UW-Madison BIOCHEM 660 - DeepView - Basic Molecular Modeling

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Biochem 660 – 2008 153 DeepView'‐'page'‐'153 DeepView: Basic Molecular Modeling Deep View formerly known as Swiss PDB Viewer (http://us.expasy.org/spdbv/) is a free program developed by Glaxo Smith Kline R&D & the Swiss Institute of Bioinformatics. It has many features available in other programs, but with an array of additional features not commonly found in free software. It is available on many platforms, including Mac OSX, Windows and Unix, therefore providing a wide distribution. - e - 1 DeepView - Exercise A: Starting DeepView and opening a molecule The exact location of the DeepView program will be provided by the instructor. On OSX it may be available on the task bar, on Windows it may be available within the Start>Programs button. ✔ TASK 1) Double click on the DeepView icon 2) You are immediately prompted to open a PDB file with a dialog window. Select the file “hrv2-2A-2HRV.pdb” from the PDB files directory “PDB-files-for-lab” 3) At least 3 windows will appear concurrently: The text log window The ToolBar window The graphical display with the name of the molecule and the size of the display as the bar name. The default is a black background with the molecule shown as CPK lines colored, Rasmol style. Note: If you close the graphical windows with the “x” ( or ) closing button you can reopen the molecule again with the “File” menu which remembers a list of previously opened PDB files.Biochem 660 – 2008 154 DeepView'‐'page'‐'154 4) From the Wind menu call the “Control Panel” the “Layer Infos” and the “Sequences Alignment” windows. - e - 2 DeepView - Exercise B: Interacting with the molecular display ✔ READ The mouse can be used to rotate, translate and scale (zoom) the molecule interactively. These three functions are toggled from the “Toolbar.” Note that the currently selected function is shown with a black background, the others are shown with a gray background. Rotate: Scale: Translate: 1) The function button must be selected each time the mouse is to assume a different function. 2) The leftmost button on the Toolbar will recenter and rescale the molecule, a useful tool if you loose it. - e - 3 DeepView - Exercise C: Coloring the molecule and side chains ✔ TASK a. Color the molecule with some of the available options in the “Color” menu. b. Return to CPK color when you are done exploring. c. Engage the menus Display > Render in 3D (note that the display may become black) and then also Render in solid 3DBiochem 660 – 2008 155 DeepView'‐'page'‐'155 d. Bring the “Control Panel” from the “Wind” menu. Note for reference the 2 check marks that allow you to make the molecule visible or immobile (can move). e. Scroll down and find His25 within the list. f. Click on the 2 check marks and see how this undisplays (makes invisible) the complete amino acid or only the side chain. g. Click on the square with a minus sign at the right hand side of this line. This will open the color menu selection. h. Slide the vertical slide bar on the right to make the color brighter, and click for selecting a color within the disk (for example yellow). Note that other mode of color selections appear by clicking on the various icons at the top. The options might be slightly different depending on the operating system. i. Click OK j. Look in the display to see where His25 is located. k. Rotate the molecule to bring it to the top right of the display l. In the Toolbar click on the “?” buton (8th from the left: ) m. Click on an atom of His25, this will create a label. - e - 4 DeepView - Exercise D: Mutating a side chains Finding a mutant in the laboratory is exciting because it may help understand the function of an amino acid within the molecule. It is even more exciting to be able to create a “mutate” a 3D model with the mutation you have isolated, provided a 3D X-ray or NMR structure exists. The following exercise illustrates a method within DeepView to mutate an amino acid side-chain.Biochem 660 – 2008 156 DeepView'‐'page'‐'156 ✔ TASK 1) Click on the “Mutate” button (second from right in Toolbar) 2) Click on any atom of His25 Note that a local menu shows up 3) Mutate this His25 to His for this time around. (Note that the proposed orientation differs from the current side chain position but offers an additional H-Bond with the oxygen of Ser22.) 4) Click on the “Mutate” button again, and click “Discard” this will make His25 return to its original orientation. Note: you can click on the “?” button while the mutation takes place to identify who is doing the H-Bond. You can also click on the “Rotate” button in the Toolbar and rotate the display. 5) Mutate the side chain again to ASN and note that this time the proposed orientation makes an Hbond with the O of Glu23 6) Explore various mutations options, you can save them if you are curious. 7) Save your structure: File > Save > Layer…. Enter a PDB file name, e.g. “mutant.pdb” 8) Open the “mutant.pdb” file you just created with a word processor (e.g. TextWrangler or WordPad) and look at the PDB coordinates where you created the mutation. - e - 5 DeepView - Exercise E: 3D superimposition of 3 molecules A PDB file contains XYZ 3D Cartesian coordinates, but the origin point (0,0,0) is not necessarily the same for similar structures, as various factors can influence the final 3D file including the orientation within the crystal or choices made by the authors. It is sometimes useful to be able to superimpose 2 or more structures in 3D space to see how they align in 3D.Biochem 660 – 2008 157 DeepView'‐'page'‐'157 ✔ TASK 1) Quit and Resart DeepView if you are currently running it. 2) Open the following 3 PDB files: hrv2-2A-2HRV.pdb hrv2-3C-1CQQ.pdb polio-3C-1L1N.pdb Note: Use the File > Open PDB… menu to open the 2nd and 3rd files. 3) Use the Wind menu to bring in the Sequences Alignment 4) Use the Color menu and color by Layer. Note that the sequences change to the same color as the 3D structures. 5) Use the Wind menu can bring the Control Panel Note that you can select which molecule is being worked on by clicking on the name of the currently displayed molecule. 6) Click on the word “side” in the Control Panel and watch the side chain disappear from the display and the check marks


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UW-Madison BIOCHEM 660 - DeepView - Basic Molecular Modeling

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