NotesFAQContact Us
Search Tips
Peer reviewed Peer reviewed
Direct linkDirect link
ERIC Number: EJ1160750
Record Type: Journal
Publication Date: 2017
Pages: 9
Abstractor: As Provided
ISSN: ISSN-1470-8175
Using PyMOL to Explore the Effects of ph on Noncovalent Interactions between Immunoglobulin G and Protein A: A Guided-Inquiry Biochemistry Activity
Roche Allred, Zahilyn D.; Tai, Heeyoung; Bretz, Stacey Lowery; Page, Richard C.
Biochemistry and Molecular Biology Education, v45 n6 p528-536 Nov-Dec 2017
Students' understandings of foundational concepts such as noncovalent interactions, pH and pK[subscript 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/pK[subscript 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/pK[subscript 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/pK[subscript 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, pK[subscript a], and protein structure.
Wiley-Blackwell. 350 Main Street, Malden, MA 02148. Tel: 800-835-6770; Tel: 781-388-8598; Fax: 781-388-8232; e-mail:; Web site:
Publication Type: Journal Articles; Reports - Descriptive
Education Level: Higher Education
Audience: N/A
Language: English
Sponsor: National Science Foundation (NSF)
Authoring Institution: N/A
Grant or Contract Numbers: 1432466; 1552113