Incorporating modeling and simulations in undergraduate biophysical chemistry course to promote understanding of structure‐dynamics‐function relationships in proteins

Abstract

A project-based biophysical chemistry laboratory course, which is offered to the biochemistry and molecular biology majors in their senior year, is described. In this course, the classroom study of the structure-function of biomolecules is integrated with the discovery-guided laboratory study of these molecules using computer modeling and simulations. In particular, modern computational tools are employed to elucidate the relationship between structure, dynamics, and function in proteins. Computer-based laboratory protocols that we introduced in three modules allow students to visualize the secondary, super-secondary, and tertiary structures of proteins, analyze non-covalent interactions in protein-ligand complexes, develop three-dimensional structural models (homology model) for new protein sequences and evaluate their structural qualities, and study proteins' intrinsic dynamics to understand their functions. In the fourth module, students are assigned to an authentic research problem, where they apply their laboratory skills (acquired in modules 1-3) to answer conceptual biophysical questions. Through this process, students gain in-depth understanding of protein dynamics-the missing link between structure and function. Additionally, the requirement of term papers sharpens students' writing and communication skills. Finally, these projects result in new findings that are communicated in peer-reviewed journals.

Assessment of students' external representations of mmCIF entries and their biochemical knowledge

“…Much of the integration of molecular modeling and computational chemistry into biochemistry and chemistry classes has focused on course descriptions, anecdotal comments, and/or Likert scale type questions . This does not mean that there were no student questions or assignments, but the results were not discussed in regards to student understanding.…”

From blood to milk: Graphical systems modeling in secondary‐level biochemistry courses

“…2 Indeed, in recent years, the use of systems modeling in science curricula has continually increased. 3,4 Due to the complexity underlying biochemical transformations (i.e., metabolism) of living organisms, graphical representation of systems integration can be a useful technique to conceptualize metabolism. 5 Secondary-level educators can integrate systems modeling into their online biochemistry units through use of programs such as "Power Point" or "Google Slides," which allow students to make graphical representations that depict systems integration.…”

“…Systems modeling is a powerful approach towards integrating these perspectives to allow their exploration using a holistic approach 2 . Indeed, in recent years, the use of systems modeling in science curricula has continually increased 3,4 …”

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

“…In recent years, a number of experiments and activities to incorporate the use of molecular visualization programs as part of biochemistry lecture or laboratory courses have been developed . Activities range from students performing activities solely within molecular visualization programs to laboratory experiments to using physical models that serve as a complement to the programs .…”