Hermes in a Nutshell Version 1.0 November2016 Hermes V1.8.2 Table of Contents Hermes in a Nutshell... 1 Introduction... 2 Example 1. Visualizing and Editing the MLL1 fusion protein... 3 Setting Your Display... 4 Setting the Colour of Your Background... 4 Depth Cueing... 4 Z-Clipping... 4 Setting Style Preferences... 5 Moving the Contents of the 3D Display Area... 6 Select and Centre with Molecule Explorer... 7 Label Selected Parts of Molecules... 8 Label Protein Residues... 8 Restrict the Display to Selected Residues... 9 Measure Distances, Angles and Torsions... 10 Edit Complexes with Molecule Explorer... 11 Adding Hydrogens... 11 Save Items... 11
2 Introduction Hermes allows you to visualise & edit the 3D coordinates of proteins & small molecules Hermes also hosts interfaces to GOLD, Mogul, the CSD Ligand Overlay, descriptors for GOLD docking poses and SuperStar interaction prediction Hermes is documented in detail in the Hermes User Guide. The example Hermes_Basics_MLL1 will show you how to: load, edit and save molecules focus and render the display of protein binding sites convert coordinates from PDB-format to MOL2-format GOLD Docking and Descriptors Mogul Geometry Analysis CSD Ligand Overlay SuperStar Interaction Prediction
3 Example 1. Visualizing and Editing the MLL1 fusion protein Download Input Files As an example to get familiar with Hermes we will inspect and edit a complex between the MLL1 fusion protein and the cofactor product SAH, deposited in the PDB with the code 2w5y. MLL1 is a fusion protein expressed by blood cancer cells. S-adenosyl-Lhomocysteine (SAH) is a metabolite of the cofactor S-adenosyl methionine (SAM). Cofactor binding sites can be challenging in drug discovery projects due to the potential for off-target binding to related proteins. Interestingly, SAM is very flexible and adopts different conformations in different enzymes. Thus, SAM binding sites are considered druggable and currently investigated for the treatments of cancer and neuropsychiatric disorders. 1 The file 2w5y.pdb is provided in your example folder. Please download this folder, if you have not already done so. In this tutorial, you will learn how to: Load, save and edit molecules Insect the active site of your complex Focus on parts of the molecule Restrict the display of the molecule to its active site Label atoms and protein residues Measure distances Customize molecule rendering, colours and backgrounds MLL1 fusion protein, PDB: 2w5y 1 Arrowsmith, Cheryl H., et al. "Epigenetic protein families: a new frontier for drug discovery." Nature reviews Drug discovery 11.5 (2012): 384-400.
4 Setting Your Display Setting the Colour of Your Background You can switch between the default black background and an alternative colour by clicking: 1. Display -> Display Options 2. Background SuperStar Interaction Prediction Depth Cueing Depth cueing renders objects at the front more brightly than those at the back. 1. Click Depth Cueing in the Visualisation Options toolbar. If this toolbar is not displayed, load it by View-> Visualisation Options Toolbar 2. Optionally, customise depth cueing via Display -> Display Options -> Depth Cueing Z-Clipping With Z-clipping, you only display objects that are located between the near clipping plane and the far clipping plane. These planes are parallel to your screen and restrict the depth of your display. 1. Z-clipping can be enabled, disabled and modified by clicking Display -> Display Options -> Z-Clipping. The Enabled check box can be used to switch Z-Clipping on and off. More information on display settings can be found in the Hermes User Guide, Chapter 7.
