Building small molecules Use the Builder (right panel) to build up molecules. Start building clicking a fragment/atom in the builder and it will appear to the workspace. Continue modifying the molecule by selecting atom(s) or bonds that you want to modify and use fragments/atoms/bonds from the builder. Hint (selection): - Left-click to select an atom. - You can also select bonds by clicking them. - Hold shift to select multiple atoms. - Ctrl+left-click to select whole molecule or residue. - Double-click to select whole molecule or protein. 1. Build the following molecules (5), minimize and save them (.moe -format) Remember to Minimize your molecules in the end. Save your molecule and clear the workspace (with Close on right panel) before starting to build another molecule. Celecoxib Indomethacin Note: build the COOH group as COO - (Normally this would appear after proper structure preparation, due to time limits we do it in a quick way)
Alprazolam Phenoxymethylpenicillin Note the chirality and -COOH! Hint (chirality): - You can change the chirality by selecting a chiral atom and modifying its chirality (R/S) from the builder, and after the minimization chirality changes accordingly. Tetracycline *Note the chirality!
Examine properties / visualization of small molecules Open up one of the built *.moe ligand-file that you want to examine more deeply. Try out different representations for the molecule and colors Select whole molecule, right-click: Atoms e.g. Label: Charge gives you the point charges of the atoms Next, examine properties of the molecule with special surfaces. Go to (right panel) Surface Surfaces and Maps e.g. You can get the Molecular surface colored by lipophilicity with these settings: Hint: you can adjust the transparency of a surface (front/back) from here Try out premade visualization themes. E.g. the figure above is represented by Schematic theme.
Small molecule database You will need to combine your built molecules in a database for tomorrows docking exercise. 1. Create a combined molecular database from your ligands. New Database New Database window opens up. Name your database e.g. ligands and save it (*.mdb). Database Viewer window opens up. As you see it is empty. Now, add your molecules to the database. File Import Add Double click all your molecules to add them to the list OK OK Now, you should see your molecules in your Database Viewer You can expand the cells to see the 2D-structures by dragging from the down-right corner of the cell. Save it in.mdb format. (You need to type.mdb in the filename)
Protein preparation 1. Retrieve a human Lysozyme C structure You can download directly RCSB PDB structures in MOE. Go to File Open RCSB PDB (left panel) type 2NWD (PDB ID) to Codes: Click OK After the downloading is finished, there opens up a new interactive Load PDB File window. You can use the default settings, press OK Show all atoms As you see (e.g. from waters) that you need to prepare the structure. Use QuickPrep (right panel) Set Tether Receptor Strength 1000 and uncheck Fix Atoms Click OK You can see how atoms move and orient during the minimization process.
Now you have prepared the protein and it is ready for further analysis. Next, you will train how to hide/show specific residues. 2. Visualize all disulfide bridges of Lysozyme C You are interested in Lysozymes disulfide bridges, and where they are located. Breakage of these important bonds will result in Lysozyme s denaturation. Hide all unnecessary information and visualize disulfide bridges in a clear way (example fig.). Label them as well. From Ribbon you may change the style and color for the ribbon. Open up the Sequence Editor from SEQ (up-right) to make selections from sequence. Hint (sequence editor): - for selecting residues/chains from SEQ see that you have Select Synchronize box checked - double-click chain name (on left) to select whole chain - change display settings (e.g. one or three letter codes for amino acids) from down-right Visualize your result: Render Setup Save Picture The checklist for visualization Starting point: What do you want to say with the figure? Remove all unnecessary information from the figure. o Hide nonpolar hydrogens! Center to the point of interest. Labeling. Use colors (discreetly & sensibly), surfaces, shapes, clipping, fog, focal blur etc. to make your statement more clear. Check that the atoms are unselected in the workspace (you don t want to have a pink atom selection in the final figure!) Adjust the resolution according to your needs CMYK colors for publications
3. Prepare K-Ras protein in complex with a GTP-analog Download 3GFT structure File Open 3GFT (PDB ID) (Default settings) K-Ras is biologically active as a monomer, however, how many K-Ras proteins you find in the structure? Why? Are all chains totally similar, are there more disordered regions (missing residues) in some chains than in others? Check out the ligands in chain F, what is the additional ligand is this chain and why it s there? Obviously, you cannot prepare a structure like this. There is, for example, two options how to prepare the structure: OR 1) Delete all other chains except one, and all unnecessary things from the selected chain as well 2) Download the structure again (Close workspace before) and use the setting in Load PDB File Symmetry: Biomolecule This option will download only a biologically active unit. Now you can prepare the protein with: QuickPrep Tether Receptor Strength 1000 and use Fix Atoms option Investigate the ligand (GTP) interactions with the protein. What kind of interactions are present? You can generate a 2D-interaction diagram from: Compute Ligand interactions To isolate view only for ligands binding site use: SiteView (right-panel)