Entangle Help Page
I wanted to include a brief summary for you on what Entangle does and does not do! The basic idea of Entangle is to take in pdbs and sort the potentially good interactions on the basis of basic chemical properties such as stereochemistry.
It doesn't try to evaluate whether one interaction is better thermodynamically than another. It just sorts them and has a GUI interface that allows you to evaluate the interaction yourself.
That being said we have found that it does a great job so far! You will find the H-bonding, stacking, and electrostatics the most useful. The van der Waals and hydrophobics are still under development because we know so little about them! This is one of the ways we are using Entangle in our lab.
What Entangle does not do is molecular dynamics! It takes pdb as God's own truth and builds hydrogen onto the structure in a manner consistent with whether it is an amide or serine hydroxyl, etc.
Welcome to Entangle!
You need to run this on a PC with a reasonable processor (>350 ) and RAM (> 64 MB RAM).
It should look like this:
We suggest that you try looking at the sample PDBs we have bundled with the program.
The window will now look like this:
Note that the name of the protein appears in the protein chain box as U1A SPLICESOMAL PROTEIN and the RNA in the RNA chain box as RNA 21MER HAIRPIN. The small boxes with the letter A and P are the chain identifiers from the loaded pdbs. If you mouse over them and click you will see other chains available to you from the pdbs. Presumably you will want to use the RNA and protein chains that are interacting!
Note that the Analyze box is now highlighted in bold. This means you can analyze the pdb.
3. Click on the Analyze button (an hourglass should appear). It will take a few seconds but then the screen should change as shown below:
4. These are the H-bond potentials in the structure. You will see ARG52 NH1 group is listed twice (highlighted at left). It can make a H-bond to the O6 position of G16 and/or the N1 position of A6. Remember Entangle does not have any way to choose the best interaction. That is left to you. As in most Windows outputs the column widths can be adjusted by mousing at the top of the column and left clicking.
Van der Waals Interactions
5. Each of the tabs represents a class of interactions. Just click on the tab of interest.
6. If you hit the All interactions by residue tab you will get a handy summary. This spreadsheet summarizes the interactions by class:
Let's say you want to assess an interaction without using any fancy computers. Just click View Structure. It will probably take about 15-30 secs, but a new window pops up. If nothing happens you may be out of RAM. A good excuse to go to the boss and demand a proper machine! PLEASE DON'T TRY THE ENTIRE 30S RIBOSOME! IT'S TOO BIG! JUST USE THE CHAINS OF INTEREST.
7. You may now view the areas of interest by mousing to the lower part of the window. A drop down menu appears where you can choose which base you want to view. Choose Adenine 11.
8. The left mouse rotates the molecule, the right translates. Zoom is Alt-left MouseIt should look like this:
The H-bonds are shown as dashed lines to orient you. The polypeptide backbone is shown as the Caonly. Stacking interactions are indicated by filling in the rings of the stacking residues.
It is rendered in a basic way to avoid devouring all your memory and slowing up the ability to rotate the molecule.
9. If you want to save your interactions in a file you can go to FILE, and save information as an HTML format which you can then print. Under FILE you should see SAVE INTERACTIONS. Make sure you give an html extension! An example is u1a.html. Good Luck!
Guide to Interactions Sorting
In most cases the H-building is completely predetermined by the molecule but in others such as serine, Entangle finds the closest position along circular locus of possible positions and then finds the best hydrogen bond donor position. You can imagine cases where the H could have two good acceptors, as shown below:
In this case Entangle will give you both possibilities. If you have some nice electron density you may be able to tell which interaction is being used. Currently a cutoff of 90o is used to determine a proper H-bond (see html documents cited below).
Entangle also uses the geometry to to look for a proper H-bond. If the geometry is very poor the interaction may still qualify as an electrostatic interaction and be sorted as such (see below). The Donor to Acceptor cutoff distance is 3.9 Å . The Hydrogen to Acceptor cutoff is 2.5 Å.
Pretty obvious, in the protein-RNA world there is only one possibility, Lys/Arg with the phosphate oxygen. There are no other formal charges on the RNA. The default cutoff for these interactions is currently set at <7.0 Å. This is overly generous but we wanted you to see all the possibilities. Based on your experiences we will refine these numbers into a more reasonable value.
Clearly one of Entangle's best features is its search for stacking between the aromatic amino acid sidechains and the bases of the RNA. We have also included arginine in this search because we have observed the guanidinium moiety of arginine stacking over the pi-electron of bases. Entangle checks the orientation of one to another by calculating the plane of each residue and then finding the dihedral angle between the two planes to determine the center-to-center distance. Default cutoff 3.8 Å.
Are non-polar atoms that are <5 Å apart. The importance of these interaction is clear, their assessment is not. This is one of the benefits of data mining the 50S and 30S structures, we will begin to accumulate info on this ubiquitous but hard to quantitate interaction.
Van der Waal interactions
If the distance between the
atoms is less than the sum of the two atoms, van der Waals radius + some
maximum distance. Our assumption all along has been that the structure
has been refined.