CHM 579 Assignment #1

Molecular Graphics, Structure Refinement Server and Basic Monte Carlo

Due on Wednesday, Feb 1 2017 at 3:29 PM

The objective of this assignment is three-fold: first, to become familiar with protein structures and the Protein Data Bank, to try some of the programs used to display protein structures, and to learn how these programs can be used for research and understanding; second, to be able to use the existing online servers and interpret the results; third, to be able to run a simple program in the linux environment. These skills will form the basis of future assignments in the class.

The Protein Data Bank

The Protein Data Bank, or PDB, is the best place to obtain 3-Dimensional structures of proteins, nucleic acids, peptides and other macromolecules. From their site, you can locate proteins by keyword searching or by entering the accession number for the structure file, like 1mba. Most of the structures in the PDB were determined by X-ray crystallography or NMR spectroscopy with a growing trend of using Cryo-EM. Details on the molecules in the structure file, how the structures were determined, pertinent research articles, etc. can be found on the web site but also in the pdb file itself.

PDB files are just formatted text files, so you can open them in a text editor or even Word and read them. There is a wealth of information there! The molecular viewing programs use the ATOM records in the file, which contain residue name, residue number, atom name and atom number - all of which are important when selecting molecules or parts of them to visualize. Often, the structure files include other molecules besides the protein, such as water molecules, nucleic acid and bound ligands.

Molecular Graphics Programs

There are quite a few programs used to view molecules.. Each has its advantages and disadvantages. We provide links to the programs discussed in the lectures (and their manuals/documentation) on the Programs Page.

PyMol
PyMol is a relatively new and very promising molecule viewing program. It is available for all Unix/Linux platforms, Windows and Mac OSX. It uses a combination of menus, a powerful selection sidebar, demonstrated in the lecture, and a command line interface. It has a logging feature to remember commands as they are executed, allows for scripting and has a nice movie feature. We have created a PyMol tutorial for you to get started with the program. There is also a tutorial on the PyMol website. Also check out the PyMol Wiki for more help and tips.
- PyMol is free to download for versions pre 1.0. You can download it here: Pymol version 0.99. Don't worry about the "builds are obsolete" message. Version 0.99 is fine for this class. If you really want a newer version and are a student (i.e. not going to use it for industry or professional work) you can apply to download the educational version.
Visual Molecular Dynamics (VMD)
VMD is new and very promising molecule viewing program developed at University of Illinois at Urbana-Champaign. It is available for all Unix/Linux platforms, Windows and Mac OSX. It uses a combination of three windows: a terminal window, a viewing window and a main window. The terminal window (DOS window on Windows machines) is useful in that error messages and command output. The view window is where your molecules will appear, and the main window is where most of the controls for VMD are found. We have created a VMD tutorial for you to get started with VMD. We strongly encourage you to go through the VMD tutorial also which can be found on the VMD website, if you need more information to create this assignment. VMD is a very important tool which would be helpful for further assignments as well.
- VMD is under rapid development, so get the latest program from the VMD Web Site.

There are a number of different molecular graphics programs out there (rasmol, molmol, swissPDBviewer, Chimera, to name a few) but we feel that Pymol and VMD together offer the best features for this course. You are free to experiment with other programs but for this assigmnet we require that you use VMD and Pymol.

Structure Refinement Server

The 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 assignment outlines as follows.

Basic Monte Carlo Program

Monte Carlo is a method that involves random numbers and probability to solve problems in a variety of areas, including, computational chemistry, computational physics, finance, weather prediction, etc. You can read all about Monte Carlo here and we will also cover this topic in our lectures in detail. Here we want to compile and use a simple monte carlo program in a step-wise manner to understand the process of working in the linux environment, see the details of a simple program written in Fortran, and play with parameters to understand the results. A basic introduction to linux and other items for the linux environment is available here for your reference.

