The BioMolViz Project: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Kristen Procko, Josh Beckham, Jaime Prilusky, Karsten Theis

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 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.
+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 [https://biomolviz.org/framework/ BioMolViz website].
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 '''[[:Category:Topology and Connectivity|Topology and Connectivity (TC)]]''' ‐ Following the chain direction through the molecule, translating between 2D topology mapping and 3D rendering.
-== An Example Assessment ==
+== Framework Examples ==
+<StructureSection load='' size='450' side='right' caption='One of the 12 overarching themes is MI, molecular interactions, illustrated here by the lambda repressor bound to the major grooves of double-stranded DNA' scene='86/865933/Molecularinteraction/1'>
+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.
+'''[[:Category:Atomic Geometry|Atomic Geometry (AG)]]''': A ring form of <scene name='85/857774/Ag/1'>D-glucose (ß-D-glucopyanose)</scene> 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.''
+'''[[:Category:Alternate Renderings|Alternate Renderings (AR)]]''': An <scene name='85/857774/Ar/5'>alpha helix</scene> (<jmol>
+  <jmolCheckbox>
+    <scriptWhenUnChecked>animation off;
+       </scriptWhenUnChecked>
+    <scriptWhenchecked>animation mode loop 0.0 0.0; animation FPS 1; animation on
+       </scriptWhenchecked>
+    <checked>true</checked>
+    <text>animation</text>
+  </jmolCheckbox></jmol>) 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.''
+'''[[:Category:Construction and Annotation|Construction and Annotation (CA)]]''': The structure of <scene name='85/857774/Ca/1'><jmol>
+  <jmolLink>
+    <script>select protein and *:A; isosurface ignore (not selected) SASURFACE 1.2  MAP property color translucent 0.6
+       </script>
+    <text>with surface</text>
+  </jmolLink>
+</jmol>bovine rhodopsin with bound retinal </scene> (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)''
+'''[[:Category:Ligands and Modifications|Ligands and Modifications (LM)]]''': <scene name='85/857774/Lm/1'>Deoxymyoglobin (PDB ID: 1a6n) bound to the heme ligand</scene>. 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)''
+'''[[:Category:Macromolecular Assemblies|Macromolecular Assemblies (MA)]]''': A <scene name='85/857774/Ma/1'>peripheral membrane protein</scene> (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)''
-<StructureSection load='2yvk' size='340' side='right' caption='Caption for this structure' scene=''>
-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 prior to inclusion in the repository. These assessments are designed using the Framework. For example, a learning goal within the '''[[:Category:Alternate Renderings|Alternate Renderings (AR)]]''' Overarching Theme is:
+'''[[:Category:Macromolecular Building Blocks|Macromolecular Building Blocks (MB)]]''': A <scene name='85/857774/Mb/1'>glycosylated peptide</scene> 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.
-:'''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:
+:''MB1.02 Given a rendered structure, students will be able to divide the polymer into its monomer units. (Novice)''
-:'''AR1.04:''' Students can infer information from rendering a structure in different ways.
-An '''assessment''' to test if this learning objective has been met would be:
+'''[[:Category:Molecular Dynamics|Molecular Dynamics (MD)]]''': The NMR structures of the <scene name='85/857774/Md/1'>dimeric C-terminal domain of HIV-1 capsid protein </scene>(<jmol>
+  <jmolCheckbox>
+    <scriptWhenUnChecked>animation off; delay 1; model 1
+       </scriptWhenUnChecked>
+    <scriptWhenchecked>animation mode loop; animation on
+       </scriptWhenchecked>
+    <checked>false</checked>
+    <text>animation</text>
+  </jmolCheckbox>
+</jmol>):
+(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.
-: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.
+:''MD1.01 Students can recognize that biological molecules have different conformations. (Novice, Amateur)''
-To show mastery, the learner will first focus on <scene name='86/865933/Unit_a/5'>subunit A of the complex</scene>, hiding subunit B for clarity. An <scene name='86/865933/Zoom_ligand_spacefill/1'>unobscured view of the ligand</scene> 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 <scene name='86/865933/Zoom_ligand_stick/2'>stick representation</scene>. To view the interacting residues, the learner shows amino acid residues within 5Å of the active site <scene name='86/865933/Zoom_ligand_plus_as_stick/3'>as sticks and displays them with CPK coloring</scene>. 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 <scene name='86/865933/As_no_cartoon/1'>hide the cartoon rendering of the protein</scene>, and then show the <scene name='86/865933/As_no_cartoon_-_resi_labeled/1'>active site residues with labels</scene>. Finding polar contacts to nearby residues is generally quite straightforward in most molecular visualization software programs.
+'''[[:Category:Molecular Interactions|Molecular Interactions (MI)]]''': The <scene name='85/857774/Molecularinteraction/1'>DNA binding motif of the lambda repressor protein (ribbons) is shown bound to the operator of lambda phage viral DNA</scene> (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)''
+'''[[:Category:Symmetry/Asymmetry Recognition|Symmetry/Asymmetry Recognition (SA)]]''': A <scene name='85/857774/Sa/1'>homodimer of the large kinase Tel1 protein from the bacterium Chaetomium thermophilum</scene> (PDB ID: 6sl0) with each monomer arranged symmetrically around the vertical axis.  A 180 degree rotation <jmol>
+  <jmolButton>
+    <script>rotate Y 180 50</script>
+    <text>rotate by 180</text>
+  </jmolButton>
+</jmol> 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)''
+'''[[:Category:Structure‐Function Relationship|Structure‐Function Relationship (SF)]]''': Active site of the <scene name='85/857774/Chymotrypsin/3'>serine protease, chymotrypsin</scene> (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)''
+'''[[:Category:Structural Model Skepticism|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 <scene name='85/857774/Sk/1'>Streptococcal Protein G in complex with the FC domain of human IgG</scene> (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)''
+'''[[:Category:Topology and Connectivity|Topology and Connectivity (TC)]]''': Three consecutive <scene name='85/857774/Tc/1'>zinc finger domains from a transcription factor III bound to an RNA</scene> 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)''
 </StructureSection>
 == References ==
 <references/>
@@ Line 64: / Line 141: @@
 [[Category: BioMolViz]]
 [[Category: Alternate Renderings]]
+[[Category: Atomic Geometry]]
 [[Category: Construction and Annotation]]
 [[Category: Ligands and Modifications]]
 [[Category: Macromolecular Assemblies]]
 [[Category: Macromolecular Building Blocks]]
+[[Category: Molecular Dynamics]]
 [[Category: Molecular Interactions]]
 [[Category: Structure‐Function Relationship]]
-[[Category: Topology and Connectivity]]
 [[Category: Symmetry/Asymmetry Recognition]]
 [[Category: Structural Model Skepticism]]
+[[Category: Topology and Connectivity]]