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From Pipe Cleaners and Pony Beads to Apps and 3D Glasses: Teaching Protein Structure

    Author: Pamela A. Marshall1
    VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: School of Mathematical and Natural Sciences, New College of Interdisciplinary Arts and Sciences, Arizona State University at the West Campus, Phoenix, AZ 85069
    AUTHOR AND ARTICLE INFORMATION AUTHOR AND ARTICLE INFORMATION
    • Published 15 December 2014
    • †Supplemental materials available at http://jmbe.asm.org
    • Corresponding author. Mailing address: School of Mathematical and Natural Sciences, New College of Interdisciplinary Arts and Sciences, Arizona State University at the West campus, MC 2352, P.O. Box 37100, Phoenix, AZ 85069. Phone: 602-543-6143. Fax: 602-543-6073. E-mail: [email protected].
    • ©2014 Author(s). Published by the American Society for Microbiology.
    Source: J. Microbiol. Biol. Educ. December 2014 vol. 15 no. 2 304-306. doi:10.1128/jmbe.v15i2.714
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    Abstract:

    Students often self-identify as visual learners and prefer to engage with a topic in an active, hands-on way. Indeed, much research has shown that students who actively engage with the material and are engrossed in the topics retain concepts better than students who are passive receivers of information. However, much of learning life science concepts is still driven by books and static pictures. One concept students have a hard time grasping is how a linear chain of amino acids folds to becomes a 3D protein structure. Adding three dimensional activities to the topic of protein structure and function should allow for a deeper understanding of the primary, secondary, tertiary, and quaternary structure of proteins and how proteins function in a cell. Here, I review protein folding activities and describe using Apps and 3D visualization to enhance student understanding of protein structure.

Key Concept Ranking

Protein Folding
0.6245984
Protein G
0.5294118
Streptomyces clavuligerus
0.5051873
DNA Replication
0.41196245
Amino Acids
0.4111589
0.6245984

References & Citations

1. Crochetiere H 2007 Protein folding demo. Presentation at the New Jersey Science Convention. [Online.] www.btanj.org/demo/2007/protein.pdf. Accessed December 1, 2013
2. DeBruyn JM 2012 Teaching the central dogma of molecular biology using jewelry J Microbiol Biol Educ 13 62 64 10.1128/jmbe.v13i1.356 23653786 3577301 http://dx.doi.org/10.1128/jmbe.v13i1.356
3. Derrick JP, Wigley WP 1994 The third IgG-binding domain from streptococcal protein G J Mol Biol 243 906 918 10.1006/jmbi.1994.1691 7966308 http://dx.doi.org/10.1006/jmbi.1994.1691
4. Jittivadhna K, Ruenwongsa P, Panijpan B 2009 Making ordered DNA and protein structures from computer-printed transparency film cut-outs Biochem Mol Biol Educ 37 220 226 10.1002/bmb.20299 21567740 http://dx.doi.org/10.1002/bmb.20299
5. Kohn C 2012 Pipe cleaner protein modeling. Agricultural Sciences Semester II Curriculum 2014 [Online.] http://wuhsag.weebly.com/uploads/1/4/0/9/14095127/pipe_cleaner_protein_modeling.docx. Accessed June 6, 2014
6. Nelson A, Goetze J 2004 Modeling protein folding and applying it to a relevant activity Am Biol Teach 66 287 289
7. Office of Science Outreach, University of Indiana. 2010 Build and fold a model protein. Protein folding. [Online.] http://www.indiana.edu/~oso/lessons/prot/folding1.htm#model. Accessed December 26, 2013
8. Ormo M, Cubitt AB, Kallio K, Gross LA, Tsien RY, Remington SJ 1996 Crystal structure of the Aequorea victoria green fluorescent protein. Science 273 1392 1395 10.1126/science.273.5280.1392 http://dx.doi.org/10.1126/science.273.5280.1392
9. Oster LM, et al 2006 Insights into cephamycin biosynthesis: the crystal structure of CmcI from Streptomyces clavuligerus. J. Mol. Biol. 358 546 558 10.1016/j.jmb.2006.02.004 16527306 http://dx.doi.org/10.1016/j.jmb.2006.02.004
10. Preece D, Williams SB, Lam R, Weller R 2013 “Let’s get physical”: advantages of a physical model over 3D computer models and textbooks in learning imaging anatomy” Anatom Sci Educ 6 216 224 10.1002/ase.1345 http://dx.doi.org/10.1002/ase.1345
11. Priano C 2013 Shaping tRNA Amer Biol Teach 75 708 709 10.1525/abt.2013.75.9.14 http://dx.doi.org/10.1525/abt.2013.75.9.14
12. Sigismondi L 1989 A paper model of DNA structure and replication Amer Biol Teach 51 422 423 10.2307/4448969 http://dx.doi.org/10.2307/4448969
13. White B 2006 A simple and effective protein folding activity suitable for large lectures CBE Life Sci Educ 5 264 269 10.1187/cbe.05-12-0136 17012218 1618698 http://dx.doi.org/10.1187/cbe.05-12-0136

