Hydrogen Bond Network Filter
This post previews an upcoming Bonus Filter in Foldit design puzzles - the Hydrogen Bond Network Filter.
We are introducing this filter to overcome a major challenge in protein interface design, and something we've observed in many Foldit designs.
A lot of designs we've seen so far have used lots of hydrophobic residues in their interfaces. This works because these hydrophobic residues are buried in the core of the symmetric complex, sandwiched between two copies of the protein.
However, when you are designing proteins with interfaces, you have to consider that placing hydrophobics on the interface means that these residues will be on the surface of each of the individual pieces. This is a problem, because it means that these hydrophobics are exposed in each of the isolated pieces, making each piece unlikely to fold up correctly on its own. If the pieces don't fold up on their own, they wont be around to interface with one another!
To combat this problem, protein designers in the Baker Lab have been using Hydrogen Bond Networks.
A Hydrogen Bond Network is a 'web' of hydrogen bonds that connects the sidechains of multiple residues. When constructed across protein interfaces, these networks help to make the interface more stable. You can see an example of such a network below:
And unlike a hydrophobic core, these networks can be made out of polar hydrophilic residues. Because of this, the network will work well as a surface for each piece - and will still work well as an interface between the pieces!
The other major advantage of Hydrogen Bond Networks is that they increase the specificity of the interface. Since the networks are very carefully joined together like a jigsaw puzzle, each piece will be most happy when it's allowed to network with the other pieces. This helps to ensure that the pieces of your protein will interface with each other like you intended!
Hydrogen Bonds are an interaction between a donor and an acceptor. As the name suggests, the donor donates a hydrogen atom, and the acceptor accepts it.
In Foldit, you can see these donors and acceptors using certain view options that are available when you've enabled 'Show Advanced GUI' in General Options.
Using the Score/Hydro+CPK Color scheme will color donors blue and acceptors red, like you see in the example above.
Donors have a partial positive charge, and acceptors have a partial negative charge. This causes the donor and acceptor to be attracted. But the opposite charges are not the full story; the charges are in specific locations and directions, and it's the geometry of the h-bond that really dictates its strength.
To get a better idea of how to improve your geometry, you can use the Stick+polarH option in 'View Protein'. This view option will let you see the hydrogen atoms themselves, shown in white.
Hydrogen Bond Networks
When multiple Hydrogen Bonds connect across multiple sidechains, they form a Hydrogen Bond Network. To get credit for a network in Foldit, you must have at least 3 hydrogen bonds, and at least 1 hydrogen bond that connects across an interface (these criteria may change from puzzle to puzzle).
In puzzles where the Hydrogen Bond Network Filter is enabled, you can visualize them using the filter. To do so, open the drop-down Filter Panel beneath the score panel, and click the 'show' checkbox for the HBond Network filter.
Valid networks will show up as a web of blue bonds. Each valid network that you form will get a score, which is then added to your total score as a bonus.
But what makes a good Hydrogen Bond Network?
Well, first off, your hydrogen bonds have to be good! A weak hydrogen bond wont work to extend a network. Remember that the strength of a Hydrogen Bond depends on its geometry. The donor and acceptor must be at the correct distance and angle to be strong enough for a network. Bonds that are too weak will show up in red on the visualization.
Once you have a network of good bonds, the score of a Hydrogen Bond Network is evaluated as follows:
Score = SCORE_SCALE * percent_polars_satisfied * num_intermolecule_bonds
So what do these mean?
SCORE_SCALE - This is just a constant that we set on a per-puzzle basis to decide how much Hbond Networks are worth.
percent_polars_satisfied - A good hydrogen bond network will minimize the number of unsatisfied polar atoms. If there's a blue or red atom in your network, it should be bonded to something - in some cases, multiple times. You want your network to satisfy most or all of its polar atoms.
num_intermolecule_bonds - The more bonds that your network forms across the symmetric interfaces of your protein, the higher it will score!
