Understanding Structure: A Computer-Based Macromolecular Biochemistry Lab Activity

McLaughlin, Krystle J.

doi:10.1021/acs.jchemed.6b00464

Cited by 15 publications

(15 citation statements)

References 9 publications

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“…As an illustration, we employed the MAtCH model to briefly review and suggest possible modifications for three protein-folding and dynamics educational materials published this year ( Helgren and Hagen, 2017 ; Lipchock et al. , 2017 ; McLaughlin, 2017 ; see Supplemental Table S1). Lipchock et al.…”

Section: Discussionmentioning

confidence: 99%

How Four Scientists Integrate Thermodynamic and Kinetic Theory, Context, Analogies, and Methods in Protein-Folding and Dynamics Research: Implications for Biochemistry Instruction

Jeffery

Pelaez

Anderson

2018

LSE

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Section: Discussionmentioning

confidence: 99%

How Four Scientists Integrate Thermodynamic and Kinetic Theory, Context, Analogies, and Methods in Protein-Folding and Dynamics Research: Implications for Biochemistry Instruction

Jeffery

Pelaez

Anderson

2018

LSE

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“…PDB‐101 content is primarily developed by RCSB PDB team members. A quarterly Education Corner publishes descriptions of how other researchers and educators (e.g., 51–59 ) are using PDB data in classrooms, art, and science outreach.…”

Section: Community Interactions and Impactmentioning

confidence: 99%

PDB‐101: Educational resources supporting molecular explorations through biology and medicine

et al. 2021

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The Protein Data Bank (PDB) archive is a rich source of information in the form of atomic‐level three‐dimensional (3D) structures of biomolecules experimentally determined using macromolecular crystallography, nuclear magnetic resonance (NMR) spectroscopy, and electron microscopy (3DEM). Originally established in 1971 as a resource for protein crystallographers to freely exchange data, today PDB data drive research and education across scientific disciplines. In 2011, the online portal PDB‐101 was launched to support teachers, students, and the general public in PDB archive exploration (http://pdb101.rcsb.org). Maintained by the Research Collaboratory for Structural Bioinformatics PDB, PDB‐101 aims to help train the next generation of PDB users and to promote the overall importance of structural biology and protein science to nonexperts. Regularly published features include the highly popular Molecule of the Month series, 3D model activities, molecular animation videos, and educational curricula. Materials are organized into various categories (Health and Disease, Molecules of Life, Biotech and Nanotech, and Structures and Structure Determination) and searchable by keyword. A biennial health focus frames new resource creation and provides topics for annual video challenges for high school students. Web analytics document that PDB‐101 materials relating to fundamental topics (e.g., hemoglobin, catalase) are highly accessed year‐on‐year. In addition, PDB‐101 materials created in response to topical health matters (e.g., Zika, measles, coronavirus) are well received. PDB‐101 shows how learning about the diverse shapes and functions of PDB structures promotes understanding of all aspects of biology, from the central dogma of biology to health and disease to biological energy.

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“…Many exercises use free stand-alone or web-based tools [4] making incorporation of bioinformatics achievable. Students used bioinformatics to investigate multiple topics such as drug design [5,6,7,8,9], visualization of protein structure [10,11,12,13,14], homology modeling [15,16,17], genomics/proteomics [18,19] and genetic diseases [20]. The work described here is distinct because students use bioinformatics to investigate a genetic disease and explores the racial disproportionality of this disease.…”

Section: Introductionmentioning

confidence: 99%

Using Molecular Visualization as a Tool for Culturally Competent and Culturally Relevant Teaching: A Guided-Inquiry Biochemistry Activity

McCarthy¹,

Williams²,

Hughes‐Darden³

et al. 2020

JOCSE

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The central dogma is a key foundational concept in biochemistry. The idea that DNA mutations cause change at the protein level can be abstract for students. To provide a real-world example of the effect of mutation on protein function, a molecular visualization module was developed and incorporated into two biochemistry courses. This inquiry-based activity explored the molecular basis and cultural relevance of sickle cell anemia. Hemoglobin structural changes from the disease were examined. Participants used free tools including NCBI, RCSB PDB, LALIGN and Swiss PDB DeepView protein visualization software from EXPASY. This module was an active, engaging exercise which exposed students to protein visualization and increased cultural awareness.

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Understanding Structure: A Computer-Based Macromolecular Biochemistry Lab Activity

Cited by 15 publications

References 9 publications

How Four Scientists Integrate Thermodynamic and Kinetic Theory, Context, Analogies, and Methods in Protein-Folding and Dynamics Research: Implications for Biochemistry Instruction

How Four Scientists Integrate Thermodynamic and Kinetic Theory, Context, Analogies, and Methods in Protein-Folding and Dynamics Research: Implications for Biochemistry Instruction

PDB‐101: Educational resources supporting molecular explorations through biology and medicine

Using Molecular Visualization as a Tool for Culturally Competent and Culturally Relevant Teaching: A Guided-Inquiry Biochemistry Activity

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