Protein Structure and Function *
AbstractHow a biological system functions is a consequence of the 3-D structures of biological macromolecules like proteins and protein complexes. Proteins can be categorized into different protein families based upon sequence, structure, and function. Typically, proteins in the same family have similar biochemical functions. You can investigate the structure of a protein by using protein databases (Entrez Protein, SwissProt, PDB) and 3-D computational models. You can compare the structures of different proteins with similar function to see if they have similar geometries, like molecules that bind ATP or DNA. You can compare homologous proteins from different species to see how the structure varies by searching the PDB taxonomic database. You can also search for proteins that are linked to a particular disease in PDB, and compare the normal and abnormal structures. Many proteins in the PDB database have structural data for different mutations, so you can compare the mutant structures to identify structurally important residues. When choosing a protein of interest from the structure database, consider the following questions. Does the protein occur in different conformations or isoforms? Is there a model of the active site, substrate or ligand? Is the protein part of a larger protein complex? Is there a structure that has been solved with a mutation, ion or ligand? Is the protein part of a larger family of proteins with similar structures? Are there structures available of homologous proteins from different species? Are there portions of the protein which are conserved between different species? Are there any mutations which may cause a change in 3-D structure? Are there any post-translational modifications that may affect structure, like phosphorylation or ubiquitination? (PDB, 2006)
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Last edit date: 2017-07-28
BibliographyPDB, 2006. "Structural Genomics Information Portal," The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) [accessed 3/25/06] http://sg.pdb.org/.
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