The BioMolViz Project

Project OverviewProject Overview

The BioMolViz Framework is a guide for biomolecular visualization (BMV) instruction. Designed and amended by teams of biochemistry and molecular biology instructors, the Framework divides visual literacy into 12 Overarching Themes. Each theme is subdivided into several broad learning goals, which are further partitioned into a series of specific learning objectives. The objectives describe discrete tasks for the BMV learner to accomplish. By considering the Overarching Theme, learning goals, and objectives, instructors can create BMV assessments using backward design, considering their course aims in the design process. Likewise, the BMV learner can utilize the Framework to guide their own learning by exploring the BMV topics and skills instructors consider key for development of visual literacy.

Rationale: Deliberate Visual Literacy InstructionRationale: Deliberate Visual Literacy Instruction

Biochemistry and molecular biology instructors frequently use images in their instruction, and some incorporate biomolecular visualization tools and software. However, the most common classroom use of BMV is exposure, not explicit instruction how to use the images (e.g. choosing a representation, manipulating a structure for presentation, or thinking about how that structure may be used in a biological context). As instructors guide students through the process of evaluating images and effectively creating them, they will need assessments to evaluate their instructional techniques.

The Framework provides a basis for the design of such assessments, and BioMolViz workshops facilitate team-driven crafting of these tools. The assessments that are in development will be validated by teams of experts, and made widely available for instructors to use.

Framework Overarching ThemesFramework Overarching Themes

The twelve overarching themes of the Framework are outlined below, and the associated learning goals and objectives, can be viewed on the BioMolViz website.

Atomic Geometry (AG) ‐ three‐atom and four‐atom dihedral/torsion angles, metal size and metal‐ligand geometries, steric clashes.

Alternate Renderings (AR) ‐ Rendering of a macromolecular structure such as a protein or nucleic acid structure in various ways from the simplest possible way (connections between alpha carbons) to illustration of secondary structure (ribbons) to surface rendering and space filling.

Construction and Annotation (CA) ‐ Ability to build macromolecular models, either physical or computerized, and, where possible, add commentary, either written or verbal, to tell a molecular story.

Ligands and Modifications (LM) ‐ Metals and metal clusters, additions such as glycosylation, phosphorylation, lipid attachment, methylation etc.

Macromolecular Assemblies (MA) ‐ Polypeptides, oligosaccharides, and nucleic acid and lipid superstructures.

Macromolecular Building Blocks (MB) ‐ Recognition of native amino acids, nucleotides, sugars, and other biomonomer units/building blocks. Understanding of their physical and chemical properties, particularly regarding functional groups.

Molecular Dynamics (MD) ‐ Animated motion simulating conformational changes involved in ligand binding or catalysis, or other molecular motion/dynamics.

Molecular Interactions (MI) ‐ Covalent and noncovalent bonding governing ligand binding and subunit‐subunit interactions.

Symmetry/Asymmetry Recognition (SA) ‐ Recognition of symmetry elements within both single chain and oligomeric macromolecules.

Structure‐Function Relationship (SF) ‐ Active/binding sites, microenvironments, nucleophiles, redox centers, etc.

Structural Model Skepticism (SK) ‐ Recognition of the limitations of models to describe the structure of macromolecules.

Topology and Connectivity (TC) ‐ Following the chain direction through the molecule, translating between 2D topology mapping and 3D rendering.

An Example AssessmentAn Example Assessment

The broader goal of the BioMolViz project is to build a repository of assessments that instructors can use in their courses to evaluate visual literacy gains. These assessments are written in teams, peer reviewed, and will undergo validation by an expert panel. Using the Framework, these assessments are designed from the learning objectives. As an example, a repository contributor might identify the Alternate Renderings (AR) Overarching Theme as an area they wish to target with their assessment. One learning goal within the AR theme is: AR1: Students can create meaningful molecular images to convey features such as secondary structure, CPK coloring, active sites and molecular interactions. A learning objective encompassed by this goal is: AR1.04: Students can infer information from rendering a structure in different ways. An assessment that can be used test if this learning objective has been met can explore protein-ligand interactions. An example of how this assessment may be described to the learner is provided below. Given the structure of 5-methylthioribose 1-phosphate(MTRu-1-P) isomerase bound to MTRu-1-P (PDB ID: 2yvk chain A), use Jmol (or another molecular visualization tool such as Chimera or PyMOL) to identify the amino acids in the protein that interact with the ligand. Example Assessment Solution Clicking on any of the green links in the following paragraph will show an example of how the learner's model may look at that stage of the process To show mastery, the learner will first focus on , hiding subunit B for clarity. An is obtained by rotating the macromolecule and zooming in. To display interactions, the learner will first replace the spacefilling representation of the ligand with a . To view the interacting residues, the learner shows amino acid residues within 5Å of the active site . For contrast, the learner colors the ligand magenta. In this view, water molecules within 5Å of the ligand are displayed as well. The view has gotten busy, so to focus in on the active site residues, the learner can , and then show the . The learner then executes a command to within the active site, including those to the ligand, or measures polar contacts manually.

spinqualitylabelsall models Caption for this structure Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

ReferencesReferences

Bateman, Robert C., and Paul A. Craig. 2010. “Education Corner: A Proficiency Rubric for Biomacromolecular 3D Literacy.” PDB Newsletter 45: 5–7.

Dries, Daniel R., Diane M. Dean, Laura L. Listenberger, Walter R.P. Novak, Margaret A. Franzen, and Paul A. Craig. 2016. “An Expanded Framework for Biomolecular Visualization in the Classroom: Learning Goals and Competencies.” Biochemistry and Molecular Biology Education. https://doi.org/10.1002/bmb.20991.