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This is the place where we will describe some of the outcomes and results of your folding work, provide a glimpse of future challenges and developments, and in general give you a better sense of where we are and where foldit hopes to go in the future.

Aflatoxin: a cancer-causing glue

In our previous blog post, we announced our Aflatoxin Challenge – a new series of Foldit puzzles designed to tackle a common poison known as aflatoxin. This week, Baker Lab scientist ianh offers a more detailed picture of the chemistry behind aflatoxin's harmful effects.

Most people on Earth consume aflatoxins every day. Aflatoxins are compounds produced by certain fungi that can grow in or on almost all grains and groundnuts. Aflatoxins are known hepatocarcinogens, meaning they cause liver cancer in high doses. Liver cancer is the third leading cause of cancer death globally, with 83% of cases occurring in East Asia and sub-Saharan Africa where aflatoxin exposure is highest.

What makes aflatoxin so toxic?

Surprisingly, aflatoxin itself isn’t toxic. Once ingested, our body uses its normal metabolic processes to try to break it down. It turns out a metabolic product of aflatoxin – not aflatoxin itself – is harmful, and the chemistry behind its toxicity is both frightening and familiar.

One of the metabolic enzymes that acts on aflatoxin is CYP3A4, a vitally import liver enzyme tasked with breaking down different complex molecules. Its normal targets are molecules produced by our own bodies, like the sex hormones testosterone and estrogen, but CYP3A4 can also safely chew up some of the complex chemicals we put in our body, such as caffeine (found in coffee and tea) and lidocaine (a local anesthetic commonly used by dentists).

When CYP3A4 metabolizes a chemical it changes that molecule’s structure in some way. When it acts on aflatoxin, it adds a chemical feature – chemists call this new feature an epoxide group.

Extreme chemistry

Epoxide groups are highly reactive, meaning they are unstable on their own and like to bond with other nearby chemicals. This extreme reactivity can be harnessed for many practical applications, including adhesion, electrical insulation, and industrial manufacturing. Some of the strongest glues ever made – epoxy glues – are based on epoxide chemistry.

Once CYP3A4 converts aflatoxin into epoxy-aflatoxin, the compound doesn’t wait around for long. It quickly reacts with other chemicals in our cells, especially amines.

One of the best places to find amines in our cells in our DNA. Each of the four letters of DNA – A, T, G, and C – is an amine. Epoxy-aflatoxin reacts especially strongly with guanosine (G), forming a nearly-unbreakable bond. This permanently damages DNA.

Cancer-causing mutations

DNA damage is problematic, not only because it interferes with the natural processes of the damaged cell, but because this damage can be passed on to descendants when the damaged cell replicates. In this way, a single error in a single cell may be amplified over time to affect a large population of cells.

The liver is especially prone to this cascade because it (1) expresses high levels of the CYP3A4 protein that metabolizes aflatoxin, and (2) because liver cells reproduce at faster rates than cells of other organs, allowing DNA mutations to accumulate and propagate much more quickly.

Human DNA includes a gene that encodes for the tumor-suppressing protein p53. The normal role of the p53 protein is to police DNA damage in the cell. It recognizes DNA damage and can initiate DNA repair processes or, in extreme cases, induce cell death. Without functional p53 protein, DNA damage runs rampant in a cell. Dysfunctional p53 is strongly associated with many forms of cancer in humans.

It seems that one particular guanosine in the p53 gene is especially susceptible to aflatoxin damage. Damage to this guanosine is propagated to descendant cells as a G -> T mutation in the p53 gene; the G -> T mutation in the p53 gene results in a ARG -> SER mutation in the p53 protein. The p53 protein falls victim to the very type of DNA damage it is meant to avert! This mutated version of p53 is exceedingly common in liver cancer patients.


In summary: aflatoxin causes DNA damage in the liver, resulting in a population of cells with defective p53 and prompting tumor growth.

Help us design a protein to break down this toxic compound by playing the latest Foldit puzzle, 1445: Aflatoxin Challenge: Round 2 with Insertions!

( Posted by  ianh 78 1451  |  Tue, 10/31/2017 - 17:26  |  1 comment )
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New Classroom Puzzle Series

As many of you know, playing Foldit can be a very effective way to learn about protein structure and folding, as well as other topics in biochemistry. Many teachers have taken advantage of this facet in the past, asking students to play Foldit as part of the class. However, we have not typically designed puzzles in Foldit for the express purpose of biochemistry education.

This winter, Professor Scott Horowitz will be teaching a biochemistry course at the University of Denver, with an emphasized use of Foldit to illustrate specific biochemical topics. Students will read primary literature in biochemistry, and will have access to custom Foldit puzzles that are designed to complement the assigned papers. Ideally, the puzzles will give the students an intuitive feel for the biochemical systems they are learning about, and enable them to better understand the papers they are reading. (And yes, the students will be graded, in part, based on their Foldit score.)

But first, we’re asking for the help of you, the Foldit community! Before assigning these puzzles to students, we’d like to get some feedback from our regular Foldit players—veterans and newcomers alike. Over the next couple of months, we’ll be posting a series of “Classroom” puzzles, with the course reading when possible, and we want to hear your thoughts and opinions about how to make them more useful for undergraduate students.

