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Structural Studies of Phycobiliproteins from Spirulina: Combining Spectroscopy, Thermodynamics, and Molecular Modeling in an Undergraduate Biochemistry Experiment
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Abstract
Molecular modeling provides a powerful mechanism for students to connect molecular-level structural changes with macroscopically observable properties. We describe an experiment that integrates spectroscopy, thermodynamics, and molecular modeling into a single activity examining structural changes in phycobiliproteins upon denaturation with urea. Phycobiliproteins contain a covalently attached chromophore, phycocyanobilin, which is constrained in a planar conformation by the folded protein. Upon denaturation of the protein, the chromophore undergoes a conformational change, leading to a significant alteration of the absorption spectrum. By measuring the absorbance at 625 nm as a function of urea concentration, the free energy of unfolding can be determined. Students determine the dihedral angles in the chromophore and map the contacts between protein and chromophore using Protein Explorer, a structure visualization program freely available on the Internet. The change in absorption wavelength can be related to the difference between the LUMO and HOMO energies, obtained using PC Spartan Pro, for the chromophore in the folded and unfolded phycobiliprotein. This experiment could be used in a physical chemistry class in a curriculum that integrates biochemistry throughout the course work as well as in a traditional biochemistry course.
Keywords (Audience):
Upper-Division UndergraduateKeywords (Domain):
BiochemistryKeywords (Pedagogy):
Hands-On Learning / ManipulativesKeywords (Subject):
Biophysical ChemistryCiting Articles
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- Received: August 03, 2009
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