The BioMolViz Project: Difference between revisions

Examples of structures that would probe some of 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 could serve as an image to accompany an assessment within that Overarching Theme. An example of a potential assessment is described below, and the targeted learning objective given in italics.  

</jmol>bovine rhodopsin with bound retinal </scene> (PDB ID: 1gzm) is shown, with discrete hydrophobic (green) and hydrophilic (red) 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.  

'''[[: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> (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.  

'''[[:Category:Symmetry/Asymmetry Recognition|Symmetry/Asymmetry Recognition (SA)]]''': A <scene name='85/857774/Sa/1'>(<jmol>

</jmol>)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 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.  

'''[[: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'>SK</scene>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.