Check out the first puzzle of the series, 1434: Classroom Puzzle: Phosphates in Biology! This puzzle focuses on the structure of RNA, and the role of phosphorus in biology. The puzzle description links to two related articles: the first is a landmark 1987 paper by Frank Westheimer discussing the unique role of biological phosphates; the second is a controversial 2010 paper by Wolfe-Simon et al. suggesting arsenic as a viable substitute for phosphorus. Please leave comments and suggestions on the puzzle page!

( Posted by  bkoep 78 544  |  Wed, 09/27/2017 - 21:41  |  1 comment )
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Introducing Small Molecule Design Puzzles

Hi everyone,

Today we are officially launching the Foldit small molecule drug discovery game mode.

To kick off the new game mode, we are releasing a new puzzle on acquired immunodeficiency syndrome (AIDS). It has been over three decades since the CDC reported on the discovery of AIDS and its cause, the human immunodeficiency virus (HIV). Currently, 17 million people globally are being treated for HIV with antiretroviral therapy (WHO Global AIDS Update 2016). A total of 2.1 million people were infected with HIV in 2015 and 1.1 million people died from AIDS, with the majority of patients being from in Africa.


(Source: UNAIDS Global AIDS Update 2016)

Current treatment therapies focus on blocking the enzymes used by HIV to reproduce. One such enzyme is HIV protease, an enzyme which the virus uses to cleave polypeptide precursors. Without a functioning HIV protease, the virus cannot make the proteins needed to produce new virus particles. Several small molecule drugs have been created to block HIV protease, such as saquinavir and amprenavir. These compounds inhibit HIV protease by binding in the enzyme active site, a large cleft running through the middle of the protein, which prevent the enzyme's substrates from binding to the enzyme. HIV protease is a good test case for small molecule design, as there's a wealth of information about what sorts of compounds bind to the enzyme.

For this puzzle, we are interested in what small molecule inhibitors you can design for HIV protease 1. As a starting point, we're giving you the base fragment for saquinavir in the binding pocket. What we'd like you to do is use the new small molecule design tools to alter the chemical structure of the inhibitor ligand to get a better binding (better scoring) ligand.

We recommend that you use the selection interface (Menu->Selection Interface) for this process, as it gives you the most control, but you can also access some of the drug design tools through the "Modes" entry of the original interface. In particular, the Ligand Design tool will be your main tool for altering the identity of the ligand.

In the selection interface, the Ligand Design tool will pop up after clicking on the ligand. (In the original interface, click Ligand Design from the modes menu before clicking on the ligand.) You can then click one or more individual atoms to change the atom's element, or to add and delete bonds, atoms and groups. Keep in mind the advanced GUI (Main/Menu->General Options->Show advanced GUI) enables additional options under View that may help in working with small molecules. (I like the "Cartoon Ligand" view, myself, as it allows you to select ligand hydrogen atoms.)

Explore the tools and different designs you can make for the small molecule! Remember, you can use the Upload for Scientists button for designs that you want us to look at, even if they are not the best-scoring solutions!

-rmoretti & freeradical


P.S. Didn't follow the development of the drug design mode? Catch up with these previous blog posts:

* Foldit drug design introduction
* Foldit Drug Design Part Two
* Foldit Drug Design Blog: Interface Update
* Drug design puzzles coming your way!
* Let's Get Ready for Drug Design Puzzles!
* Devprev Drug Design Update
* Drug Design Update: Tool Talk
* Drug Design Update: Merk Molecular Force Field
* Big Update: Experimental Client (Drug Design)

(Note that some features discussed are for older versions and have changed since.)

( Posted by  rmoretti 78 654  |  Tue, 09/19/2017 - 23:11  |  0 comments )
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A Visit from a Veteran Foldit Player

A couple of weeks ago, the Foldit team had the pleasure of meeting with veteran Foldit player, Timo van der Laan! Timo, who was visiting Seattle from his home in the Netherlands, met with us to discuss volunteering his programming expertise. Timo's background in automating development processes and structuring documentation will be a huge asset as he works with our team on improving Foldit.

The team discussed numerous potential projects and afterward, bkoep took Timo on a tour of the lab where proteins designed by Foldit players are tested. They examined samples of plasmid DNA, each of which encodes the amino acid sequence of a Foldit player designs, which are inserted into E. coli cells. Then they visited the E. coli incubators where the bacteria are grown, with shaking platforms that keep the growth medium turbulent and well-aerated. Timo was introduced to some of the instruments are used to purify proteins, like a column for size exclusion chromatograph (SEC); as well as other instruments that are used to characterize proteins, like the circular dichroism (CD) spectrometer. Lastly, they viewed some of the protein crystallization trays that have been set up for the numerous projects of the Baker Lab.


bkoep and Timo
bkoep and Timo van der Laan on a tour of the Baker Lab

We thoroughly enjoyed meeting Timo after all these years and are looking forward to working with him on whatever project ends up getting nailed down!

You can read more about these instruments and the design testing process in our previous blog post.

( Posted by  smortier 78 1451  |  Wed, 06/21/2017 - 20:17  |  2 comments )
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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, RosettaCommons