5 Setting Style Preferences To set ligands apart from the protein structure, you can suite a style that suits your needs. 1. Click Display -> Style Preferences... 2. Set Ligand to Stick 3. You can experiment with different settings for Colours to suit your needs
6 Moving the Contents of the 3D Display Area A complete description on how to move Hermes s display can be found in Chapter 5 of the Hermes User Guide. 1. To translate: hold the middle mouse button or the Ctrl key + left mouse button or Ctrl + 2. To rotate: hold the left mouse button: x and y rotation shift key + the left mouse button: z rotation, Shift + 3. To scale: hold the right mouse button 4. You can also use the Alignment and Orientations toolbar in Hermes to move the display without having to click in the model itself 5. If the toolbar is not visible, please: right click in the area underneath the top Hermes menu bar and choose Alignment and Orientation Operations
7 Select and Centre with Molecule Explorer 1. Ensure that Molecule Explorer is displayed by clicking View and checking that Molecule Explorer is ticked. 2. The Molecule Explorer window can be selected with the left mouse button and dragged to any position on your screen. 3. In Molecule Explorer, components can be opened by selecting the icon on its left: Windows: > Unix, MacOS: + Click on the icon adjacent to 2W5Y under All Entries. 4. The protein is broken down by category into: Chains, Ligands, Metals and Waters. Each of these has a corresponding icon adjacent to it. Each successive time the icon is selected, the component it corresponds to is broken down further. This way it is possible e.g. to identify specific protein residues or atoms in a ligand 5. You may need to increase the width to display the full labels. Do this by selecting and moving vertical column dividers 6. Display styles, colours and labels and selection options are available via the right mouse button. Open 2W5Y -> Ligands -> A. Right click on A to bring up a menu controlling the content and style of the display 7. Select Center & Zoom 3D View to focus on the active site
8 Label Selected Parts of Molecules To label a molecule or a protein residue in Hermes: 1. Click an atom in the display with the left mouse. The atom will be highlighted in yellow 2. Right click near the selected atom to bring up a menu Depending on the exact position of your mouse, the selection of options may slightly vary, but a sub-option Labels should always be available. 3. In the menu select a Labels. 4. In the Labels submenu, select Label by Atom Label. 5. Your molecule will now carry an atom label. Label Protein Residues To label protein residues: 1. Crtl-A to select all residues, or right click in the display and choose Selection->Select All. 2. Right click in the screen to bring up the display menu. 3. Choose Labels. 4. Choose Label Alpha Carbons by Protein Residue. 5. After a short delay, residues will display labels.
9 Restrict the Display to Selected Residues To inspect an active site, you may wish to restrict the display to residues interacting with your ligand. 1. Left click on any atom in the ligand SAH. Right click in the display to bring up the Molecule Area Pull Down Menu (MAM). 2. Click Select -> Select Molecule to select the whole ligand. 3. Ensure the selected molecule is highlighted in yellow, then click on Selection in the top menu bar and open the Define Complex Selection menu. 4. Enter AS as a name for your selection. 5. Activate the Residues that are within radio button and enter a value of 6Å into the text field. 6. Press the Add button. 7. More atoms will appear in the field Atoms currently selected. 8. Click save to save your subset. 9. The subset will become visible in the Atom selection drop down in the menu bar. Select it from there. The selected atoms will get highlighted. 10. Right click in the display to bring up the MAM. 11. In the M, click Show/Hide -> Show only to restrict your display to the AS selection. 12. You will see the ligand with the active site residues on your screen.
10 Measure Distances, Angles and Torsions We want to measure the distances between the amide nitrogen of ASN3958 and the peptide oxygen of Ile 3838. 1. Right click on the display to bring up the molecular area pull down menu. 2. Select Measure -> Measure Distances. 3. Click on a combination of atoms. 4. A distance measurement will appear on the screen.
11 Edit Complexes with Molecule Explorer Molecule Explorer allows you to delete components of your macromolecule. 1. In Molecule Explorer, open 2W5Y using your left mouse, if not open already 2. Select Waters with a right mouse click to bring up a dialogue in Molecule Explorer 3. Left click Delete to delete all water molecules from the complex 4. In the same way as 2. and 3., delete all ligands from Molecule Explorer (not illustrated) Note: Molecule Explorer may collapse the All Entries tree after a delete step, please reopen to access the level you require. Adding Hydrogens Add Hydrogens by: 1. Ctrl + H or 2. Edit -> Add Hydrogens Note: You may have to select the Show hydrogens box in the top level toolbar (i.e. Visualisation Options) to show the hydrogen atoms. Save Items To save your protein to as a MOL2 file, use: 1. File -> Save As and enter 2w5y_protonated.mol2 as the name for your molecule.