You can see the stats for each individual network by hovering over one of the bonds of that network. This will also highlight all bonds of that network in yellow:
It's important to note that while Hydrogen Bond Networks are awesome for stabilizing the interface between your symmetric proteins, you should have some hydrophobics on the interface as well. The best solutions will have a balance! Ideally, you want a very connected, perfectly satisfied network, with tight hydrophobic packing around it.
To go along with the release of this filter, we've posted a new puzzle http://fold.it/portal/node/2000714. In this puzzle, the backbone is fixed - your job is to mutate and move the sidechains to form networks of hydrogen bonds. Some players have already created some amazing networks in the devprev version of this puzzle! We're very excited to see what you can do, too!( Posted by jflat06 111 1097 | Thu, 04/30/2015 - 23:54 | 7 comments )
Foldit Drug Design Blog: Interface Update
It's time for another update on the process we have been using to update the graphics for Foldit drug design!
This project started awhile ago with a very simple interface.
The idea that we had was to use the graphical user interface for designing proteins. In the image above, you see that we have a pi-menu pop up when you select an atom to design. While this is a pretty cool concept, the main problem that we encountered was that the pi-menu hid the ligand that you were supposed to be designing. It was very difficult to perform modifications and see how it effected the protein/ligand.
This difficulty resulted in a move to a separate menu.
In this menu, which we call the Ligand Design Panel, you can select atoms to design and then click on the design panel to change those atoms. The cool thing is now you can move the design panel around and view the protein and the ligand without interference with the menu. There are of course, some problems with this menu. We have some mixed opinions on this, and invite you to share your thoughts in our thread below.
The elements that you can choose from are just labeled with the element name: C-carbon, N-nitrogen, O-oxygen, P-phosphorus, etc. Also, the fragments shown below the elements, are kind of an ugly magenta. Further, when you click on an atom, then a fragment, you have no idea where that new fragment will be placed, spatially. So, we needed to update the ligand panel.
The new ligand panel is much more colorful! The elements are colored based on their CPK coloring and the fragments have been replaced with high-resolution images. Further, now, when you select a fragment, a glowing outline of that fragment is drawn onto the structure! No more guessing where a new fragment will be placed.
Additionally, we added the ability to modify bonds. Which brings us to the next graphical improvement. Before, everything was shown as a single bond. Now, the small molecule is drawn with its bonds shown and a new way of viewing the protein, called the Cartoon Ligand view option (under advance settings, View Protein: Cartoon Ligand) is available.
We have added new ways of viewing interactions within the protein.
We have also added a ligand viewing panel, which allows for turning the isosurface on only around the small molecule, showing areas where there are a hydrogen bond acceptor/donor, and finally, where there is repulsion between atoms. You can also change the transparency of everything on the fly, which allows you more direct manipulation of the settings.
Finally, we have added functionality that helps notify you if you are trying to design something that is not chemically feasible.
We hope everyone enjoys all the new additions. Let us know what other things you would like to see in the graphics department.( Posted by free_radical 111 3722 | Tue, 03/24/2015 - 15:50 | 10 comments )
Through the eyes of a scientist: Part 2 - Puzzle 1052
In addition to highlighting some of our favorite Scientist-Shared solutions, we'll look at several lower-scoring designs to illustrate issues relating to:
- hydrogen bond networks
- buried, unsatisfied polar atoms
Check it out and leave your questions in the comments below!( Posted by bkoep 111 1355 | Sat, 02/28/2015 - 00:25 | 12 comments )
Player designs enter the wet lab
Last week the Baker Lab ordered materials to construct the latest batch of Foldit designs in the lab for experimental testing! The following eight protein designs were selected based on visual inspection by our scientists and folding predictions by the Rosetta@home distributed computing project. For each design below, we've included an image of the Foldit player's design on the left; and on the right, a folding funnel with the energy and Cα-RMSD for 100000s of Rosetta@home predictions in red, as well as an image of the lowest-energy prediction. We like to see that the lowest-energy prediction also has a low RMSD (explained here).
