CHM 579 Assignment #2
Structure Refinement Server, Protein Structure Morphing and Normal Modes
Due on Friday, Feb 7 2020 at 11:59 PM
The purpose of this assignment is to familiarize you with different online tools for the analyis of protein structures and
how they move. For this assignment, you will select a protein of interest and submit it to these servers for analysis and
present your findings on your CHM579 webpage (in the assignment2 folder). You may select a protein that you used in assignment1
or pick a new one.
Structure Refinement Server
KoBaMIN server is an internet service for very
fast protein structure refinement. The refinement protocol is composed
of two steps: (1) energy minimization using a knowledge-based potential of mean force and (2) stereochemistry correction.
Users submit one or more protein structures and KoBaMIN likely brings them closer to the native-like conformation. Energy
minimization is a technique to relax the system of atoms by moving to a local minimum over the potential energy surface.
This is achieved by moving the coordinates of atoms in order to reach the minimum of the potential energy surface. At the
minimum of the potential energy surface, the gradient is equal to zero and the Hessian is positive definite. You will be
using this refinement server on your choice of protein structures in the following assignment outline.
Run one of your favorite protein structure you have chosen for this assignment for structure refinement server using the
KoBaMIN server and download the results when the job is finished.
- Run the server by unchecking the box
"Perform post-refinement stereochemistry correction with MESHI."
- More information about the server is given
here with an example output page shown
here. Look at the output page and explain what you observe by linking the output page from the server as well as
including any screenshots, if you prefer for clarity.
- Download the final refined structures as well as other files including log files and link them to your webpage.
- Is the total energy minimized from this simulation? What is the change in energy after refinement? How long did it take
to run for your structure?
- Read the ENCAD log files and answer the following questions:
- Display the chemical formula or the amino acid sequence (3-letter code) for your structure.
- The output file lists the 'strains' in the system: Display visually and list the top 5 most strained bond lengths, bond
angles, torsion angles, and phi-psi torsions for your refined structure. What are the starting and ending total bond
length and bond angle energy excluding the water molecules? Does this make sense for minimization? Why?
Protein Structure Morphing
is a part of the
Database of Macromolecular Movements, a web based database designed by Mark Gerstein, a professor at Yale University.
There you can find all sorts of information about protein motion, as well as software, links and movies. It's a fun site
to explore to learn more about conformational changes in proteins. When the morph server is fed 2 conformations of the
same protein, it will return a set of morphed intermediates. What the morphed intermediates represent is a hypothetical
trajectory for the motion that would need to occur for a protein to transition from one conformation to the other.
Notice the impressive number of output formats that the morph server generates!
- Visit the
Database of Macromolecular Movements
- Find a protein that has more than one experimentally determined conformation. The bigger the difference in conformations,
the more dramatic the effects of the morph server will be, and the better the results. One great source of such proteins
are those that bind ions or other ligands and exhibit conformational changes upon binding. It is OK to use a protein whose
results have already been submitted to the morph server. Just make sure to resubmit everything yourself! We certainly
don't expect you to find proteins nobody else has ever looked at before.
- Find the
on the above website, and submit your pdbs to it. Feel free to play with the different options. For instance, selecting more
frames will result in a smoother morph. Notice that depending on the PDB files you submit (give them PDB ID's or upload
them), you could experience problems. Be prepared to try more than one option. Check out their
page for suggestions. We can try to help with any problems, but we offer no guarantees!
The morph server expects to find the same protein in each of the submitted pdb files (just in different conformations).
Check the pdbs you are submitting to make sure they only have one molecule in them, there are no large gaps (missing
coordinates) in either pdb file, and that the protein sequences are identical or very similar. I recommend downloading
the pdbs and looking at them in a text editor. You can remove heteroatoms or extra protein chains and submit your modified
pdbs using the upload option on the web page.
- Play with the output! The automatically generated movies are usually very nice, but you are stuck with their default viewing
angle. Also download the files with each of the individual frames of the movie and use your favorite molecule viewer to
look at the superimposed conformations simultaneously. It is recomended that you use PyMOL or VMD to create a movie detailing your findings.
Normal Mode Analysis
Karsten Suhre Lab developed the server
elNemo, which can be used to calculate normal modes.
- Visit the elNemo Server and submit one conformation of the same protein you submitted to the morph server. Calculate
a few of the lowest normal modes, but remember that the first 6 normal modes are rotational and translational. (Hint:
normal mode analysis of "open" conformations gives better results than the analysis of a "closed" conformation).
- The output of the server will be a number of PDBs along with animation files, each representing the motion due to one normal mode. Upload the files
to your favorite molecular viewer and observe the mode-induced movements.
Make a webpage that showcases the motion of your selected protein.
Include the following:
- Describe the biological function of the (
one) protein you chose. Remember that there is a great deal of information in the PDB header, including references
to papers by the groups that did the structure determination. Please list the PDB ID's of the two structures you used
in your morph.
- Describe the differences between the structures in your two submitted pdbs. They might show the protein in the presence/absence
of ligands or heteroatoms, might include different mutants, may show the protein under different environmental conditions
(pH, salt concentration, etc.), or something else altogether.
- Include the morph you generated, or a link to it. Also include images that showcase the conformational change. You can
include the ones generated by the server, but
also make some of your own that do a better job of illustrating the motion. Animated movies are not necessary.
Well constructed "still" images are just fine. Show how the trigger described above induces the conformational change.
Is the motion large or small? How much of the protein is involved? Would you describe the motion as predominately shear
- Describe the motion induced by the three lowest normal modes ("breathing", twisting, hinging...) and include some stills.
Is there a low frequency normal mode that is similar to the motion seen in the morph server? Can the biologically relevant
motion be described by a small number of low frequency normal modes?
- Describe why the motion of your protein is BIOLOGICALLY interesting (one or two paragraphs) and any information that you
think the morph, the normal mode analysis, or data generated on the server webpages may have revealed.