This blog post introduces a new tool for Foldit protein design. The Blueprint Panel displays the amino acid sequence and secondary structure of your protein. By default, each letter of the sequence is colored according to the φ and ψ torsions at that position in the structure, following the same ABEGO coloring scheme used by the Rama Map. Above the sequence, a secondary structure diagram reflects the sheet and helix assignment at each position. The Auto Structures button will detect sheets and helices, and make the appropriate secondary structure assignments.
The Blueprint panel is accompanied by the Building Blocks panel. Building blocks represent discrete patterns of protein backbone that can be applied to your protein structure. The building blocks provided here correspond to specific loops that are frequently observed in natural proteins (they were previously known as "Ideal Loops" in the Rama Map). All building blocks are meant to connect secondary structure elements directly, with a sheet or helix on either side. The appropriate use of a building block is dependent on this secondary structure "context." For example, a Helix-Sheet building block would make a good connection between a helix at position 20 and a sheet at position 23, but would not work well if the helix and sheet positions were reversed.
Click-and-drag a building block onto the Blueprint panel to apply the building block to your structure. Applied building blocks will remain outlined in the Blueprint panel. Applied building blocks will continue to exert torsional constraints wherever they are placed—these constraints behave like rubber bands for φ and ψ torsions, and will try to keep residues close to the original building block shape whenever you use Wiggle.
Click-and-drag a building block off of the Blueprint panel to remove the building block; this will also remove the associated torsional constraints. It is recommended that you leave building blocks and torsional constraints in place while you continue to fold a protein.
The Building Block panel includes two special building blocks next to the Context menu: one block is all-helix and another is all-sheet. These special building blocks can be placed on the Blueprint panel to shape residues into ideal helices and ideal sheets. They do not exert torsional constraints, and disappear immediately after they are applied.
The Blueprint Panel will be enabled in specific design puzzles. It can be accessed from the Actions menu in the Original Interface, or from the Main menu in the Selection Interface. Try it out now in Puzzle 1305!( Posted by bkoep 71 398 | Thu, 10/27/2016 - 22:14 | 2 comments )
New Tool Preview!
We’re excited about a new Foldit tool that has been developed for protein design! The Blueprint panel, alongside its partner Building Blocks panel, is meant to ease the construction of “ideal” loops. Check out the video below to see a prototype in action! We hope to start testing the new feature in devprev in a matter of days!( Posted by inkycatz 71 1514 | Tue, 10/25/2016 - 15:10 | 0 comments )
Foldit Plays for Jain Foundation / DYSF
As another example of applying Foldit to human disease, this month we have a puzzle on the protein dysferlin. The deficiency or absence of dysferlin causes one genetic type of Limb Girdle Muscular Dystrophy. Muscular dystrophy caused by dysferlin has autosomal recessive inheritance (meaning it is equally likely to affect females and males) and typical onset between the ages of 15 and 30. The UW Institute for Protein Design is conducting a research project on the structure and function of dysferlin for the Jain Foundation, a nonprofit foundation based in Seattle which supports research and the development of treatments for dysferlinopathy. The exact function of dysferlin is not completely understood, but it is thought to be involved in repair of the muscle cell membrane if it is damaged, and in resetting the muscle to a quiescent state following contraction. Sept. 30 is Limb Girdle Muscular Dystrophy Awareness Day, and we are introducing Puzzle 1291: Dysferlin C2B Domain to commemorate this day and to spread awareness to the Foldit community.
The following video features an interview with a neurologist on Limb Girdle Muscular Dystrophy, and with a patient who has dysferlin deficiency.
