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Using PyMOL to Explore the Effects of pH on Noncovalent Interactions between Immunoglobulin G and Protein A: A Guided‐Inquiry Biochemistry Activity
Author(s) -
Roche Allred Zahilyn D.,
Tai Heeyoung,
Bretz Stacey Lowery,
Page Richard C.
Publication year - 2017
Publication title -
biochemistry and molecular biology education
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.34
H-Index - 39
eISSN - 1539-3429
pISSN - 1470-8175
DOI - 10.1002/bmb.21066
Subject(s) - non covalent interactions , chemistry , protein–protein interaction , biochemistry , psychology , hydrogen bond , computational biology , organic chemistry , biology , molecule
Abstract Students' understandings of foundational concepts such as noncovalent interactions, pH and p K a 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/p K a . 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/p K a 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/p K a 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, p K a , and protein structure. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(6):528–536, 2017.