The RCSB PDB "Molecule of the Month": Inspiring a Molecular View of Biology

Abstract

The Research Collaboratory for Structural Bioinformatics (RCSB) Molecule of the Month series provides a curated introduction to the 3-D biomolecular structures available in the Protein Data Bank archive and the tools that are available at the RCSB website for accessing and exploring them. A variety of educational materials, such as articles, videos, posters, hands-on activities, lesson plans, and curricula, build on this series for use in a variety of educational settings as a general introduction to key topics, such as enzyme action, protein synthesis, and viruses. The series and associated educational materials are freely available at www.rcsb.org.

Fig 1. Molecules highlighted in the MotM features.

As of the end of 2014, 180 different molecules have been presented in Molecule of the Month features. Topics are selected to promote understanding of biomolecular structure and function and connections to human health and disease as well as biotechnology. Some of the more popular subjects are depicted herein. From top to bottom: DNA polymerase [16], ribosome [17,18], hemoglobin [19], ATP synthase [20,21], a G-protein bound to a G-protein-coupled receptor (GPCR) [22], and the collagen triple helix [23].

Fig 2. Images from MotM features.

For the 2010 column on the ribosome, structures were chosen to exemplify discrete mechanistic steps in protein synthesis, including the elongation phase (top) [–26]. The style of the illustration highlights major molecular players: ribosomal subunits in blue (large) and green (small), transfer RNA in yellow, messenger RNA in red, and elongation factors in purple. The non-photorealistic style is designed to focus attention on overall shape, size, and molecular interactions, while still giving a sense of the component atoms. An interactive JSmol was also included in the "Exploring the Structure" section of the column, allowing users to explore firsthand the codon-anticodon interaction (bottom). This illustration shows a close-up of the "decoding center" of the ribosome.

Fig 3. Protein modeling at the Science Olympiad.

The Protein Modeling event uses MotM features to provide a scientific foundation. An example of how the models of the Major Histocompatibility Complex [27] are built in the competition is shown. Illustrations (left panel) and descriptions introduce the competition’s topic and the section on Exploring the Structure (central panel) and JSmol interactive views show details of the functionally important regions of the protein model. Students visualize the assigned molecules in the CBM MSOE environment to guide their model building. An example of student-built toober model is shown (top model in the right panel) along with a 3-D printed model of the same protein (lower model in the right panel, lacking the bound peptide) that event officials use for judging the model. Images in the right panel were kindly provided by Tim Herman, with permission.

Fig 4. Molecular machines at High Tech High.

Parag Chowdhury and his students at High Tech High in North County San Diego, California, combined art and science to explore molecular machines. Using the RCSB PDB MotM features as starting points, they created original paintings of biomolecules and wrote one-page descriptions of the role played by each biomolecule in the cell. They then combined all of this creative work into a book, Molecular Machines: How Are We Assembled?, currently available through the on-demand publisher Blurb. The painting of a bacterial virus or bacteriophage [28], shown above, was used on the cover of the book, and was kindly provided by Parag Chowdhury with permission.

Fig 5. Molecular origami.

Templates for paper models of selected MotM-featured structures present the opportunity to make low cost and easily accessible physical models. Integrating these models with the MotM features provides new perspectives on these molecules. Examples of a few paper models include: DNA double helix (left panel), green fluorescent protein (center panel) [29], and HIV capsid (right panel) [30]. These and other paper models and associated MotM features are available for download from http://www.pdb.org/pdb/101/static101.do?p=education_discussion/educational_resources/index.html.

Fig 6. HIV/AIDS curriculum.

Selected MotM features and educational materials developed at the RCSB PDB, such as this image of the anatomy of HIV and the proteins encoded by the HIV genome, are combined with other public resources in a curriculum that explores immunity and our defenses against HIV. The modular curriculum includes three main components: (i) review of the structure and function of biological molecules; (ii) introduction to the human immune system; and (iii) module on HIV/AIDS biology, treatments, and global impact. Two versions of the curricula are available for use in general biology and AP biology classrooms together with suggestions for assessing student learning. In addition to curricular material, pre- and post-tests are included. The curricula conform to current science teaching standards and core curricula and are available at http://education.rcsb.org/curriculum.