User:Eric Martz/Introduction to Structural Bioinformatics I, 2014: Difference between revisions
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Section 2: "1-3 character" | |||
Sec 8: Start with "show me ONE hydrogen bond". Describe which atoms participate in the hydrogen bond, including their residue names and sequence number. If you show more than one distance, indicate which bond you are describing. I need enough detail to be able to reproduce what you are reporting. | |||
Renumber sections to enumerate inline 4A and 5A. | |||
Consider adding exptl vs full length sequence lengths and alignment. | |||
Hydrophobic core: mention "per domain". Cf. 1acc. | |||
If students have problems or get stuck, they should contact the TA. If the TA cannot confidently answer the question, TA should contact me (give cell phone). | |||
In 2014, 3 people picked 1mbo, so have them register and avoid dups! | |||
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<center> | <center> | ||
<span style="font-size:160%">How to | <span style="font-size:160%">How to visualize, understand and share/present 3D protein molecular structures</span><br> | ||
<span style="font-size:130%">by Eric Martz, <font color="magenta"> | <span style="font-size:130%">by Eric Martz, 2014<!--<font color="magenta"> DRAFT UNDER REVISION</font>--></span> | ||
<br> | <br> | ||
<span style="font-size:115%">for [http://www.micro.umass.edu/faculty-and-research/steven-sandler Prof. Steven Sandler's] course [http://www.micro.umass.edu/courses/catalog/microbio-565-laboratory-in-molecular-genetics Microbiology 565: Laboratory in Molecular Genetics]</span> | <span style="font-size:115%">for [http://www.micro.umass.edu/faculty-and-research/steven-sandler Prof. Steven Sandler's] course [http://www.micro.umass.edu/courses/catalog/microbio-565-laboratory-in-molecular-genetics Microbiology 565: Laboratory in Molecular Genetics]</span> | ||
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<imagemap> | <imagemap> | ||
Image:1000px-Amino Acids.svg.png|200 px| | Image:1000px-Amino Acids.svg.png|200 px| | ||
default [http://proteopedia.org/wiki/images/1/13/1000px-Amino_Acids.svg.png] | default [http://proteopedia.org/wiki/images/1/13/1000px-Amino_Acids.svg.png] | ||
</imagemap> | </imagemap> | ||
|} | |} | ||
:<span style="font-size:130%">1. [[Amino acid]] '''sequence''' + protein chain '''conformation''' = protein '''function'''.</span> | :<span style="font-size:130%">1. [[Amino acid]] '''sequence''' + protein chain '''conformation''' = protein '''function'''.</span> | ||
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==IV. Choose a Molecule to Explore== | ==IV. Choose a Molecule to Explore== | ||
*Choose a molecule to use for your report. | *Choose a molecule to use for your report. | ||
**Each student should choose a ''different'' molecule. | |||
**It must have protein. | **It must have protein. | ||
**It will be more interesting if it contains some non-protein: DNA, RNA or ligand. | **It will be more interesting if it contains some non-protein: DNA, RNA or ligand. | ||
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# Search by molecule name or amino acid sequence at [http://www.pdb.org www.pdb.org], but remember that less than 10% of proteins have known structure. | # Search by molecule name or amino acid sequence at [http://www.pdb.org www.pdb.org], but remember that less than 10% of proteins have known structure. | ||
== | ==V. Explore Your Molecule== | ||
===FirstGlance in Jmol=== | |||
The main tool we will use is '''FirstGlance in Jmol''': [http://firstglance.jmol.org FirstGlance.Jmol.Org]. (To google it later, use the single word (no space) '''firstglance'''.) | The main tool we will use is '''FirstGlance in Jmol''': [http://firstglance.jmol.org FirstGlance.Jmol.Org]. (To google it later, use the single word (no space) '''firstglance'''.) | ||
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*In the ''Views'' tab, there are 10 links at the top that show you different aspects of the molecule. Try them all, as well as any of the other tools in FirstGlance that interest you. | *In the ''Views'' tab, there are 10 links at the top that show you different aspects of the molecule. Try them all, as well as any of the other tools in FirstGlance that interest you. | ||
:FirstGlance does NOT use '''Java''' unless you tell it to. Larger proteins will be slow to load and rotate, and to change the view, unless you use Java. Use ''Safari (or Firefox) for Java'' on Macs because Chrome does not support Java on Macs. On Windows, Internet Explorer is good for Java. In your Java-compatible browser, display a molecule in FirstGlance, and then click on the ''Preferences'' tab in FirstGlance. Java is installed and working in the BCRC. Simply give it permission when asked (several times). | :FirstGlance does NOT use '''Java''' unless you tell it to. Larger proteins will be slow to load and rotate, and to change the view, unless you use Java. Use ''Safari (or Firefox) for Java'' on Macs because Chrome does not support Java on Macs. On Windows, Internet Explorer is good for Java. In your Java-compatible browser, display a molecule in FirstGlance, and then click on the ''Preferences'' tab in FirstGlance. Java is installed and working in the BCRC. Simply give it permission when asked (several times). | ||
