CHM 579 Assignment #3

Molecular Simulations - Morph Server, Normal Modes & Molecular Dynamics

Due on Wednesday, Mar 22, 2017 at 3:29 PM

Overview:

The idea of this assignment is to simply have some fun with molecular simulations and get a flavor for other techniques apart from molecular dynamics. Unfortunately, due to the complexity and computational intensity of Molecular Dynamics software packages, we can't have you all run 100 ns MD simulations on your favorite system. Instead, here we will learn how to run Interactive Molecular Dynamics (IMD) to view the simulation as time progresses on your local machine to give you a visual sense of what is happening to the system. Then you would run Steered MD for 500ps long simulations and analyze the output of MD for one of the parts of the assignment. Also, you will be looking at conformational changes in proteins and how these motions are important for their biological function. The assignment has 3 parts: The Morph Server, Normal Mode Analysis, Molecular Dynamics using NAMD and VMD (Deca-alanine and carbon nanotube systems) and setting-up systems (acetone in water and protein in water) with Gromacs. You should realize that the protein folding is a hard problem. In nature, a protein folds in the order of milli-second to few seconds and we are just simulating pico-second regime here. This is because on the a huge-amount of computer time is need to simulate a protein with time-steps of the order of femto seconds (1e-15 sec), as bond vibration is of the order of femto-seconds. Thus to avoid resonance in these molecules we cannot have time-steps more than a few femto-seconds (typically 2 fs). Of course, there are other methods to take care of resonance and increase the time-step, which we will cover in later parts of this course.

The Assignment:

Part 1 - The Morph Server:

The Morph Server 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!

  1. Visit the Database of Macromolecular Movements

  2. 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.

  3. Find the Morph Server 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 FAQ page for suggestions. We can try to help with any problems, but we offer no guarantees!

  4. 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.

Part 2 - Normal Mode Analysis:

The Delarue Group Web Services provide tools for online normal mode calculation, as well as other valuable services and plenty of references.

  1. Visit the Delarue Group 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).

  2. The output of the server will be a number of PDBs, 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:
  1. 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.

  2. 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.

  3. 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 or hinge-like?

  4. 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?

  5. 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.

Part 3A - Molecular Dynamics with NAMD & VMD

This part of the assignment deals with running simulations and understanding how to analyze output from Molecular Dynamics (MD) simulations. The output of a MD program is a series of time-resolved coordinates for all of the atoms in the simulation. The code widely used in the MD community is GROMACS. It is one of the fastest MD software out there. Due to the complexity of using the code (only for Linux and MacOS and assumes Linux/Unix background), it would not be fair for all students to run simulations with it. Thus, we have decided to use NAMD, a MD simulation program developed by Theoretical and Computational Biophysics Group at UIUC in conjunction with VMD, the molecular viewing program. VMD has the capability to work with NAMD in order to display the results of a simulation as they are calculated (Interactive MD). As new atomic coordinate timesteps are generated by the simulation process, they can be transferred directly over to VMD, which can then animate the molecule. A major new feature in VMD is the ability to add perturbative steering forces to a running simulation, which are incorporated directly into the dynamics calculation. You will run both Interactive MD and Steered MD for this assignment.

In order to complete this assignment, you will require to have up-to-date versions of the following software, properly installed on your computer, as mentioned on the NAMD tutorial website:

For windows users, a proper work path should be set for the installed softwares. Suppose these softwares are installed under the following directories:

The work path can be created in different ways. One can either append the following command in C:\autoexec.bat and execute it or type this command in a DOS prompt:

path=C:\Program Files\University of Illinois\VMD;C:\NAMD;

Part 3A (I): Deca-alanine in vacuum

To make things simple for you we have chosen a tutorial from the NAMD website which you can replicate with different parameters and actually run simulations on your computer. You would be simulating deca-alanine in vacuum. A biologically relevant simulation would involve water molecules but in this case one can get to know a lot about structural features in deca-alanine in vacuum as time progresses in the simulation.

The deca-alanine tutorial will get you started with NAMD. You can get the pdf file for the tutorial here. Please NOTE that only pages 1-11 are relevant in the tutorial, though you can read further to get an idea of TCL. A feature of NAMD is that we can use TCL scripting language for analysis and simulation. We do not expect you to do any programming in TCL for the purpose of this assignment. Thus, we would be providing all the files needed to start the simulation. You should use VMD Extension for analysis as mentioned in the VMD tutorial on the VMD website. Please feel free to look for any good tutorials for VMD analysis for MD online, but ALWAYS reference it. We would try to update the VMD tutorial as well, to help with this assignment. You would only need to change the parameters for different simulations as asked below:

  1. Download and install the latest version of VMD and NAMD on your computer. Download the tar-zipped set-up files to get you started with the simulation. Please make sure that the current directory contains all the files downloaded. For windows users, create a folder files and download all the set-up files in this directory. At the command prompt make files as the current directory.

  2. The Interactive MD is for you to see how does the deca-alanine behaves with simulation. Follow the instructions in the tutorial for Interactive MD:

  3. Run Steered Molecular Dynamics (SMD) for 500 ps on deca-alanine in vacuum at 300K, 400K and 450K by changing the parameters in the smd.namd file. Note this is not an interactive MD but you should analyze the MD trajectory using VMD. You will notice that the SMD uses smd.tcl file for the force it applies on the atoms in simulation as explained on page 9 of the tutorial. Feel free to change the force-constant (k) paramter in the smd.tcl file to make the simulation work for 500ps.

    4. Part 3A (II) : Simulation of water permeation through nanotubes

Part 3B - Molecular Dynamics set-up with Gromacs

This part of the assignment deals with running simulations and understanding how to set-up simple systems with Gromacs and understand the output from Molecular Dynamics (MD) simulations. For this part of the assignment, please follow the instructions in the PDF files given below and answer the questions asked in the files:

Part 3B (I): Molecular Dynamics of Solvated Acetone

Part 3B (II): Molecular Dynamics of Lysozyme in Water

NOTE:

Please feel free to email the instructor if you have any questions about this assignment. Start early!!!

Handing Things In:

  1. First of all, we would like the URL of the original morphing submission (the server automatically generates a webpage for you). This should be an ORIGINAL morph that you submitted!
  2. Secondy, we need the address of your webpage. The page should include a picture(s) of the motion, the biological relevance, and answers to the questions. Please use a white background for the webpage, as it makes things nicer!
  3. Please remember to properly cite scientific papers/web pages you used for your assignment! You can find the reference to VMD, NAMD and GROMACS on their website. It is required to cite these references if you are using VMD or NAMD in your assignment. Plagiarism will not be tolerated. It is OK to include some well-written quotes in your assignment, but your descriptions should be mostly in your own words, so we can evaluate your understanding of the material.

How You Will Be Graded

  1. Parts 1 and 2 (the morph server and normal mode analysis) - You must include images you made yourself that specifically highlight the points you make in your discussion. We will only grade the morph and discussion for ONE protein.
  2. Part 3 (Molecular Dynamics) - You answer all the questions asked on this page as well as in the linked PDF files of tutorials and labs.
  3. It is important to show that you understand things and not merely say 'yes' or 'no' for answers to the questions and grading will be done on your reasons/explanations to things that are asked in this assignment.
  4. Feel free to include any movies and illustrations for all parts of the assignment. Like we have discussed - think of the assignment as a research online paper where you can include illustrations to elaborate the points you are making as part of your results and discussions.

    Submit your work



Problems? Questions about the Page or the Class? Contact the instructor