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

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 ==II. Protein Structure and Structural Bioinformatics==
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+Image:1000px-Amino Acids.svg.png|200 px|
+default [http://proteopedia.org/wiki/images/1/13/1000px-Amino_Acids.svg.png]
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 :<span style="font-size:130%">1. [[Amino acid]] '''sequence''' + protein chain '''conformation''' = protein '''function'''.</span>
-::A. Conformation can be a '''stable fold''' or '''[[Intrinsically Disordered Protein|intrinsically unstructured]]'''. Both commonly exist in the same protein molecule.
+::A. [http://www.umass.edu/molvis/workshop/allstruc/whycare.htm Why do we care?]
-::B. Conformation is specified by sequence.
+::B. Conformation can be a '''stable fold''' or '''[[Intrinsically Disordered Protein|intrinsically unstructured]]'''. Both commonly exist in the same protein molecule.
+::C. Conformation is specified by sequence.
 :::*Folded domains fold spontaneously (Anfinson, 1960's<ref>For a brief overview of Anfinson's protein folding experiments in the 1960's, see the first paragraph at [[Intrinsically Disordered Protein]].</ref>), or with the help of [[chaperonins]].
 :::*The '''denaturation''' (unfolding) of a folded domain destroys its function.
-:<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:
 :::*[[X-ray crystallography]], 88%.
+::::*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%.
 ::::*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%.
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 ==III. Choose a Molecule to Explore==
-*Choose a molecule that includes '''protein and ligand'''. It may also include nucleic acid, but must have protein and ligand.
+*Choose a molecule that includes '''protein'''. It may also include ligand and/or nucleic acid, but must have protein.
 *Be sure to note the '''4-character PDB code''' of the molecule you choose. The PDB code makes it easy to retrieve the molecule and information about it. Here are some ways to find a protein with known structure:
 # Atlas of Macromolecules ([http://atlas.molviz.org Atlas.MolviZ.Org]). Choose a "straightforward" molecule that has ligand.
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 :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''.
-: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.
 ::See [[Introduction to Evolutionary Conservation]].
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 *Water-soluble proteins have polar/charged amino acids nearly everywhere on their surfaces (Examples: small [[2hhd]], large [[1igy]]). Patches of hydrophobic amino acids on the surfaces of soluble proteins are usually less than ~10 &aring; in their smaller diameter, and usually recessed.
 *Hydrophobic surface patches may be buried in chain-to-chain contacts -- check the [[#Section_6:_Biological_Unit|biological unit]] (example: [[Lac_repressor#Structure_of_the_lac_repressor|lac repressor homodimer]]).
-*Large, protruding hydrophobic surface areas (>25 &Aring; in their smaller diameter) may indicate transmembrane proteins (insoluble; example: [[1bl8]]).
+*Large, protruding hydrophobic surface areas (>25 &Aring; in their smaller diameter) may indicate transmembrane proteins (insoluble). Examples:
+**[[1bl8]]
+**showing [http://opm.phar.umich.edu/protein.php?pdbid=1r3j bilayer boundaries] (click on "Jmol"; ligand toggles boundaries).
+**[[Gramicidin Channel in Lipid Bilayer]].
 ====B. Charge====
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 ==V. Powerpoint Report==
-Save your report with the filename yourLastName-565.pptx, for example <font color='red'><b>sandler-565.pptx</b></font>. When completed, your Powerpoint report is to be emailed to '''emartz@microbio.umass.edu''' for grading.
+Save your report with the filename '''yourLastName-565.pptx''', for example <font color='red'><b>sandler-565.pptx</b></font>. When completed, your Powerpoint report is to be emailed to '''emartz@microbio.umass.edu''' for grading.
 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>
+<br>
+[http://www.umass.edu/molvis/martz/lectures/labmolgen/martz-565-2012.ppt Sample Completed Powerpoint Assignment] (You may download it, rename the file, and use it as a template.)
 ===Section 1: Identity===
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 ===Section 3: Evolutionary Conservation===
 Does your molecule have a highly conserved region? If so, what is its function? If there is no highly conserved region, is there a highly variable region? Show a <font color='e000e0'><b>snapshot</b></font> illustrating a highly conserved (or variable) region.
-:<font color='gray'>Click on ''Evolutionary Conservation'' in Proteopedia. Toggle the ''quality'' button to high quality. Use the ''popup'' button to enlarge the high quality image.</font>
+:<font color='gray'>Click on ''Evolutionary Conservation'' in Proteopedia. Toggle the ''quality'' button to high quality. Use the ''popup'' button to enlarge the high quality image. Problems? See [[How to see conserved regions]].</font>
 ===Section 4: Hydrophobic/Polar===
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 ===<font color='gray'>Section 8 - Optional: Contacts/Non-covalent Bonds</font>===
+#Use the ''Contacts'' tool in FirstGlance.
+#Change target selection to ''Residues/Groups''.
+#Click on something small to select it as a "target", such as a ligand, or a single amino acid.
+#Click the link to ''Show atoms contacting target''.
+#Click ''Center contacts''.
+#Uncheck ''Backbones''.
+#Zoom in (and click ''Return to Contacts'' if necessary).
+#Uncheck all categories of non-covalent bonds.
+#Check ''hydrogen-bonded non-water''. (Review [[Hydrogen_bonds#Donor_and_Acceptor_Atoms|hydrogen bonds]].)
+#Double click the hydrogen bond donor and acceptor atoms to insert a distance monitor.
+Describe the moiety you selected as a target. Include a <font color='e000e0'><b>snapshot</b></font> showing a hydrogen bond.
 ==VI. See Also==