Utilizing Mechanistic Cross-Linking Technology To Study Protein–Protein Interactions: An Experiment Designed for an Undergraduate Biochemistry Lab

Finzel, Kara; Beld, Joris; Burkart, Michael D.; Charkoudian, Louise K.

doi:10.1021/acs.jchemed.6b00453

Cited by 5 publications

(3 citation statements)

References 20 publications

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“…Consistent with this, a large number of publications focused on constructing laboratory instruction platforms where a variety of experiment skills were integrated, such as NMR spectroscopy, , fluorescence spectroscopy, circular dichroism, UV spectroscopy, and surface plasmon resonance . In many cases, the constructions of laboratory instructions were coupled with the introduction of key concepts in biochemistry courses. ,,− …”

Section: Resultsmentioning

confidence: 98%

Knowledge-Map Analysis of Undergraduate Biochemistry Teaching Research: A Bibliometric Study from 2012 to 2021

He,

Li,

Chen

et al. 2024

J. Chem. Educ.

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Biochemistry is becoming increasingly crucial for undergraduates majoring in biology, chemistry, agriculture, and medicine. In recent years, much research has been carried out on promoting this course's teaching outcomes. However, the knowledge structure of undergraduate biochemistry teaching research has yet to be formed. Here, 715 validated publications from 2012 to 2021 were retrieved from the Web of Science Core Collection. The annual publications, journals/cited journals, countries, institutions, authors/cited authors, keywords, and cited references were analyzed using CiteSpace. As revealed in our study, the United States is the most productive country, and Biochemistry and Molecular Biology Education, the Journal of Chemical Education, and CBE Life Sciences Education are the most influential journals. Most studies focused on introducing or designing creative laboratory courses to improve students' hands-on abilities. Interestingly, we found that the studies in this period can be divided into two stages: the research topics in the first stage were highly diverse, and in the second stage, the subfield of course-based undergraduate research experiences attracted much attention. Taken together, this study offers insights into the historical development of undergraduate biochemistry educational research, which will have implications for scientists conducting future investigations in this promising field and teachers for better learning outcomes.

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Section: Resultsmentioning

confidence: 98%

Knowledge-Map Analysis of Undergraduate Biochemistry Teaching Research: A Bibliometric Study from 2012 to 2021

He,

Li,

Chen

et al. 2024

J. Chem. Educ.

View full text Add to dashboard Cite

show abstract

“…C-terminally His-tagged ACP hydrolase (Pseudomonas aeruginosa AcpH) was prepared as described previously (Kosa et al, 2012) except that the purification was performed in a cold room (6 C). The four enzymes used for loading the cross-linking probes, Sfp, CoaA, CoaD and CoaE, were prepared as described previously (Finzel et al, 2017).…”

Section: Protein Expression and Purificationmentioning

confidence: 99%

Mechanism-based cross-linking probes capture the Escherichia coli ketosynthase FabB in conformationally distinct catalytic states

Mindrebo¹,

Davis²,

Kim³

et al. 2022

Acta Cryst Sect D Struct Biol

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Ketosynthases (KSs) catalyse essential carbon–carbon bond-forming reactions in fatty-acid biosynthesis using a two-step, ping-pong reaction mechanism. In Escherichia coli, there are two homodimeric elongating KSs, FabB and FabF, which possess overlapping substrate selectivity. However, FabB is essential for the biosynthesis of the unsaturated fatty acids (UFAs) required for cell survival in the absence of exogenous UFAs. Additionally, FabB has reduced activity towards substrates longer than 12 C atoms, whereas FabF efficiently catalyses the elongation of saturated C14 and unsaturated C16:1 acyl-acyl carrier protein (ACP) complexes. In this study, two cross-linked crystal structures of FabB in complex with ACPs functionalized with long-chain fatty-acid cross-linking probes that approximate catalytic steps were solved. Both homodimeric structures possess asymmetric substrate-binding pockets suggestive of cooperative relationships between the two FabB monomers when engaged with C14 and C16 acyl chains. In addition, these structures capture an unusual rotamer of the active-site gating residue, Phe392, which is potentially representative of the catalytic state prior to substrate release. These structures demonstrate the utility of mechanism-based cross-linking methods to capture and elucidate conformational transitions accompanying KS-mediated catalysis at near-atomic resolution.

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“…Finzel et al developed an interdisciplinary experiment to study protein interactions in natural product biosynthetic pathways by mechanistic cross-linking probes. This experiment combined the elements of organic chemistry, protein biochemistry, and computational docking and provided students with a platform to learn chemoenzymatic synthesis . As an integration of polymer chemistry and colloid chemistry, the polymeric surfactant can effectively function as a bridge to help students easily comprehend these topics, so it thus has good potential for pedagogical application.…”

Section: Introductionmentioning

confidence: 99%

Designing, Synthesizing, and Analyzing a Comb-like Polymeric Surfactant, Poly(acrylic acid-co-octadecyl acrylate), in a Multidisciplinary Laboratory Experiment

et al. 2021

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As an outcome of multidiscipline integration, the polymeric surfactant is of growing importance in modern industry and scientific research. However, the instructional introduction on polymeric surfactants is still insufficient in universities nowadays. In order to effectively guide undergraduates to study polymeric surfactant, a new polymeric surfactant, poly(acrylic acid-co-octadecyl acrylate), was designed and synthesized by copolymerization between acrylic acid and octadecyl acrylate. Moreover, its surface activity and rheological performance were also analyzed by contact angle meter, laser scanning confocal microscope, polarizing microscope, and rotary rheometer. Generally, as a combination of the hands-on exercise with theoretical lecture, this laboratory experiment enabled students to understand the key concepts and chemical nature of polymeric surfactants in depth. In addition, the ability to incorporate multidiscipline concepts into the practical issues students must solve was also cultivated by this exercise.

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Utilizing Mechanistic Cross-Linking Technology To Study Protein–Protein Interactions: An Experiment Designed for an Undergraduate Biochemistry Lab

Cited by 5 publications

References 20 publications

Knowledge-Map Analysis of Undergraduate Biochemistry Teaching Research: A Bibliometric Study from 2012 to 2021

Knowledge-Map Analysis of Undergraduate Biochemistry Teaching Research: A Bibliometric Study from 2012 to 2021

Mechanism-based cross-linking probes capture the Escherichia coli ketosynthase FabB in conformationally distinct catalytic states

Designing, Synthesizing, and Analyzing a Comb-like Polymeric Surfactant, Poly(acrylic acid-co-octadecyl acrylate), in a Multidisciplinary Laboratory Experiment

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