Feedback on the last Marburg design puzzle
Happy Canada Day to our Canadian players!
We're about to give you a Marburg design puzzle, but I first wanted to provide a little bit of feedback on the last Marburg puzzle that we ran (puzzle 1073: Marburg Binder Design with Disulfides). We got some pretty good-looking designs back, but curiously, all of the best designs were ones that were shared with us using the "Share with Scientists" feature; they were not the top-scoring designs. This reflects one of the big challenges, for us, in giving these puzzles to the Foldit community: it's hard for us to figure out how to translate our qualitative idea of what a "good" design will look like into a set of quantitative rules that allow a computer to assign a higher score to a better design, and we didn't quite get it right on that puzzle.
We're going to revisit the 37-residue Marburg binder design in the new puzzle, but this time, we'll tweak the scoring and the filters to try to promote the features that we want to see. In particular, we'd like to see:
-- Compactness. Our favourite designs were the ones that were not so elongated. It's good to try to imagine how the peptide would look in the absence of the Marburg glycoprotein. If its structure depends on its interaction with the glycoprotein, and if it's floppy and unstructured in isolation, this means that the binding event must confer order on the peptide. This is entropically unfavourable (it's hard to increase the order of a physical system), and the price of ordering the peptide must be paid by a reduction in binding affinity. So nice, compact peptides that are likely to retain their structure in isolation are best for binding. We'll be including a core existence filter in the new puzzle to help to promote this.
-- Long-range disulfides. Disulfide bonds are a great way of enforcing order in a peptide, but this only works if they're holding together parts that would otherwise be inclined to move apart. A disulfide between two amino acids that are close together in linear sequence doesn't do a whole lot. Often, the best disulfide-bonding patterns (and the ones frequently seen in structured natural peptides) are "leapfrog" patterns. For example, you might link residue 1 to residue 20, and residue 10 to residue 30. This maximizes the linear separation between disulfide-bonded cysteine residues while minimizing the length of stretches of amino acids that contain no disulfide.
-- Lots of secondary structure. Many of the best designs had at least one helix lying across a sheet of at least two strands.
-- Lots of proline residues and few glycine residues. Proline helps to rigidify a peptide in a desired conformation. Glycine, on the other hand, is too flexible, and increases the number of possible alternative conformations, making folding into a single unique conformation more difficult. Although glycine is sometimes necessary (there are sometimes loops in which one residue has to be in an unusual conformation that no other amino acid type could access), we'd like to see few glycine residues if possible. In the new puzzle, we'll be increasing the penalty for glycine and increasing the bonus for proline.
-- Void-free packing. We recommend turning on the cavity or void display in the view options. This draws red spheres wherever there is an empty space in the core of the peptide being designed or at the interface with the Marburg glycoprotein. These red spheres are bad -- there shouldn't be empty spaces! If you can eliminate them, please do so (you should find that it helps your score, too).
-- Additional interactions with the glycoprotein. Although much of the interaction with the glycoprotein comes from the loop taken from the antibody crystal structure, the peptide is likely to have more affinity and specificity for its target if you can design additional interactions with the surface of the glycoprotein. Shape and charge complementarity beyond the antibody loop are good things! Now, this comes with a caveat: don't go for additional interactions at the expense of ordered structure. A peptide that lies entirely along the glycoprotein surface, forming lots of interactions with the surface and no interactions with itself, is likely to be too disordered to bind. If you can design in additional interactions with the surface that come off of well-ordered secondary structure elements that pack well with the rest of the peptide, though, that would be terrific.
Here are some of the solutions that we particularly liked:
retiredmichael of the Beta Folders had a nice design in which an alpha helix lies across one face of a three-stranded beta-sheet. This design had lots of secondary structure, a pretty good hydrophobic core (in which most of the secondary structure elements contribute), a nice disulfide bonding pattern, and relatively few voids in the interior of the peptide. The only criticism I'd have of this design is that one strand in the sheet does not contribute to the hydrophobic core; aside from this, this design looks very good.
mimi of the Contenders created a very interesting topology with helices sandwiching a three-stranded beta-sheet. This creates a lot of opportunities for interaction with the surface of the Marburg glycoprotein. The one thing to watch out for, here, is that this design has a bit less of a hydrophobic core, which might hinder its folding.
MurloW of Anthropic Dreams made a design with a topology somewhat similar to retiredmichael's, albeit with the helix in a different orientation and a fourth strand on the beta-sheet. This also opens up possibilities for interactions with the glycoprotein -- but be careful about those voids at the interface!
eusair's design put the helix on the opposite face of the beta-sheet to that chosen by retiredmichael or MurloW, and this allowed eusair to stick a valine very nicely into a cleft created by two prolines on the glycoprotein surface. I like this design quite a bit -- but be careful about those edge strands, that don't always contribute to the hydrophobic core.
Congratulations to all of these players, and good luck to everyone on the next puzzle!
Your handy guide to Marburg, Ebola, and Foldit
We're revisiting Ebola and the Marburg virus with an upcoming series of puzzles! The team has indicated we'll be starting with some Marburg puzzles, although it is highly likely more Ebola puzzles will also appear.
Marburg virus disease (MVD) (formerly known as Marburg haemorrhagic fever) is a severe and highly fatal disease caused by a virus from the same family as the one that causes Ebola virus disease.
With that in mind and to get everyone back up to speed on this topic, we've compiled some of our previous efforts in this area. Feel free to check out our previous blogs:
Review our blog post, talking about Puzzle 1000
Continuing the battle against Ebola
As well as check out previous related puzzles:
1073: Marburg Binder Design with Disulfides
1000: Breach Ebola's Defences!
975: Ebola glycoprotein 30-residue inhibitory peptide design
971c: Ebola glycoprotein peptide inhibitor design
884b: 74 Residue Ebola Binder Design
879: Ebola Binder Design with Disulfides
846: Ebola hotspot discovery
For more reading, when we were running frequent puzzles of these types before, spmm noted that Science/AAAS has a suite of free Ebola articles which are interesting, reasonably easy to read, and also have links to more complex papers and articles.
As always, the Foldit team remains committed to research in this area and appreciates everyone's assistance on these puzzles!( Posted by inkycatz 105 1577 | Tue, 06/30/2015 - 22:01 | 1 comment )
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 105 1129 | 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 105 3728 | 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 105 1407 | Sat, 02/28/2015 - 00:25 | 12 comments )