Here are two Views in FirstGlance that will be used in your Powerpoint report: | |||
Powerpoint report: | |||
====A. Hydrophobic/Polar==== | ====A. Hydrophobic/Polar==== | ||
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*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]]). | *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 Å in their smaller diameter) may indicate transmembrane proteins (insoluble). Examples: | *Large, protruding hydrophobic surface areas (>25 Å in their smaller diameter) may indicate transmembrane proteins (insoluble). Examples: | ||
**[ | **[http://firstglance.jmol.org/fg.htm?mol=1bl8 1bl8] | ||
**showing [http://opm.phar.umich.edu/protein.php?pdbid=1r3j bilayer boundaries] (click on "Jmol"; ligand toggles boundaries). | **showing [http://opm.phar.umich.edu/protein.php?pdbid=1r3j bilayer boundaries] (click on "Jmol"; ligand toggles boundaries). | ||
**[[Gramicidin Channel in Lipid Bilayer]]. | **[[Gramicidin Channel in Lipid Bilayer]]. | ||
====B. Charge==== | ====B. Charge==== | ||
Most proteins have roughly equal numbers of positive and negative charges intermixed on their surfaces. Surface patches of exclusively positive charge often bind nucleic acids (negatively charged because of their phosphates). For example, examine the protein surface charges where the gal4 transcriptional regulator binds DNA ([ | Most proteins have roughly equal numbers of positive and negative charges intermixed on their surfaces. Surface patches of exclusively positive charge often bind nucleic acids (negatively charged because of their phosphates). For example, examine the protein surface charges where the gal4 transcriptional regulator binds DNA ([http://firstglance.jmol.org/fg.htm?mol=1d66 1d66]). | ||
== | ==VI. 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. You will ''not'' be asked to present your report in class. | ||
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''. | ||
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<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> | ||
<br> | <br> | ||
[http:// | <span style="font-size:140%;background:#c0ffc0;">[http://bioinformatics.org/molvis/ppt/martz-565-2014rev2.ppt Sample Completed Powerpoint Assignment]</span> (You may download it, rename the file, and use it as a template.) | ||
===Section 1: Identity=== | ===Section 1: Identity=== | ||
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*A <font color='e000e0'><b>snapshot</b></font> of your molecule. | *A <font color='e000e0'><b>snapshot</b></font> of your molecule. | ||
<center><table border="0" width="80%" style="background:#ffffa0;"><tr><td><center> | <center><table border="0" width="80%" style="background:#ffffa0;"><tr><td><center><span style="font-size:130%"> | ||
[http://firstglance.jmol.org/slides.htm How to make a snapshot], | [http://firstglance.jmol.org/slides.htm How to make a snapshot],</span> | ||
<br> | <br> | ||
is also linked at the bottom left in ''FirstGlance''. | is also linked at the bottom left in ''FirstGlance''. | ||
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===Section 3: Evolutionary Conservation=== | ===Section 3: Evolutionary Conservation=== | ||
See [[Introduction to 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. | 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. | ||
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===Section 4: Hydrophobic/Polar=== | ===Section 4: Hydrophobic/Polar=== | ||
Do you think your molecule is water soluble? Support your conclusion with a <font color='e000e0'><b>snapshot</b></font>. <font color='gray'>Be sure to use the ''Hydrophobic/Polar'' view from FirstGlance in a snapshot. Optionally, you may show other views in other snapshots.</font> | Do you think your molecule is water soluble? Support your conclusion with a <font color='e000e0'><b>snapshot</b></font>. <font color='gray'>Be sure to use the ''Hydrophobic/Polar'' view from FirstGlance in a snapshot. Optionally, you may show other views in other snapshots.</font> | ||
===Section 4A: Hydrophobic Core=== | |||
Is there a hydrophobic core in your molecule? Support your conclusion with a <font color='e000e0'><b>snapshot</b></font>. <font color='gray'>Be sure to use the ''Hydrophobic/Polar'' view from FirstGlance and turn on the ''Slab'' button.</font> | |||
===Section 5: Charge=== | ===Section 5: Charge=== | ||
Are there any areas on the surface of your molecule with only positive (or negative) charges? Show <font color='e000e0'><b>snapshots</b></font> illustrating your conclusions. <font color='gray'>Be sure to use the ''Charge'' view from FirstGlance in a snapshot.</font> | Are there any areas on the surface of your molecule with only positive (or negative) charges? Show <font color='e000e0'><b>snapshots</b></font> illustrating your conclusions. <font color='gray'>Be sure to use the ''Charge'' view from FirstGlance in a snapshot.</font> | ||
===Section 5A: Cation-Pi Interactions=== | |||
