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

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 ==II. Protein Structure and Structural Bioinformatics==
-:<span style="font-size:130%">1. Amino acid '''sequence''' + protein chain '''conformation''' = protein '''function'''.</span>
+{| align="right"
-::A. Conformation can be a '''stable fold''' or '''[[Intrinsically Disordered Protein|intrinsically unstructured]]'''. Both commonly exist in the same protein molecule.
+|-
-::B. Conformation is specified by sequence.
+|
+<imagemap>
+Image:1000px-Amino Acids.svg.png|200 px|
+default [http://proteopedia.org/wiki/images/1/13/1000px-Amino_Acids.svg.png]
+</imagemap>
+|}
+:<span style="font-size:130%">1. [[Amino acid]] '''sequence''' + protein chain '''conformation''' = protein '''function'''.</span>
+::A. [http://www.umass.edu/molvis/workshop/allstruc/whycare.htm Why do we care?]
+::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]].
 :F. The ''popup'' button for enlarging the molecular scene.
 :G. A link to display the molecule in ''FirstGlance in Jmol'' (in the ''Resources'' block under the molecule).
-===2. Continue in FirstGlance===
+===2. Continue in FirstGlance in Jmol===
 In Proteopedia, use the link to ''FirstGlance'' in the ''Resources'' block under the molecule to display your molecule in ''FirstGlance in Jmol''.
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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, ''Section #'' is complicated, so you might have the answer in two slides, labeled ''Section 1A'' and ''Section 1B''.
+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 2: Ligands and Non-Standard Residues===
+Give the 3-letter abbreviations and full names for all ligands and non-standard residues. If none, so state. ([[Standard residues]])
+:<font color='gray'>Proteopedia lists the 1 to 3-letter abbreviations for each ligand and non-standard residue in green links under the molecule. Click on each one to see its full name shown in red at the bottom of the molecule.</font>
 ===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. Problems? See [[How to see conserved regions]].</font>
 ===Section 4: Hydrophobic/Polar===
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 ===Section 5: Charge===
-Are there any areas on the surface of your molecule with only positive (or negative) charges? Show a illustrating your conclusions.
+Are there any areas on the surface of your molecule with only positive (or negative) charges? Show a <font color='e000e0'><b>snapshot</b></font> illustrating your conclusions.
 ===Section 6: Biological Unit===
+How many polymer chains (protein, DNA or RNA) are in the biological unit? The asymmetric unit?
+:A. The asymmetric unit is what you see in Proteopedia or FirstGlance, when you use the PDB code.
+:B. In a new browser tab, go to [http://watcut.uwaterloo.ca/cgi-bin/makemultimer/ MakeMultimer].
+:C. Enter your PDB code. Leave all other options at their defaults. Click Submit.
+:D. Pay attention to the tables, especially the "Chain" column (model made by MakeMultimer), vs. the "original" column (original chain names).
+:E. Click "View in FirstGlance".
+Show side-by-side <font color='e000e0'><b>two snapshots</b></font> comparing the asymmetric unit with the biological unit. The ''Cartoon'' representation in FirstGlance is best for these snapshots. Make sure to label which is which.
 ===Section 7: Animation from Polyview-3D===
+Minimal steps to make an animation:
+<!--
+#Use the Firefox browser. (Initial orientation, Set by Jmol does not work in Safari.)-->
+#Go to [http://polyview.cchmc.org/polyview3d.html Polyview-3D].
+#Enter your PDB code in the PDB ID slot near the top.
+#Change "Type of request" from "Single slide" to "Animation". It is under the ''Image Settings'' section near the bottom.
+#Click any "Preview" link.<font color='gray'>
+#Optional: If you want to modify the orientation or zoom of the molecule, click on ''View by Jmol / Set orientation'' under ''Quick links'' at the upper left of the page. Use the mouse to rotate and zoom in Jmol. Then click the ''Set and close'' button.
+#Optional: If you want to change the colors, hide portions of the molecule, emphasize certain residues, etc. feel free to try out these options in the form, using ''Preview'' to check your results.</font>
+#In the "Animation Settings" section at the bottom of the page, set Delay to 10/100.
+#Change "Angle step" to 5 degrees.
+#Check "Rocking".
+#Change "angle range" for rocking to 30 degrees.
+#Click "Get 3D Image".
+The above steps are the minimum for an animation that avoids putting a heavy load on the server. Feel free to try other options, but while the class is in session, please don't make a large (>300 pixel) animation, or increase the angle range, or decrease the angle step size. Otherwise, the server may get overloaded and take a very long time to produce results. After class is over, feel free to submit more demanding jobs. If you highlight specific residues, please explain why.
+In Powerpoint, animations move only when the slides are projected (full-screen).
+'''Windows Powerpoint''': Simply drag the animation directly from the Polyview-3D web page and drop it into a Powerpoint slide.
+'''Mac Powerpoint''': The method below produces a slide that will animate continuously. Other methods we have tried do not.
+#Control-Click on the animation in the Polyview-3D web page, and select Save Image As ...
+#Save the image to the Desktop.
+#Drag the image file (filename ending in .gif) from the Desktop and drop it into a Powerpoint slide.
+#As stated above, the animation will run only when the saved .ppt file is projected (full screen).
+===<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.
-===Section 8 - Optional: Contacts/Non-covalent Bonds===
+Describe the moiety you selected as a target. Include a <font color='e000e0'><b>snapshot</b></font> showing a hydrogen bond.
 ==VI. See Also==