technologies. This international effort is the foundation of the new field of structural genomics.

Recent and expected advances in technology promise an accelerating pace of protein structure determination. The storehouse for all of this data is the Protein Data Bank (PDB). The PDB may be found on the web at http://www.rcsb.org/pdb/.

Finding the amino acid or primary sequence is just the beginning of studying a protein. Proteins fold locally into secondary structures such as alpha helices, beta-strands, and turns. Two or three adjacent secondary structures might combine into common local folds called " motifs” or “supersecondary” structures such as beta sheets or alpha-alpha units. These building blocks then fold into the 3D or tertiary structure of a protein. Finally, one or more tertiary structures may be combined as subunits into a quaternary structure such as an enzyme or a virus.

Without knowing how a protein folds into a 3D structure, you are less likely to know what the protein does or how it does it. Even if you know that the protein is implicated in a disease, ...