The BioMolViz Project: Difference between revisions
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'''[[: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 | '''[[: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> | <jmolCheckbox> | ||
<scriptWhenUnChecked>animation off; delay 1; model 1 | <scriptWhenUnChecked>animation off; delay 1; model 1 | ||
| Line 102: | Line 97: | ||
<text>animation</text> | <text>animation</text> | ||
</jmolCheckbox> | </jmolCheckbox> | ||
</jmol>) (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. | </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. | |||
:''MD1.01 Students can recognize that biological molecules have different conformations. (Novice, Amateur)'' | |||
'''[[: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)'' | :''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'>(<jmol> | '''[[: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> | <jmolButton> | ||
<script>rotate Y 180 50</script> | <script>rotate Y 180 50</script> | ||
<text>rotate by 180</text> | <text>rotate by 180</text> | ||
</jmolButton> | </jmolButton> | ||
</jmol> | </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)'' | :''SA1.02 Students can rotate a given, rendered molecule and identify axes of symmetry. (Amateur)'' | ||
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'''[[: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' | '''[[: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)'' | :''SK2.01 Students will evaluate a crystal structure for crystal packing effects. (Novice, Amateur, Expert)'' | ||