For more information about the types of experiments in store for these Foldit player-designed proteins, see our previous blog post.
In monomer designs, we were looking particularly for diverse topologies containing some β-sheet secondary structure. Such topologies are significantly more difficult to design than the helical bundles that have been so successful in the past. Consequently, these folding funnels may appear less pristine, but we are still very excited to experiment with them in the lab!
Symmetric Oligomer Designs
For designs of symmetric homooligomers, we do a similar analysis to make sure the monomer will fold up as expected.
We also want to make sure that, once folded, the monomer units are likely to bind to each other in the correct orientation. The most common reason a design fails this "docking" test is that its interface is completely hydrophobic and featureless. In such a case, two properly folded monomers can usually come together in a number of different ways to bury the same amount of hydrophobic surface. The best way to ensure specific binding in the correct orientation is to design rugged, complementary surfaces (e.g. large interdigitated side chains) and incorporate hydrogen bond networks at the interface.
The following symmetric designs performed decently for both monomer folding and docking tests (data not shown), and we are excited to try them out—however, we think there is room for improvement in the design of specific interfaces!
The players responsible for the above designs certainly deserve recognition, but there are many, many more exciting designs that just missed the cut or are still under analysis. We can't wait to see what Foldit players come up with next—keep up the great folding!( Posted by bkoep 111 1355 | Tue, 02/10/2015 - 15:57 | 8 comments )
Foldit Drug Design Part Two
My name is Sandeep Kothiwale (aka fragmentor). I am continuing the Foldit drug design blog this week. I am a graduate student at Vanderbilt University and developing the drug design module of Foldit. This blog describes the shake/wiggle feature for small molecules which is analogous to the one for protein molecule.
Drug molecules (small molecules) bind to a target molecule (protein in our case) and effect the function of the protein. This change in protein function leads to the desired physiological effect of relieving disease or its symptoms. For example, Imatinib (Gleevec) binds and blocks an enzyme whose over-activity causes leukemia.
As with imatinib, all drug molecules bind their targets in a specific pocket in a particular 3D arrangement. For successful drug design, one needs to recapitulate the expected binding pose of the putative drug (ligand) to the protein. This requires that 3D structure of ligand be determined which is able to bind the target. Spatial arrangement that atoms in a molecule can adopt with respect to each other is called a conformation. A molecule can adopt multiple freely convertible conformations by rotations about individual single bonds. Thus enumeration of 3D conformations is essential in modeling ligand binding in Foldit. As you might know, we use the wiggle feature for enumerating side-chain conformations. This is accomplished using a set of rules that have been identified for 20 or so amino acids from known protein structures in the Protein Data Bank (PDB). As you can imagine enumeration of small molecule conformation is substantially more complex than wiggle for 20 or so amino acid side chains because of large chemical space.
Foldit will use an algorithm that I helped develop for sampling conformations of ligands. It uses information contained in the Cambridge Structure Database (CSD), a repository of small molecule crystal structures (on a side note, the CSD group has let us use their database free of charge!). The algorithm uses a CSD-derived database, the csd-rotamer library that contains statistics about most commonly seen conformations of small molecular fragments. Given a molecule of interest, the algorithm determines which smaller fragments are part of it and uses information in the csd-rotamer library to sample conformations.
During the drug-design process ligand will be built by adding fragments to the base fragments. One could hit the ligand-wiggle button to sample conformations of ligands and let Rosetta (Foldit’s engine) choose the conformation that best fits the binding pocket. We have a video of this cool technology above (and at the link). The video first shows adding a fragment to the base small molecule (shown in orange) and then at 26s, the new fragment rotates. We are using HIV protease as a test case. Check it out!( Posted by fragmentor 111 3722 | Mon, 02/02/2015 - 18:14 | 4 comments )