User:Eric Martz/Introduction to Structural Bioinformatics I: Difference between revisions

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:<span style="font-size:130%">2. Structure Knowledge.</span>
:<span style="font-size:130%">2. Backbone Representation.</span>
 
::A. [http://www.umass.edu/molvis/tutorials/hemoglobin/pepstruc.htm Peptides and Backbones] (within a tutorial on hemoglobin)
::B. [http://firstglance.jmol.org/fg.htm?mol=1pgb Small Protein in FirstGlance] (use Vines, Cartoon)
 
 
:<span style="font-size:130%">3. Structure Knowledge.</span>


::A. Although sequence specifies fold, scientists '''cannot yet predict the fold from the sequence'''. Therefore, fold must be determined by empirical (experimental) methods. The most common methods for determining the 3D structure of a protein molecule are:
::A. Although sequence specifies fold, scientists '''cannot yet predict the fold from the sequence'''. Therefore, fold must be determined by empirical (experimental) methods. The most common methods for determining the 3D structure of a protein molecule are:
:::*[[X-ray crystallography]], 88%.
:::*[[X-ray crystallography]], 88%.
::::Cannot determine the structure of [[Intrinsically Disordered Protein|intrinsically unstructured]] loops or molecules.
::::*Cannot determine the structure of [[Intrinsically Disordered Protein|intrinsically unstructured]] loops or molecules.
::::*Result is a single model representing the average of the molecules in the crystal.
::::*[[Resolution]] reflects the degree of order or disorder in the crystal.
:::*[[Nuclear magnetic resonance]] (NMR) in aqueous solution, 11%.
:::*[[Nuclear magnetic resonance]] (NMR) in aqueous solution, 11%.
::::*NMR is limited to small proteins (30 kD or smaller).
::::*NMR is limited to small proteins (30 kD or smaller).
::::*Result is an ensemble of models consistent with the data. Examples: [[2bbn]]
:::*High resolution cryo-electron microscopy, 0.5%.
:::*High resolution cryo-electron microscopy, 0.5%.


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::E. Crystallographers publish the [[asymmetric unit]] of the crystal. It may be identical with the [[biological unit]] (the functional form of the molecule), or it may be only part of the biological unit, or it may contain multiple copies of the biological unit. See [[Biological unit#Examples|examples]].
::E. Crystallographers publish the [[asymmetric unit]] of the crystal. It may be identical with the [[biological unit]] (the functional form of the molecule), or it may be only part of the biological unit, or it may contain multiple copies of the biological unit. See [[Biological unit#Examples|examples]].
:::Interchain contacts that occur in the asymmetric unit that are absent in the biological unit are an artifact of crystallization, termed [[crystal contacts]].
:::Interchain contacts that occur in the asymmetric unit that are absent in the biological unit are an artifact of crystallization, termed [[crystal contacts]].
:<span style="font-size:130%">3. Backbone Representation.</span>
::A. [http://www.umass.edu/molvis/tutorials/hemoglobin/pepstruc.htm Peptides and Backbones] (within a tutorial on hemoglobin)
::B. [http://firstglance.jmol.org/fg.htm?mol=1pgb Small Protein in FirstGlance] (use Vines, Cartoon)


==III. Choose a Molecule to Explore==
==III. Choose a Molecule to Explore==
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:B. The abstract of the publication about this structure, which usually mentions the '''function of the molecule''' if known.
:B. The abstract of the publication about this structure, which usually mentions the '''function of the molecule''' if known.
:C. The '''number of polymer chains''' under ''About this Structure''.
:C. The '''number of polymer chains''' under ''About this Structure''.
:D. Full '''names of ligands and non-standard residues''' (displayed when their green links are clicked beneath the molecule). Example: [[2src]].
:D. Full '''names of ligands and non-standard residues''' (displayed when their '''<font color="#00c000">green links</font>''' are clicked beneath the molecule). Example: [[2src]].
:E. Evolutionary conservation.
:E. Evolutionary conservation.
::See [[Introduction to Evolutionary Conservation]].
::See [[Introduction to Evolutionary Conservation]].
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Each slide MUST be labeled at the top with its section number, e.g. ''Section 1''.
Each slide MUST be labeled at the top with its section number, e.g. ''Section 1''.


Each question below may be answered in a single slide, or multiple slides. For example, suppose you want to show two snapshots for ''Section 3'', and make separate comments. You may choose to use two slides, labeled ''Section 3A'' and ''Section 3B''.
Each Section below may be answered in a single slide, or multiple slides. For example, suppose you want to show two snapshots for ''Section 3'', and make separate comments. You may choose to use two slides, labeled ''Section 3A'' and ''Section 3B''.


<font color='e000e0'>This is not a test. It is to help you learn by doing. Ask for help!</font>
<font color='e000e0'>This is not a test. It is to help you learn by doing. Ask for help!</font>
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