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1. Implementing the CURE: Combining Wet-Lab Protein Biochemistry with Computational Analysis to Provide Gains in Student Learning in the Biochemistry Teaching Lab

   Pikaart, Michael J (April 2018, The FASEB journal)

   Most undergraduates studying biochemistry and molecular biology get their broadest exposure to wet-lab techniques in protein and nucleic acid chemistry (and, increasingly, computer/visualization) in their upper-level laboratory courses. These tend to be juniors and seniors with well-defined career goals. Some of these students will have already have a research background in a traditional one-to-one (or one-to-few) research mentoring setting, for example a summer research program. This approach has proved effective at increasing student learning and persistence in the sciences. At the same time, extended full-time PI-directed research is limited in the number of students served, and can even present a barrier. To broaden the impact of teaching through research, many practitioners have adopted a CURE, or Course-based Undergraduate Research Experience, approach.This presentation reports on “BASIL” (Biochemical Authentic Scientific Inquiry Laboratory), a team of faculty who have worked to bring computational and wet-lab protein science to the biochemistry teaching lab. Together, we have developed a protein biochemistry CURE to determine enzymatic function of proteins of unknown activity. This work leverages the results of the Protein Structure Initiative, a fifteen-year NIH-funded effort which concluded in 2015 with the publication and distribution of more than 5000 previously uncharacterized proteins. The great majority of these are “orphans,” with high quality structures and pre-cloned expression plasmids available, but no research on their enzymatic function or role in native organisms. The BASIL consortium of undergraduate biochemistry faculty and students seeks to identify functional properties of a subset of these uncharacterized proteins, seeking to unify structure and function relationships. Currently, implementable modules are available for faculty who wish to adopt them, and expected student results will be presented.Support or Funding InformationSupported by NSF IUSE 1709278This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal. 

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2. Integrating Computation and Wet Lab Methods in a Biochemistry Lab Course-Based Undergraduate Research Experience (Cure)

   https://doi.org/10.1016/j.bpj.2019.11.1786  

   Koeppe, Julia R.; Ringer McDonald, Ashley; Roberts, Rebecca; Craig, Paul A. (February 2020, Biophysical Journal)
3. Combining molecular visualization with bench methods in a hypothesis-driven undergraduate biochemistry lab course

   https://doi.org/10.1096/fasebj.30.1_supplement.666.2  

   Craig, Paul A; Mills, Jeffrey L; Daubner, Colette; Pikaart, Michael J (April 2016, The FASEB journal)

   We are seeking to incorporate authentic inquiry into an undergraduate biochemistry lab course. Students on six campuses are combining computational (“in silico”) and wet lab (“in vitro”) techniques as they characterize proteins whose three dimensional structures are known but to which functions have not been previously ascribed. The in silico modules include protein visualization with PyMOL, structural alignment using Dali and ProMOL, sequence exploration with BLAST and Pfam, and ligand docking with PyRX and Autodock Vina. The goal is to predict the function of the protein and to identify the most promising substrates for the active sites. In the wet lab, students express and purify their target proteins, then conduct enzyme kinetics with substrates selected from their docking studies. Their learning as students and their growth as scientists is being assessed in terms of research methods, visualization, biological context, and mechanism of protein function. The lab course is an extension of successful undergraduate research efforts at RIT and Dowling College. The modules that are developed will be disseminated to the scientific community via a web site (promol.org), including both protocols and captioned video instruction in the techniques involved. Over the course of the project, we will also be following changes in faculty and teaching assistant competence in two areas: effective teaching with structural biology tools and the development of skills in the area of measuring learning gains by students. As we conduct the lab on these different campuses, we will also focus on advantages of our approach and barriers to implementation that exist on each campus, from the level of student acceptance and faculty training, to resources that are needed to changes in the culture at the departmental and institutional levels. As we analyze the feasibility of this approach on other campuses, we will seek input from other potential adopters about their level of interest and the barriers that they anticipate on their campuses. 

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4. Using structure to predict function in protein biochemistry: a combined computational and wet lab approach

   https://doi.org/10.1016/j.bpj.2021.11.2877  

   Koeppe, Julia R.; Craig, Paul A. (February 2022, Biophysical Journal)
5. Abstract 156: The Biochemistry Authentic Scientific Inquiry Lab (BASIL) provides a framework for learning Michaelis-Menten kinetics

   https://doi.org/10.1016/j.jbc.2023.103481  

   Roberts, Rebecca (January 2023, Journal of Biological Chemistry)