The Assignment

Learn to download structure files. Some structure files are often provided with the viewer programs for demonstration purposes, but you should download the structures of different proteins from the PDB.
Learn to use Two Different Molecule Viewing Programs (Pymol and VMD).
- Learn to rotate and zoom in on different parts of the structure.
- Play with different structure representations.
- Learn how to select different molecules, protein chains, residues and atoms.
- Learn how to output the structures in different image formats.
Choose Two Protein Structures (of Two Different Proteins).
- These should be structures that you download from the PDB, not ones that were supplied with the graphics programs.
- If you don't have the slightest idea what structures to choose, you can try the Molecule of the Month..
- There are links to articles related to each structure in the database, and there is also important information within the header section of the pdb file itself. Learn about the proteins and the other molecules in the structure files.
Use the programs to generate illustrations of interesting aspects of the structure of these proteins.
- You can export images from the programs themselves or capture images straight of the screen, as discussed the lecture. Only submit compressed image file formats, like jpeg or gif. Tiff, pict and other raw formats generate massive files. You should include images generated by both viewing programs in your submission.
- Each image should illustrate some property of the protein's structure or function. We do not just want pretty pictures - the biology needs to be there too! Some ideas:
  - Try some of the examples that were shown in the lecture.
  - Show the architecture of the protein, secondary structure, packing, surface, fold, etc.
  - Show some examples of interactions that stabilize the structure.
  - If your pdb file has other molecules besides the protein in it, show them and how they interact with the protein. What is the biological relevance of their presence?
  - Is your protein oligomeric or part of a complex? How can that be clearly shown?
  - Zoom in to clearly show interesting details.
  - Show how the structure might affect the dynamics of the molecule.
- Use one or more images to show how the structure of the protein relates to its function.
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?
Follow the instructions and answer questions for the monte carlo program given in the PDF file here. We will go over this part in the lab session. This part of the assignment will help you get comfortable with the linux environment to run programs and interpret the output. The goal of this lab is to get familiar with a simple Monte Carlo program and to be able to compile and run it on a Linux server.
- Please download the zip file associated with this part of the assignment and unzip it in mc-001 folder.
- Transfer the entire folder to scholar.rcac.purdue.edu using the following commands:
  - Open 'Terminal' on Mac/Linux and 'Secure FX' on windows.
  - Connect to scholar.rcac.purdue.edu using your username and password. On a mac/linux machine you don't need to do this and follow the next step. On windows you need to connect SecureFX to this server to transfer your folder
  - On a mac/linux machine type the command on the terminal: scp -r (folder_current_path) (username)@scholar.rcac.purdue.edu:~/
  - Using SecureCRT on Windows and using SSH on mac/linux login to scholar.rcac.purdue.edu where you will find your folder.
  - Transfer this folder and change directory to ${RCAC_SCRATCH} using the following commands:
    - mv mc-001 ${RCAC_SCRATCH}
    - cd ${RCAC_SCRATCH}
  - Follow the instructions in the PDF file to complete this part of the assignment.
Make a Web Page!
- Include your images/illustrations with a short explanation of the biological concept you are presenting.
- We are looking for a maximum of eight images on this assignment (preferably 4 from each program). Images beyond the first 8 will not be graded. These do not include any additional images you will make for the Structural Refinement Server part of the assignment.
How you will be graded:
- The assignment is worth 10 points. If the minimum requirements are met, 8 points will be awarded. The requirements are:
  - Provide images generated by Pymol and VMD.
  - Provide images of two different protein structures.
  - Demonstrate the ability to show different aspects of the structures by rendering the molecules in different ways.
  - Include a short, clear description of the biological idea conveyed in each image and answer / explanations to all questions asked in the assignment.
- The remaining 2 points are at the discretion of the instructor, and will be awarded for providing aesthetically pleasing images of biologically relevant aspects of protein structures with short, lucid and thoughtful discussion. We want to see how your understanding of the function of the protein was improved by looking at the structures.
- Please do not submit more than 8 images for grading not including any additional images you will make for the Structural Refinement Server part of the assignment.
  - Remember, the assignments are done in webpage format only.
  - Webpage Design Primer
  - BareBones Guide to HTML
  - IMPORTANT: Please do not make any plugins (Chime, etc) necessary in order to view your webpage! Use GIF/PNG/Jpeg images only, since the plugins are not available for all browsers and might make grading difficult.

Submit your work

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