Below is the database schema used by the RCSB Protein Data Bank Each box indicates a separate...
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• Below is the database schema used by the RCSB Protein Data Bank • Each box indicates a separate attribute set • Bioinformatics databases are very large PROTEIN STRUCTURE PROTEIN STRUCTURE DATABASE SCHEMA DATABASE SCHEMA Source: http://www.rcsb.org/pdbschema/
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Transcript of Below is the database schema used by the RCSB Protein Data Bank Each box indicates a separate...
• Below is the database schema used by the RCSB Protein Data Bank
• Each box indicates a separate attribute set• Bioinformatics databases are very large
PROTEIN STRUCTURE PROTEIN STRUCTURE DATABASE SCHEMADATABASE SCHEMA
Source: http://www.rcsb.org/pdbschema/
• The goal of structure databases is to explore the relationship between the three-dimensional structure of a macromolecule (such as a protein) and it’s function
• A protein is a linear chain of amino acids that folds and bonds with itself
• Only 20 different amino acids contribute for protein synthesis.
• How a protein folds is determined by it’s amino acid composition
• Understanding how structure affects function is essential to creating synthetic proteins
STRUCTURE STRUCTURE DATABASESDATABASES
• Primary Structure: The simple linear chain of amino acids connected by peptide bonds.
• Secondary Structure: Collection of the alpha helixes and beta sheets formed by the interaction of amino acids in the sequence.
• Tertiary Structure: The overall 3-dimensional shape of a single protein. The chain folds and bonds with disulfide bridges.
• Quaternary Structure: The structure formed by the bonds between different polypeptide chains.
Source: http://academic.brooklyn.cuny.edu/biology/bio4fv/page/prot_struct-4143.JPG
PROTEIN STRUCTURE PROTEIN STRUCTURE TERMINOLOGYTERMINOLOGY
• One of the goals of bioinformatics is to be able to determine the shape taken by a protein just by analyzing it’s primary structure
• Applications:– Drug design, such as improving insulin– Agriculture, such as developing fruits that stay ripe
longer– Synthesizing enzymes to perform industrial tasks
• An average cell creates 15,000 different kinds of proteins, so there is still much left to discover in this area
GOALS AND GOALS AND APPLICATIONSAPPLICATIONS
RASMOLRASMOL• RasMol is a free tool for
viewing protein structure• Available at
http://www.openrasmol.org/ and many other websites
• Viewable data for RasMol can be obtained from the RCSB Protein Data Bank at http://www.rcsb.org/pdb/Welcome.do
