L16 Unit D: Protein Structure Visualization PDF

Protein structure visualization  Tools for molecular visualization Protein structure visualization tools are software applications that allow users to view, manipulate, and analyze the three-dimensional (3D) structures of proteins and other biomolecules. These tools are essen...

Protein structure visualization  Tools for molecular visualization Protein structure visualization tools are software applications that allow users to view, manipulate, and analyze the three-dimensional (3D) structures of proteins and other biomolecules. These tools are essential for understanding the molecular architecture, function, and interactions of proteins, as well as for designing new drugs, vaccines, and biotechnologies. There are a number of tools (free and commercial) are available to visualize the biomolecules, each with different features, capabilities, and limitations. Some of them are standalone applications that can be installed on a local computer, while others are web-based applications that can be accessed through a browser. The most commonly used are: 1. PyMol 2. RasMol 3. Chime 4. MolMol 5. Protein explorer 6. Kinemage Cn3D 7. Swiss PDB viewer 8. PDBsum PyMOL PyMOL is a popular and powerful molecular graphics software for viewing, editing, and analyzing 3D structures of proteins and other biomolecules. PyMOL is written in Python and C, and can be extended and customized with Python scripts and plugins. PyMOL is available for Windows, Linux, and Mac OS X, and can be downloaded for free for educational and non-commercial use, or purchased for commercial use. To use PyMOL, users can download and install the software on their local computer, and then open it and load a structure file from their local disk or from the internet. Users can also use the PyMOL command line or graphical user interface to manipulate and modify the structure, such as changing the display mode, color, style, size, orientation, lighting, and transparency. Users can also perform various calculations and analyses on the structure, such as measuring distances, angles, dihedrals, contacts, surface area, volume, electrostatics, and hydrogen bonds. Users can also create animations, movies, and ray-traced images of the structure, and export them in various formats. Running PyMOL Running PyMOL is like running nearly any other program on your computer. When you run PyMOL, you will be presented with the main display  In Windows, this display is set up across two windows. The top window constitutes the “External GUI,” and contains the menu options as well as buttons for advanced visualization. It contains a large text area as well, which logs the commands you have used in the viewer. The bottom window contains the “Visualization Area,” which is the main area where molecules will be displayed. The visualization area can also display text, like help text. When in text mode, the visualization area displays similar information to what is displayed in the external GUI text box. The bottom window also contains another “Internal GUI.” This GUI will contain a list of molecular objects once you have loaded a protein structure. The bottom of this GUI has a matrix displaying the current mouse configuration, namely what mouse button combinations control which functions. It also contains additional buttons for making molecular movies  Opening PDB File High-resolution molecular structures are determined by one of two methods, namely X-ray crystallography or NMR spectroscopy. Once the three-dimensional atomic coordinates are determined, they can be formatted into a text file that programs like PyMOL can read. These files are called “PDB” files, short for the “Protein Data Bank.” the coordinates are submitted to the Research Collaboratory for Structural Bioinformatics (RCSB). This organization maintains the PDB, and it ensures that all PDB files have the proper format and supporting data. The PDB website is available at http://www.pdb.org/ Database entries in the PDB are given a characteristic four-character code that is used to identify the structure. For example, 1SNC is an entry for the protein staphylococcal nuclease. Visit the PDB website page for 1SNC and download the file. At the right hand side of the screen is an option to “Download Files.” When you click this link, you’ll be presented with the option to download the PDB file as text. Save this file to a convenient location To open the PDB file, select “File ---- Open” in the external GUI window, and select the 1SNC PDB file that you downloaded. The PDB file will load, and you will see the “lines” representation of the protein  Basic Viewing Functions and Navigation Within the viewing window, you can click and drag with the left mouse button to rotate the molecule. Dragging with the right mouse button will allow you to zoom in and out. Finally, dragging with the middle mouse button will translate the structure in the X-Y plane of your monitor. Using a combination of rotations, translations, and zoom operations, it’s possible to position yourself anywhere within the molecular frame, although it does take some getting used to. PyMOL also allows you to interact with the molecule itself, selecting individual residues (or atoms) by clicking on them. When you click on the protein, the atoms in the selected residue are highlighted with pink boxes. You can select multiple residues with the mouse by clicking on additional atoms, or you can unselect residues by clicking the same residue again (not a double click; two single clicks). Whenever you make or modify a selection, you can see the number of atoms in the external GUI window. To unselect all residues, click on an area of the viewer window with no atoms.  