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2014-12-15
2019-10-24

Abstract:

Students often self-identify as visual learners and prefer to engage with a topic in an active, hands-on way. Indeed, much research has shown that students who actively engage with the material and are engrossed in the topics retain concepts better than students who are passive receivers of information. However, much of learning life science concepts is still driven by books and static pictures. One concept students have a hard time grasping is how a linear chain of amino acids folds to becomes a 3D protein structure. Adding three dimensional activities to the topic of protein structure and function should allow for a deeper understanding of the primary, secondary, tertiary, and quaternary structure of proteins and how proteins function in a cell. Here, I review protein folding activities and describe using Apps and 3D visualization to enhance student understanding of protein structure.

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Author and Article Information

  • Published 15 December 2014
  • †Supplemental materials available at http://jmbe.asm.org
  • Corresponding author. Mailing address: School of Mathematical and Natural Sciences, New College of Interdisciplinary Arts and Sciences, Arizona State University at the West campus, MC 2352, P.O. Box 37100, Phoenix, AZ 85069. Phone: 602-543-6143. Fax: 602-543-6073. E-mail: [email protected].
  • ©2014 Author(s). Published by the American Society for Microbiology.

Figures

From Pipe Cleaners and Pony Beads to Apps and 3D Glasses: Teaching Protein Structure
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Citation: Marshall P. 2014. From pipe cleaners and pony beads to apps and 3d glasses: teaching protein structure . J. Microbiol. Biol. Educ. 15(2):304-306 doi:10.1128/jmbe.v15i2.714
/content/jmbe/10.1128/jmbe.v15i2.714.f1-jmbe-15-304
FIGURE 1.

Examples of pipe cleaner protein structures. For details please see Appendix 1 .

jmbe/15/2/jmbe-15-304f1_thmb.gif
jmbe/15/2/jmbe-15-304f1.gif
Image of FIGURE 1.

Click to view

FIGURE 1.

Examples of pipe cleaner protein structures. For details please see Appendix 1 .

Source: J. Microbiol. Biol. Educ. December 2014 vol. 15 no. 2 304-306. doi:10.1128/jmbe.v15i2.714
Download as Powerpoint
/content/jmbe/10.1128/jmbe.v15i2.714.f2-jmbe-15-304
FIGURE 2.

Tangle Proteins Building Set, the 3 IgG binding domain of Streptococcal protein G ( 3 ); instructions in the kit.

jmbe/15/2/jmbe-15-304f2_thmb.gif
jmbe/15/2/jmbe-15-304f2.gif
Image of FIGURE 2.

Click to view

FIGURE 2.

Tangle Proteins Building Set, the 3 IgG binding domain of Streptococcal protein G ( 3 ); instructions in the kit.

Source: J. Microbiol. Biol. Educ. December 2014 vol. 15 no. 2 304-306. doi:10.1128/jmbe.v15i2.714
Download as Powerpoint
/content/jmbe/10.1128/jmbe.v15i2.714.f3-jmbe-15-304
FIGURE 3.

Green fluorescent protein (1EMA) ( 8 ) rendered with iMolview. (a) Visualized as a ribbon structure colored N to C. (b) Visualized with 3D surfaces (skin) drawn.

jmbe/15/2/jmbe-15-304f3_thmb.gif
jmbe/15/2/jmbe-15-304f3.gif
Image of FIGURE 3.

Click to view

FIGURE 3.

Green fluorescent protein (1EMA) ( 8 ) rendered with iMolview. (a) Visualized as a ribbon structure colored N to C. (b) Visualized with 3D surfaces (skin) drawn.

Source: J. Microbiol. Biol. Educ. December 2014 vol. 15 no. 2 304-306. doi:10.1128/jmbe.v15i2.714
Download as Powerpoint
/content/jmbe/10.1128/jmbe.v15i2.714.f4-jmbe-15-304
FIGURE 4.

Cephalosporin hydroxylase from (2BM8) ( 9 ). Rendered with iMolview. (a) Protein structure. (b) Anaglyph structure.

jmbe/15/2/jmbe-15-304f4_thmb.gif
jmbe/15/2/jmbe-15-304f4.gif
Image of FIGURE 4.

Click to view

FIGURE 4.

Cephalosporin hydroxylase from (2BM8) ( 9 ). Rendered with iMolview. (a) Protein structure. (b) Anaglyph structure.

Source: J. Microbiol. Biol. Educ. December 2014 vol. 15 no. 2 304-306. doi:10.1128/jmbe.v15i2.714
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