Ferlins are a family of transmembrane proteins which contain multiple C2 domains. The N-terminus is located inside the cell, and there is a single transmembrane domain near the C-terminus, which is located on the cell’s exterior. Ferlins are thought to participate in membrane fusion events and are involved in a variety of functions in many organisms. The first ferlin to be described is fer-1 in C. elegans, which is required for sperm function and hence fertility (giving rise to the name “fer”). Ferlins has also been described in drosophila and sea urchins. Deficiencies in two of the five mammalian ferlins have been associated with human disease. Otoferlin is required for transduction of signals from the inner ear to the nervous system for hearing, and its deficiency is a genetic cause of deafness. The most abundant dysferlin isoform in skeletal muscle is 2080 amino acids long, and contains at least seven C2 domains as well as additional protein domains of other types.( Posted by inkycatz 71 1514 | Thu, 09/29/2016 - 19:33 | 1 comment )
One goal frequently cited by citizen scientists is to work on problems that benefit human health. Foldit is uniquely positioned to enable this because the game allows players to fold and design proteins, which are often implicated in human disease. In particular, Foldit players can have a huge impact on rare and neglected diseases, which are more common in developing nations than in Western nations and generally receive less attention from pharmaceutical companies. Foldit can help through structure-based drug design (SBDD). The steps involved in SBDD are 1) identification of a target (a protein), 2) crystallization of the target, and 3) design of small-molecule drugs for the target. Through collaboration with the non-profit organization Infectious Disease Research Institute (IDRI), we would like Foldit players to experience this process. We hope that Foldit players will be able to positively impact a specific neglected disease: tuberculosis (TB).
TB is caused by the bacillus Mycobacterium tuberculosis. TB disproportionally impacts impoverished communities and killed 1.5 million people in 2014 alone (2014 is the most recent year that data is available). Additionally, it is estimated that 9.6 million people have fallen ill with TB in 2014, a number that includes 5.4 million men, 3.2 million women, and 1 million children. Figure 1 shows an estimate for incidence rates of TB from the World Health Organization (WHO).
A major issue in treating TB is that the bacterium has evolved to become resistant to current treatments – most notably, antibiotics and even combinations of antibiotics (see WHO for more information on the problem of antibiotic-resistant tuberculosis). The medical community needs a new drug to kill the bacteria; a target and crystal structure for SBDD will greatly accelerate design of new drugs.
Scientists at the non-profit organization Infectious Disease Research Institute (IDRI), and at Eli Lilly, have been working together to identify a suitable target and drug for TB. Their TB Drug Discovery collaboration is embodied in the following video.
These scientists have identified an essential enzyme in M. tuberculosis, LepB, as a target; unfortunately, there is no crystal structure available for the protein to perform SBDD. This protein target is notoriously difficult to work with since it is bound to the cytoplasmic membrane and only small amounts of the protein are available for crystallization trials. More accurate models can be used to guide protein engineering, with the goal of producing more soluble and crystallizable protein. Once crystals have been obtained and X-ray diffraction data obtained, the models will be used for molecular replacement (this is similar to the HIV retroviral puzzle that Foldit players helped solve in 2011). LepB is a difficult target in both experiments and in modeling. The closest homolog to the Protein Data Bank shares ~25% sequence similarity.
This is where citizen scientists can help! We would like to use models created from Foldit players to help solve the crystal structure, once crystals are obtained. These models will have a direct impact on human health, as this target is currently being actively investigated for drug design. Further, this is a prime example of how crowd-sourced citizen scientists, non-profit organizations, and a pharmaceutical company can work in harmony to develop cures for neglected diseases.
The work done here will be published, regardless of the results (e.g., if no crystal structure is obtained due to experimental difficulties, we will still publish Foldit players' models and the players’ names will be on the paper). If crystals are created and a structure is obtained, the players who have models that help with determination of the structure will be on the publication. Rest assured, we will publish what we have so that the whole scientific community can have access to it and help to fight TB.
We are hoping that we can take this puzzle and work through the whole drug design process (through the SBDD process). After models are created, and hopefully a structure is determined, we would like to use the new drug design game elements to design small-molecule drugs against TB as well. You can see in Figure 1 just how much the scientific community needs this.
This puzzle is currently scheduled to appear on Tuesday, 12 July 2016.( Posted by free_radical 71 1514 | Thu, 07/07/2016 - 17:30 | 6 comments )
Little update: Experimental Client (Drug Design)
There is a new update to the experimental drug design group. The changes include:
Change the format for the Ligand Queue tool to follow the Remix tool
Fix several spelling errors in drug design tools
Fix selecting/deselecting atoms in selection interface not properly selecting atoms
Fix incorrectly disabling certain buttons in Selection interface design menu that should be disabled
Add proper protonation and charges to designed molecules
Slightly modify Similarity Filter for better results
Fix mismatch between counting donors/acceptors in Rule of Five Filter and View Options
Fix some issues surrounding crashes in MMFF
Please respond to bug reports in this thread.( Posted by free_radical 71 1514 | Wed, 06/08/2016 - 15:37 | 0 comments )