Show a <font color='e000e0'><b>snapshot</b></font> of an energetically significant [[Cation-pi_interactions|cation-pi interaction]]. Include a distance monitor in your snapshot. Also paste in the report from CaPTURE confirming its energetic significance. <font color='gray'>The cation-pi interaction tool, and instructions for measuring distances, are in the ''Tools Tab''.</font> | |||
===Section 6: Biological Unit=== | ===Section 6: Biological Unit=== | ||
How many polymer chains (protein | In FirstGlance, in the ''molecule information tab'' click ''Biological Unit''. (It is also in the ''Resources Tab''.) | ||
How many total polymer chains (protein + DNA + RNA) are in the asymmetric unit? The Biological unit? | |||
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. | 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. | ||
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#Use the Firefox browser. (Initial orientation, Set by Jmol does not work in Safari.)--> | #Use the Firefox browser. (Initial orientation, Set by Jmol does not work in Safari.)--> | ||
#Go to [http://polyview.cchmc.org/polyview3d.html Polyview-3D]. | #Go to [http://polyview.cchmc.org/polyview3d.html Polyview-3D]. | ||
#Enter your PDB code in the PDB ID slot near the top. | #Enter your PDB code in the PDB ID slot near the top. (If the slot is not visible, open the section ''Source of Structural Data''.) | ||
#Change "Type of request" from "Single slide" to "Animation". It is under the ''Image Settings'' section near the bottom. | #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'> | #Click any "Preview" link.<font color='gray'> | ||
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#Check "Rocking". | #Check "Rocking". | ||
#Change "angle range" for rocking to 30 degrees. | #Change "angle range" for rocking to 30 degrees. | ||
#Click " | #Click "Submit". | ||
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. | 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. <font color="gray">Optional: After class is over, feel free to submit more demanding jobs. If you highlight specific residues, please explain why. </font> | ||
In Powerpoint, animations move only when the slides are projected (full-screen). | 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. | '''Windows Powerpoint''': Simply drag the animation directly from the Polyview-3D web page and drop it into a Powerpoint slide. If the result does not animate when you project the slide, try the instructions for Mac below. | ||
'''Mac Powerpoint''': The method below produces a slide that will animate continuously. Other methods we have tried do not. | '''Mac Powerpoint''': The method below produces a slide that will animate continuously. Other methods we have tried do not. | ||
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#As stated above, the animation will run only when the saved .ppt file is projected (full screen). | #As stated above, the animation will run only when the saved .ppt file is projected (full screen). | ||
=== | <span style="font-size:140%;background:#c0ffc0;">[http://bioinformatics.org/firstglance/fgij/ppt/polyview-3d-examples.ppt Powerpoint Slides with Polyview-3D Animations]</span> (These slides are only to show you what is possible. These are not in your assignment.) | ||
# | |||
---- | |||
===Section 8 - Contacts/Non-covalent Bonds=== | |||
#Click ''Contacts'' in the ''Tools Tab'' in FirstGlance. | |||
#Change target selection to ''Residues/Groups''. | #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 on something small to select it as a "target", such as a ligand, or a single amino acid. Choose an amino acid with an uncharged polar side chain, such as Ser, Thr, Asn, Gln, Tyr, His. | ||
#Click the link to ''Show atoms contacting target''. | #Click the link to ''Show atoms contacting target''. | ||
#Click ''Center contacts''. | #Click ''Center contacts''. | ||
#Uncheck ''Backbones''. | #Uncheck ''Backbones''. | ||
#Click the 4th thumbnail image [[Image:Contact4.gif]] to display the contacts as balls and sticks colored by element. The element color key is at the bottom of the Contacts help panel in FirstGlance. | |||
#Zoom in (and click ''Return to Contacts'' if necessary). | #Zoom in (and click ''Return to Contacts'' if necessary). | ||
#Uncheck all categories of non-covalent bonds. | #Uncheck all categories of non-covalent bonds. | ||
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Describe the moiety you selected as a target. Include a <font color='e000e0'><b>snapshot</b></font> showing a hydrogen bond. | Describe the moiety you selected as a target. Include a <font color='e000e0'><b>snapshot</b></font> showing a hydrogen bond. | ||
== | ==VII. See Also== | ||
* [[User:Eric Martz/Introduction to Structural Bioinformatics]], a list of courses and workshops at various levels, including earlier versions of this segment. | * [[User:Eric Martz/Introduction to Structural Bioinformatics]], a list of courses and workshops at various levels, including earlier versions of this segment. | ||
== | ==VIII. Notes and References== | ||
<references /> | <references /> | ||
