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Analyzing the 3D Structure of Human Carbonic Anhydrase II and Its Mutants Using Deep View and the Protein Data Bank

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Noam J. Ship and Deborah B. Zamble

Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada

J. Chem. Educ., 2005, 82 (12), p 1805

DOI: 10.1021/ed082p1805

Publication Date (Web): December 1, 2005

Section:

History, Education, and Documentation

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.

Keywords (Audience):

Upper-Division Undergraduate

Keywords (Domain):

Biochemistry

Keywords (Feature):

Molecular Modeling Exercises and Experiments

Keywords (Pedagogy):

Computer-Based Learning

Keywords (Subject):

Molecular Modeling

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This article has been cited by 1 ACS Journal articles (1 most recent appear below).

Introduction to Protein Structure through Genetic Diseases
Tanya L. Schneider and Brian R. Linton
Journal of Chemical Education2008 85 (5), 662
- Introduction to Protein Structure through Genetic Diseases
  Tanya L. Schneider and Brian R. Linton
  Journal of Chemical Education2008 85 (5), 662
  An illuminating way to learn about protein function is to explore high-resolution protein structures. Analysis of the proteins involved in genetic diseases has been used to introduce students to protein structure and the role that individual mutations can ...
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