title: 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.
authors.affiliation: Department of Chemistry, University Wisconsin, Eau Claire, Wisconsin.
authors.forename: Sanchita
authors.initials: S
authors.lastname: Hati
authors.affiliation: Department of Chemistry, University Wisconsin, Eau Claire, Wisconsin.
authors.forename: Sudeep
authors.initials: S
authors.lastname: Bhattacharyya
mesh_terms: D001671:Biochemistry / Q000193:education*; D007753:Laboratories; D008958:Models, Molecular; D008967:Molecular Biology / Q000193:education; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000502:physiology*; D013329:Structure-Activity Relationship; D014495:Universities
chemical_list: D011506:Proteins
keywords: computers in research and teaching; integration of research into undergraduate teaching; molecular visualization; protein structure, function, and action mechanism