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Project 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 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 currently in development will be validated by teams of experts, and made widely available for instructors to use.
Framework 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.
Framework Examples
| Examples of structures that could be used probe some the Learning Objectives within each Overarching Theme of the BioMolViz Framework are illustrated below. Clicking on the green links will bring up a structure in the frame to the right, which may accompany an assessment within that Overarching Theme. An description of a potential assessment is described below, with the targeted learning objective shown in italics.
Atomic Geometry (AG): A ring form of is shown. The dihedral/torsion angle of the center bond defined by four consecutive ring atoms (C-C-C-O) is given. Learners should be able to measure bond angles and differentiate bond angles from dihedral/torsion angles and predict changes from ideal angles. An example assessment that encompasses AG3.03 would require students to display and describe the atoms involved in measuring the dihedral angle.
- AG3.03 Students can identify phi, psi, and omega torsion/dihedral angles in a three dimensional representation of a macromolecule.
Alternate Renderings (AR): An () of the protein lysin (PDB ID: 1lis) rendered in 3 different ways: sticks, cartoon and spacefill. Each representation shows an alternate rendering of the helix, which may be used to display different aspects of the alpha helix, such as the repetitive turn of the backbone (cartoon) or the atoms which may participate in intrastrand hydrogen bonding (sticks). For example, an AR2.03 assessment would require students to create models using different renderings in a modeling program and explain the utility of each display.
- AR2.03 Students can identify the best rendering, or combination of renderings, for a specific purpose.
Construction and Annotation (CA): The structure of (PDB ID: 1gzm) is shown, with discrete hydrophobic (gray) and hydrophilic (pink) regions displayed that allow this membrane protein to interact with extracellular/intracellular environments. The viewer should recognize the hydrophobic sections are most likely found in the nonpolar milieu of the bilayer while the polar sections are likely the extracellular and intracellular domains. An example of an assessment for CA2.04 would require students to display the polarity of alpha helices in different environments, comment on the hydrophobic exterior of this helix, and connect this to a probable location as a membrane-bound protein.
- CA2.04 Students can make accurate predictions of the location/function of the protein that incorporates additional protein features, such as transmembrane helices, apparent docking surfaces, etc. (Expert)
Ligands and Modifications (LM): . The heme iron is coordinated by electron pair donors from both the porphyrin ring and protein. For example, an LM1.01 assessment would require students to identify and label the iron (Fe) atom.
- LM1.02 Students can visually identify non‐protein chemical components in a given rendered structure. (Amateur)
Macromolecular Assemblies (MA): A (matrix metalloproteinase) is shown complexed to a phosphatidylcholine lipid bilayer in a large macromolecular assembly (PDB ID: 2mlr). The hydrophobic tails and polar heads of membrane lipids are shown as gray lines and colored spheres, respectively, while the protein with metal cofactors (Zn+2 and Ca+2,colored spheres) is shown as a cartoon in at top of the image. An example assessment for MA1.01 would have students examine a rendered 2D or 3D image of this complex and identify the lipid and protein structures of the complex. Additionally, this assessment would fit objective MA1.03 due to the presence of the bilayer lipid ultrastructure.
- MA1.01 Students can identify individual structures in a macromolecular assembly. (Novice, Amateur, Expert)
- MA1.03 Students recognize the various lipid ultrastructures (micelles, bicelles, vesicles, and lipid bilayers) in a 3D structure. (Novice)
Macromolecular Building Blocks (MB): A from the ice-binding protein (PDB ID: 3uyv) from an Arctic yeast with the amino acid and carbohydrate building blocks of the polymer shown in different colors. Comprising two different types of building blocks, the viewer must be able to identify the differences between the amino acid and carbohydrate structures. An example of an assessment for MB1.02 would require students to draw lines on a 2D image of the structure to indicate the connections of each building block and identify them from a table of amino acid and monosaccharide building blocks.
- MB1.02 Given a rendered structure, students will be able to divide the polymer into its monomer units. (Novice)
Molecular Dynamics (MD): The NMR structures of the ():
(PDB ID: 2kod) showing a distribution of structures accessible through dynamic conformational changes, particularly of the less ordered regions of the protein, shown in green. The animated GIF image illustrates various conformational states attainable by the structure. As an example of an assessment for MD1.01, students may be required to create a model using an NMR structure of the protein, overlay the states, and color each differently to allow them to identify the most flexible regions in the structure.
- MD1.01 Students can recognize that biological molecules have different conformations. (Novice, Amateur)
Molecular Interactions (MI): The (space-filling representation) (PDB ID: 1lmb). Noncovalent interactions occur between the repressor protein and the DNA, mediated largely through alpha-helices of the protein binding in the major groove of the viral DNA. An example of a MI1.02 assessment would require students to display and describe the interactions at the interface of the two macromolecules.
- MI1.02 Students can identify the different non‐covalent interactions given a 3D structure. (Amateur)
Symmetry/Asymmetry Recognition (SA): A (PDB ID: 6sl0) with each monomer arranged symmetrically around the vertical axis. A 180 degree rotation around the vertical axis reproduces the initial structure giving the protein C2 symmetry. As an example of an SA1.02 assessment, students would examine a 3D rendering of the structure, coloring the dimer in a way to reveal the symmetry clearly, and show two images to compare the structure as it’s rotated.
- SA1.02 Students can rotate a given, rendered molecule and identify axes of symmetry. (Amateur)
Structure‐Function Relationship (SF): Active site of the (PDB ID: 1gg6), with the active site residues highlighted and a covalently bound amino acid substrate mimic (shown in yellow). Recognition of the covalently-bound ligand and the catalytic triad, Ser 195, His 57, and Asp 102, could allow a viewer to predict the function of this enzyme as a protease. As an example of an SF1.01 assessment, students would be required to identify the ligand, color it, and describe that it is covalently-bound.
- SF1.01 Students can distinguish protein, cofactors and small molecule ligands or substrates. (Novice)
Structural Model Skepticism (SK): The structure shows unacceptably large steric clashes from backbone atoms for the experimentally-determined orientation of three amino acids (Tyr, Thr and Asn) from the (PDB 1D: 1fcc). The viewer should recognize the unfavorable geometry from the displayed clashes and short hydrogen bond lengths. An example assessment for SK2.01 would be to suggest alterations to either main chain or side chain conformations that may alleviate the strain.
- SK2.01 Students will evaluate a crystal structure for crystal packing effects. (Novice, Amateur, Expert)
Topology and Connectivity (TC): Three consecutive from 5S RNA (PDB ID: 1un6) are shown, in which the zinc fingers are formed from a continuous primary sequence of amino acids which fold to form topologically connected domains. The viewer should recognize the repeating domains in the module. An assessment example that encompasses TC2.03 would require students to display both macromolecules, and color each repeating domain to distinguish them.
- TC2.03 Students can identify connectivity features between domains or subunits in a macromolecular structure. (Amateur)
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References
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.
