Title

Using PyMOL to Explore the Effects of pH on Noncovalent Interactions between Immunoglobulin G and Protein A: A Guided-Inquiry Biochemistry Activity

Authors

Zahilyn Roche, Miami UniversityFollow
Heeyoung Tai, Miami University - Oxford
Stacey Lowery Bretz, Miami University - Oxford
Richard C. Page, Miami University - Oxford

Document Type

Article

Publication Date

5-24-2017

Publication Title

Biochemistry and Molecular Biology Education

Keywords

Protein-protein interactions, molecular visualization, guided inquiry, laboratory exercises, noncovalent interactions

ISSN

1539-3429

Volume

46

Issue/No.

6

First Page

528

Last Page

536

Abstract

Students' understandings of foundational concepts such as noncovalent interactions, pH and pKa are crucial for success in undergraduate biochemistry courses. We developed a guided-inquiry activity to aid students in making connections between noncovalent interactions and pH/pKa. Students explore these concepts by examining the primary and tertiary structures of immunoglobulin G (IgG) and Protein A. Students use PyMOL, an open source molecular visualization application, to (1) identify hydrogen bonds and salt bridges between and within the proteins at physiological pH and (2) apply their knowledge of pH/pKa to association rate constant data for these proteins at pH 4 and pH 11. The laboratory activity was implemented within a one semester biochemistry laboratory for students majoring in allied health disciplines, engineering, and biological sciences. Several extensions for more advanced students are discussed. Students' overall performance highlighted their ability to successfully complete tasks such as labeling and identifying noncovalent interactions and revealed difficulties with analyzing noncovalent interactions under varying pH/pKa conditions. Students' evaluations after completing the activity indicated they felt challenged but also recognized the potential of the activity to help them gain meaningful understanding of the connections between noncovalent interactions, pH, pKa, and protein structure.

Comments

Free Access

© 2017 The International Union of Biochemistry and Molecular Biology

Additional Comments

Research Funding National Science Foundation. Grant Numbers: MCB 15-52113, 1432466 Miami University

NSUWorks Citation

Roche, Z., Tai, H., Bretz, S. L., & Page, R. C. (2017). Using PyMOL to Explore the Effects of pH on Noncovalent Interactions between Immunoglobulin G and Protein A: A Guided-Inquiry Biochemistry Activity. Biochemistry and Molecular Biology Education, 46, (6), 528 - 536. https://doi.org/10.1002/bmb.21066. Retrieved from https://nsuworks.nova.edu/cnso_chemphys_facarticles/313

ORCID ID

https://orcid.org/0000-0003-2971-4878

DOI

10.1002/bmb.21066