Uncovering protein-protein interactions through a team-based undergraduate biochemistry course

Upper-level inter-disciplinary microbiology CUREs increase student's scientific self-efficacy, scientific identity, and self-assessed skills

Course-based undergraduate research experiences (CUREs) provide opportunities for undergraduate students to engage in authentic research and generally increase the participation rate of students in research. Students' participation in research has a positive impact on their science identity and self-efficacy, both of which can predict integration of students in Science, Technology, Engineering, and Math (STEM), especially for underrepresented students. The main goal of this study was to investigate instructor-initiated CUREs implemented as upper-level elective courses in the Biomedical Sciences major. We hypothesized that these CUREs would (i) have a positive impact on students' scientific identity and self-efficacy and (ii) result in gains in students' self-assessed skills in laboratory science, research, and science communication. We used Likert-type surveys developed by Estrada et al. (14) under the Tripartite Integration Model of Social Influence to measure scientific identity, self-efficacy, and scientific value orientation. When data from all CUREs were combined, our results indicate that students' self-efficacy and science identity significantly increased after completion. Students' self-assessment of research and lab-related skills was significantly higher after completion of the CUREs. We also observed that prior to participation in the CUREs, students' self-assessment of molecular and bioinformatic skills was low, when compared with microbiological skills. This may indicate strengths and gaps in our curriculum that could be explored further.

Bridging the biochemistry lecture and laboratory courses: Construction and application of the "Innovative Experimental Design" module

Both lecture and laboratory courses of biochemistry are important professional courses for undergraduates with biology related majors. Course optimization and update is crucial but challenging, especially for the laboratory course. Although taught separately, here we showed a strategy to bridge the two courses and promote the improvement of both. In addition to knowledge teaching, we implanted the "Innovative Experimental Design" module in the lecture course in which students were required to design and present their own experimental ideas. After evaluation by the faculty group, the best idea was supported for further experimental test. Here we described the preliminary experiments and optimization procedures about the idea of microbial fuel cells. This experiment is ready to be included into the laboratory course program in spring 2023.

Multi-Institution Research and Education Collaboration Identifies New Antimicrobial Compounds

New antibiotics are urgently needed to address increasing rates of multidrug resistant infections. Seventy-six diversely functionalized compounds, comprising five structural scaffolds, were synthesized and tested for their ability to inhibit microbial growth. Twenty-six compounds showed activity in the primary phenotypic screen at the Community for Open Antimicrobial Drug Discovery (CO-ADD). Follow-up testing of active molecules confirmed that two unnatural dipeptides inhibit the growth of Cryptococcus neoformans with a minimum inhibitory concentration (MIC) ≤ 8 μg/mL. Syntheses were carried out by undergraduate students at five schools implementing Distributed Drug Discovery (D3) programs. This report showcases that a collaborative research and educational process is a powerful approach to discover new molecules inhibiting microbial growth. Educational gains for students engaged in this project are highlighted in parallel to the research advances. Aspects of D3 that contribute to its success, including an emphasis on reproducibility of procedures, are discussed to underscore the power of this approach to solve important research problems and to inform other coupled chemical biology research and teaching endeavors.

A Research-inspired biochemistry laboratory module-combining expression, purification, crystallization, structure-solving, and characterization of a flavodoxin-like protein

Many laboratory courses consist of short and seemingly unconnected individual laboratory exercises. To increase the course consistency, relevance, and student engagement, we have developed a research-inspired and project-based module, "From Gene to Structure and Function". This 2.5-week full-day biochemistry and structural biology module covers protein expression, purification, structure solving, and characterization. The module is centered around the flavodoxin-like protein NrdI, involved in the activation of the bacterial ribonucleotide reductase enzyme system. Through an in-depth focus on one specific protein, the students will learn the basic laboratory skills needed in order to generate a broader knowledge and breadth within the field. With respect to generic skills, the students report their findings as a scientific article, with the aim to learn to present concise research results and write scientific papers. The current research-inspired project has the potential of being further developed into a more discovery-driven project and extended to include other molecular biological techniques or biochemical/biophysical characterizations. In student evaluations, this research-inspired laboratory course has received very high ratings and been highly appreciated, where the students have gained research experience for more independent future work in the laboratory. © 2019 The Authors. Biochemistry and Molecular Biology Education published by Wiley Periodicals, Inc. on behalf of International Union of Biochemistry and Molecular Biology, 47(3):318-332, 2019.