An alternative way to select residues is by directly using the protein sequence. In the external GUI window, select “Display ----Sequence.” You’ll notice that at the top of the viewer window you can now see the sequence of residues in Staphylococcal nuclease (starting at residue 7, “LHKEP…,” or “Leu, His, Lys, Glu, Pro”). The sequence starts at the N-terminus (Ala 7) and ends at the C-terminus (Ser 141). By using the scroll bar and clicking on the residues, you can select residues by number without having to find them in the structure. This is a convenient way to locate a residue if you aren’t sure of its location. Directly above the mouse mode matrix is a region in the viewing window which displays a list of visible objects available in PyMOL. At the top of this list is “all,” and clicking this will allow you to quickly show or hide all visible objects. Below this, you will see “1SNC,” which is the PDB file we are currently viewing. And, depending on whether you have atoms selected, you will see a “(sele)” below that, denoting the selection you have currently created. Next to each object name, you will see five letters: A (actions), S (show), H (hide), L (label), and C (color). Each of these buttons brings up a window with additional options for this object  Water molecules are often associated with protein structures (“crystallographic waters”), and we saw those waters in the sequence display. You can use the action menu to remove those waters. Select (A) ----“remove waters,” and you should see the “cloud” of crosses in your structure disappear. What’s left is just the protein and the substrate atoms.  Molecular Representations Scientists have developed multiple schemes for visualizing proteins and nucleic acids. Some examples are Sticks: These are similar to the lines we have been working with so far, but they are thicker, like the molecular models used in organic chemistry. Spheres: In this representation, all atoms are drawn as spheres, with radii that are characteristic of their (s) electron orbitals. This is also called CPK representation, after Corey, Pauling, and Branson, the originators of such models. Cartoons: In this representation, the side chain atoms are ignored, and smooth line is drawn through the backbone alone. Alpha helices and beta strands are drawn as coils and arrows, respectively. Each representation has its strengths and weaknesses. Cartoons, for example, work great for simplifying the structure, but it’s hard to get information about the chemistry involved in the enzyme. Sticks, on the other hand, reveal the chemical structure but are hard to interpret for large systems. Spheres make it easy to understand packing and steric hindrance, but they occlude the interior of the protein. Published figures often include some combination of these three representations.  PyMOL supports all of these representations through the show and hide commands. So, typing show spheres will show the CPK model of the protein. Typing hide spheres will hide it. There are many representations to choose You can change the colour of residues using Color comand Finally, for publications, it’s good to use a white background instead of black. You can change this by selecting “Display ----- Background --- White” in the external GUI window. Since black is easier to view on a screen, you can change back to black by selecting “Black” from the menu.  Saving Your Results Once you have an appealing image, it’s a good idea to save your results. In PyMOL, the state of the molecule along with the coordinates and object listing are saved as a session file. A session contains all the needed information to reproduce the view window, and you should save your session frequently to avoid losing work. To do this, select “File --- Save Session As…” from the external GUI window. When you restart PyMOL, you can load this session and all of the settings you used will be recalled. Given that some molecular images can take a significant amount of time to design, this feature is very useful. Saving an image is like saving a session; select “File ---- Save Image As ----- PNG” to save your file in PNG format, which is readable by nearly every word processing and presentation application available today. The advantages of using PyMOL are: It has a rich set of features and capabilities for protein structure visualization and analysis. It can be extended and customized with Python scripts and plugins, which offer more flexibility and functionality. It can handle large and complex structures and data sets, and produce high- quality graphics and images. The disadvantages of using PyMOL are: It may have a steep learning curve for beginners, and may require some technical knowledge and skills to use effectively. It may not be compatible with some file formats or features of the structure files. It may have some bugs or errors, or may not be updated or maintained regularly.