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courses:public:vmd [2016/06/20 13:03] richter [Alignment of proteins] |
courses:public:vmd [2016/06/21 09:43] stank [Visualization of electrostatic potentials] |
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//**Goal: Compare structures from different organisms or different folds**// | //**Goal: Compare structures from different organisms or different folds**// | ||
<code> | <code> | ||
- | * Sometimes similar proteins exist in different species - they may perform the same function | + | * Sometimes similar proteins exist in different species - they may perform the same function, |
- | but have different sequence. It is useful to compare structures of these proteins. | + | but have different sequences. Therefore, it is useful to compare structures of these proteins. |
To do that, one needs to align the proteins based on their sequence | To do that, one needs to align the proteins based on their sequence | ||
and sometimes also taking the structure into account. | and sometimes also taking the structure into account. | ||
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- What region displays largest difference between the two structures[[courses:hidden:vmd#Alignment of proteins|_?_]] | - What region displays largest difference between the two structures[[courses:hidden:vmd#Alignment of proteins|_?_]] | ||
<code> | <code> | ||
+ | * In the VMD Main window select the molecule of 1yer and right click on it to save its coordinates. | ||
+ | Choose only the protein part (chain A) in 'Selected Atoms' and save it in a file called 1YER_aligned.pdb and repeat these steps also for the other molecule 2ior_aligned.pdb | ||
* Close the VMD program | * Close the VMD program | ||
</code> | </code> | ||
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//**Goal: Visualize possible interaction sites on proteins**// | //**Goal: Visualize possible interaction sites on proteins**// | ||
+ | <code> | ||
+ | * Start VMD again and use the aligned Proteins from the previous section (load the previously saved coordinates). | ||
+ | The proteins should show up as aligned entities. | ||
+ | * Go to the PDB2PQR webserver: http://nbcr-222.ucsd.edu/pdb2pqr_2.1.1/ | ||
+ | * Upload one of the aligned coordinate files. | ||
+ | Choose the force field (AMBER) and naming scheme (AMBER), and click ’Submit’. | ||
+ | * Save the output files (xxxx_aligned.in, xxxx_aligned.propka and xxxx_aligned.pqr) on disk. | ||
+ | * Press "Run APBS" -> Launch | ||
+ | * Again, save the output files, espcially the *.dx.gz grid files. | ||
+ | You might want to look at the program output and error logs if there are errors or warnings. | ||
+ | * Repeat for both structures and unpack the *.dx.gz file. | ||
+ | </code> | ||
+ | In the respective pqr files, what are the net charges for the two proteins[[courses:hidden:vmd#Alignment of proteins|_?_]] | ||
+ | <code> | ||
+ | * To visualize the electrostatic potential, select in the vmd main window the molecule 1yer. | ||
+ | * Go to File-> Load data in molecule. Select the corresponding dx grid file from your apbs output Press Load. | ||
+ | * In Graphics Representation, change the standard representation to New Cartoon. | ||
+ | * Create a new representation, Color by ID (blue), Select drawing method Isosurface. Select an Isovalue of 3 | ||
+ | and draw as Solid surface. | ||
+ | * Again Create a new representation. Color by ID (red), Select again drawing method Isosurface with an Isovalue of -3. | ||
+ | also draw as Solid surface. | ||
+ | * Repeat the steps with the other molecule. | ||
+ | </code> | ||
+ | What are the differences between the electrostatic potentials of the two proteins? From which species are the respective proteins from[[courses:hidden:vmd#Alignment of proteins|_?_]] | ||
==== Tutor only ==== | ==== Tutor only ==== | ||
- | [[http://wiki.mcm.h-its.org/lib/exe/fetch.php?media=courses:hidden:visualizationstatesbasicvmdtutorial.zip|Visualization states from basic tutorial]] | + | {{courses:hidden:visualizationstatesbasicvmdtutorial.zip|Visualization states from basic tutorial}} |
+ | |||
+ | {{:courses:hidden:hsp90_aligned_electrostatics.zip|Visualization state alignment and electrostatics}} | ||
- | [[courses:hidden:visualizationstateselectrostaticsvmdtutorial.zip|Visualization state from electrostatics tutorial]] | ||