Peptoids advance multidisciplinary research and undergraduate education in parallel: Sequence effects on conformation and lipid interactions

Peptoids are versatile peptidomimetic molecules with wide-ranging applications from drug discovery to materials science. An understanding of peptoid sequence features that contribute to both their three-dimensional structures and their interactions with lipids will expand functions of peptoids in varied fields. Furthermore, these topics capture the enthusiasm of undergraduate students who prepare and study diverse peptoids in laboratory coursework and/or in faculty led research. Here, we present the synthesis and study of 21 peptoids with varied functionality, including 19 tripeptoids and 2 longer oligomers. We observed differences in fluorescence spectral features for 10 of the tripeptoids that correlated with peptoid flexibility and relative positioning of chromophores. Interactions of representative peptoids with sonicated glycerophospholipid vesicles were also evaluated using fluorescence spectroscopy. We observed evidence of conformational changes effected by lipids for select peptoids. We also summarize our experiences engaging students in peptoid-based projects to advance both research and undergraduate educational objectives in parallel.

Studying trans-acting enzymes that target carrier protein-bound amino acids during nonribosomal peptide synthesis

Nonribosomal peptide biosynthesis is a complex enzymatic assembly responsible for producing a great diversity of bioactive peptide natural products. Due to the recurring arrangement of catalytic domains within these machineries, great interest has been shown in reengineering these pathways to produce novel, designer peptide products. However, in order to realize such ambitions, it is first necessary to develop a comprehensive understanding of the selectivity, mechanisms, and structure of these complex enzymes, which in turn requires significant in vitro experiments. Within nonribosomal biosynthesis, some modifications are performed by enzymatic domains that are not linked to the main nonribosomal peptide synthetase but rather act in trans: these systems offer great potential for redesign, but in turn require detailed study. In this chapter, we present an overview of in vitro experiments that can be used to characterize examples of such trans-interacting enzymes from nonribosomal peptide biosynthesis: Cytochrome P450 monooxygenases and flavin-dependent halogenases.

The Effect of Divalent Cations on the Thermostability of Type II Polyketide Synthase Acyl Carrier Proteins

The successful engineering of biosynthetic pathways hinges on understanding the factors that influence acyl carrier protein (ACP) stability and function. The stability and structure of ACPs can be influenced by the presence of divalent cations, but how this relates to primary sequence remains poorly understood. As part of a course-based undergraduate research experience, we investigated the thermostability of type II polyketide synthase (PKS) ACPs. We observed an approximate 40 °C range in the thermostability amongst the 14 ACPs studied, as well as an increase in stability (5 - 26 °C) of the ACPs in the presence of divalent cations. Distribution of charges in the helix II-loop-helix III region was found to impact the enthalpy of denaturation. Taken together, our results reveal clues as to how the sequence of type II PKS ACPs relates to their structural stability, information that can be used to study how ACP sequence relates to function.

Collaborating with Undergraduates To Contribute to Biochemistry Community Resources

Course-based undergraduate research experiences (CUREs) have gained traction as effective ways to expand the impact of undergraduate research while fulfilling pedagogical goals. In this Perspective, we present innovative ways to incorporate fundamental benefits and principles of CUREs into a classroom environment through information/technology-based research projects that lead to student-generated contributions to digital community resources (CoRes). These projects represent an attractive class of CUREs because they are less resource-intensive than laboratory-based CUREs, and the projects align with the expectations of today's students to create rapid and publicly accessible contributions to society. We provide a detailed discussion of two example types of CoRe projects that can be implemented in courses to impact research and education at the chemistry-biology interface: bioinformatics annotations and development of educational tools. Finally, we present current resources available for faculty interested in incorporating CUREs or CoRe projects into their pedagogical practices. In sharing these stories and resources, we hope to lower the barrier for widespread adoption of CURE and CoRe approaches and generate discussions about how to utilize the classroom experience to make a positive impact on our students and the future of the field of biochemistry.