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Protein Structure and Function *

Difficulty
Time Required Very Long (1+ months)
Prerequisites Advanced biology course, or willingness to read up on such topics extensively.
Material Availability A computer with Internet access is necessary for this project.
Cost Very Low (under $20)
Safety No issues
*Note: This is an abbreviated Project Idea, without notes to start your background research, a specific list of materials, or a procedure for how to do the experiment. You can identify abbreviated Project Ideas by the asterisk at the end of the title. If you want a Project Idea with full instructions, please pick one without an asterisk.

Abstract

How 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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Science Buddies Staff. "Protein Structure and Function" Science Buddies. Science Buddies, 30 June 2014. Web. 29 Aug. 2014 <http://www.sciencebuddies.org/science-fair-projects/project_ideas/BioChem_p021.shtml>

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Science Buddies Staff. (2014, June 30). Protein Structure and Function. Retrieved August 29, 2014 from http://www.sciencebuddies.org/science-fair-projects/project_ideas/BioChem_p021.shtml

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Last edit date: 2014-06-30

Bibliography

PDB, 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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