Differences
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courses:public:vmd [2016/06/20 13:30] – [Visualization of electrostatic potentials] richter | courses:public:vmd [2017/03/21 11:35] – [Inspecting Protein Structure: The Ramachandran Plot] richter | ||
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to Backbone (protein backbone will be rendered in green and the | to Backbone (protein backbone will be rendered in green and the | ||
side chains in blue) | side chains in blue) | ||
- | * Replace | + | * Click on Create_Rep button and replace |
- | and click on Create_Rep button | + | |
* Change the Drawing_Method from Surf to Licorice and the Coloring_Method | * Change the Drawing_Method from Surf to Licorice and the Coloring_Method | ||
from Backbone to Name, and answer the following question: | from Backbone to Name, and answer the following question: | ||
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* In VMD_Main window, go to Extensions -> Analysis -> Ramachandran Plot | * In VMD_Main window, go to Extensions -> Analysis -> Ramachandran Plot | ||
* In the Molecule menu select 1HEW.pdb | * In the Molecule menu select 1HEW.pdb | ||
- | * Note that several points (on the left side of the graph) fall outside of the allowed conformational region | + | * Note that several points (on the right hand side of the graph) fall outside of the allowed conformational region |
* Click on these points (yellow squares) to identify these residues and answer the following question: | * Click on these points (yellow squares) to identify these residues and answer the following question: | ||
</ | </ | ||
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//**Goal: Compare structures from different organisms or different folds**// | //**Goal: Compare structures from different organisms or different folds**// | ||
< | < | ||
- | * 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 | + | but have different |
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: | - What region displays largest difference between the two structures[[courses: | ||
< | < | ||
+ | * 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 ' | ||
* Close the VMD program | * Close the VMD program | ||
</ | </ | ||
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< | < | ||
- | * Use the aligned Proteins from the previous section. | + | * Start VMD again and use the aligned Proteins from the previous section (load the previously saved coordinates). |
- | * Right click on each molecule and save its coordinates | + | The proteins should show up as aligned entities. |
- | | + | * Go to the PDB2PQR webserver: http:// |
- | * Go to the PDB2PQR webserver: | + | * 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, | ||
+ | * Press "Run APBS" | ||
+ | * 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. | ||
</ | </ | ||
+ | In the respective pqr files, what are the net charges for the two proteins[[courses: | ||
+ | < | ||
+ | * 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, | ||
+ | * Create a new representation, | ||
+ | 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. | ||
+ | </ | ||
+ | What are the differences between the electrostatic potentials of the two proteins? From which species are the respective proteins from[[courses: | ||
==== Tutor only ==== | ==== Tutor only ==== | ||
{{courses: | {{courses: | ||
- | {{: | + | {{: |
- | [[courses: | ||