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  Home > JCE Print > Journal of Chemical Education > Issues > 2005  > December  >
In the Laboratory
Molecular Modeling Exercises and Experiments
Analyzing the 3D Structure of Human Carbonic Anhydrase II and Its Mutants Using Deep View and the Protein Data Bank
Noam J. Ship and Deborah B. Zamble
Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
Cover
December 2005
Vol. 82 No. 12
p. 1805
Abstract
A lab was designed to teach biological chemistry students to critically analyze the 3D structure of a protein. The enzyme studied was human carbonic anhydrase (II) and students also examined mutants and protein bound to a variety of ligands, metals, and inhibitors. The coordinate files for each protein are downloaded by the students from the Protein Data Bank. The structure is viewed and manipulated with the public-domain molecular-viewing software Deep View. Students learn how to interpret Ramachandran plots, study familial homology, make virtual mutations, compare structures, analyze structural details, and produce stunning 3D images. The lab runs on personal computers with Internet access and requires minimal to no supervision. This lab can be used as an independent project or as part of a more comprehensive set of experiments, and it can be adapted to the study of other biomolecules.

Featured on the Cover.

Supplement
Instructions for the students are available.
*  Contents JCE2005p1805W.doc (Microsoft Word)
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JCE2005p1805W.pdf

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More Information
*  Citation
 Ship, Noam J.; Zamble, Deborah B. J. Chem. Educ. 2005 82 1805.
*  Keywords
 Biochemistry; Bioinorganic Chemistry; Bioorganic Chemistry; Computer-Based Learning; Graduate Education / Research; Internet / Web-Based Learning; Laboratory Instruction; Molecular Modeling; Proteins / Peptides; Upper-Division Undergraduate
*  History
 Created:
Last Updated:		 October 25, 2005
November 4, 2005
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