More Like this

1. Molecular storytelling: a conceptual framework for teaching and learning with molecular case studies

   https://doi.org/10.3389/feduc.2024.1379515  

   Trujillo, Caleb M; Dutta, Shuchismita (June 2024, Frontiers in Education)

   Molecular case studies (MCSs) provide educational opportunities to explore biomolecular structure and function using data from public bioinformatics resources. The conceptual basis for the design of MCSs has yet to be fully discussed in the literature, so we present molecular storytelling as a conceptual framework for teaching with case studies. Whether the case study aims to understand the biology of a specific disease and design its treatments or track the evolution of a biosynthetic pathway, vast amounts of structural and functional data, freely available in public bioinformatics resources, can facilitate rich explorations in atomic detail. To help biology and chemistry educators use these resources for instruction, a community of scholars collaborated to create the Molecular CaseNet. This community uses storytelling to explore biomolecular structure and function while teaching biology and chemistry. In this article, we define the structure of an MCS and present an example. Then, we articulate the evolution of a conceptual framework for developing and using MCSs. Finally, we related our framework to the development of technological, pedagogical, and content knowledge (TPCK) for educators in the Molecular CaseNet. The report conceptualizes an interdisciplinary framework for teaching about the molecular world and informs lesson design and education research. 

   more » « less
2. Helical Chirality of Supramolecular Columns and Spheres Self‐Organizes Complex Liquid Crystals, Crystals, and Quasicrystals

   https://doi.org/10.1002/ijch.202100057  

   Percec, Virgil; Xiao, Qi (August 2021, Israel Journal of Chemistry)

   Abstract Homochiral helical self‐organizations provide some of the most fundamental architectures of biological macromolecules and of their co‐assemblies although they were first discovered and elucidated only during the early 1950. Helical synthetic covalent macromolecules started to be discovered soon after and were followed by supramolecular macromolecules and their co‐assemblies few decades later. This perspective will provide a brief historical development of chiral helical self‐organizations in biology and in supramolecular chemistry. Helical covalent and supramolecular macromolecules self‐organize and co‐organize helical supramolecular columns and spherical helices that can generate complex liquid crystals, crystals including Frank‐Kasper phases, and quasicrystals. The design of new functions based on synthetic helical assemblies will also be discussed. Personal events from the life of scientists contributing to these developments are also briefly mentioned. 

   more » « less
3. Genetically targeted chemical assembly

   https://doi.org/10.1038/s44222-023-00110-z  

   Zhang, Anqi; Jiang, Yuanwen; Loh, Kang Yong; Bao, Zhenan; Deisseroth, Karl (October 2023, Nature Reviews Bioengineering)

   Cell type-specific interfaces within living animals will be invaluable for achieving communication with identifiable cells over the long term, enabling applications across many scientific and medical fields. However, biological tissues exhibit complex and dynamic organization properties that pose serious challenges for chronic cell-specific interfacing. A new technology, combining chemistry and molecular biology, has emerged to address this challenge: genetically targeted chemical assembly (GTCA), in which specific cells are genetically programmed (even in wild-type or non-transgenic animals, including mammals) to chemically construct non-biological structures. Here, we discuss recent progress in genetically targeted construction of materials and outline opportunities that may expand the GTCA toolbox, including specific chemical processes involving novel monomers, catalysts and reaction regimes both de cellula (from the cell) and ad cellula (towards the cell); different GTCA-compatible reaction conditions with a focus on light-based patterning; and potential applications of GTCA in research and clinical settings. 

   more » « less
4. Using augmented reality in molecular case studies to enhance biomolecular structure-function explorations in undergraduate classrooms

   https://doi.org/10.1128/jmbe.00019-24  

   Vardar-Ulu, Didem; Ragab, Saif Eldeen; Agrawal, Swati; Dutta, Shuchismita (August 2024, Journal of Microbiology & Biology Education)

   Westenberg, Dave J (Ed.)

   ABSTRACT Molecular case studies (MCSs) are open educational resources that use a storytelling approach to engage students in biomolecular structure-function explorations, at the interface of biology and chemistry. Although MCSs are developed for a particular target audience with specific learning goals, they are suitable for implementation in multiple disciplinary course contexts. Detailed teaching notes included in the case study help instructors plan and prepare for their implementation in diverse contexts. A newly developed MCS was simultaneously implemented in a biochemistry and a molecular parasitology course at two different institutions. Instructors participating in this cross-institutional and multidisciplinary implementation collaboratively identified the need for quick and effective ways to bridge the gap between the MCS authors’ vision and the implementing instructor’s interpretation of the case-related molecular structure-function discussions. Augmented reality (AR) is an interactive and engaging experience that has been used effectively in teaching molecular sciences. Its accessibility and ease-of-use with smart devices (e.g., phones and tablets) make it an attractive option for expediting and improving both instructor preparation and classroom implementation of MCSs. In this work, we report the incorporation of ready-to-use AR objects as checkpoints in the MCS. Interacting with these AR objects facilitated instructor preparation, reduced students’ cognitive load, and provided clear expectations for their learning. Based on our classroom observations, we propose that the incorporation of AR in MCSs can facilitate its successful implementation, improve the classroom experience for educators and students, and make MCSs more broadly accessible in diverse curricular settings. 

   more » « less
5. Protein-derived cofactors: chemical innovations expanding enzyme catalysis

   https://doi.org/10.1039/d4cs00981a  

   Graciano, Angelica; Liu, Aimin (March 2025, Chemical Society Reviews)

   Goss, Rebecca (Ed.)

   Protein-derived cofactors, formed through posttranslational modification of a single amino acid or covalent crosslinking of amino acid side chains, represent a rapidly expanding class of catalytic moieties that redefine enzyme functionality. Once considered rare, these cofactors are recognized across all domains of life, with their repertoire growing from 17 to 38 types in two decades in our survey. Their biosynthesis proceeds via diverse pathways, including oxidation, metal-assisted rearrangements, and enzymatic modifications, yielding intricate motifs that underpin distinctive catalytic strategies. These cofactors span paramagnetic and non-radical states, including both mono-radical and crosslinked radical forms, sometimes accompanied by additional modifications. While their discovery has accelerated, mechanistic understanding lags, as conventional mutagenesis disrupts cofactor assembly. Emerging approaches, such as site-specific incorporation of non-canonical amino acids, now enable precise interrogation of cofactor biogenesis and function, offering a viable and increasingly rigorous means to gain mechanistic insights. Beyond redox chemistry and electron transfer, these cofactors confer enzymes with expanded functionalities. Recent studies have unveiled new paradigms, such as long-range remote catalysis and redox-regulated crosslinks as molecular switches. Advances in structural biology, mass spectrometry, and biophysical spectroscopy continue to elucidate their mechanisms. Moreover, synthetic biology and biomimetic chemistry are increasingly leveraging these natural designs to engineer enzyme-inspired catalysts. This review integrates recent advances in cofactor biogenesis, reactivity, metabolic regulation, and synthetic applications, highlighting the expanding chemical landscape and growing diversity of protein-derived cofactors and their far-reaching implications for enzymology, biocatalysis, and biotechnology. 

   more » « less