To all of our wonderful Rosetta@Home contributors,

Here is an update about the p53-Mdm4 project: Using Rosetta@Home, we identified a set of 14 proteins that could be modified to stick to Mdm4 while ignoring Mdm4. We synthesized these proteins, tested them, and identified one that sticks to Mdm4 about 75 times better than it sticks to Mdm2. We sent this protein, called Mdm4 Binder 17 (MB17) to St. Jude's Childrens Research Hospital so the cancer experts could test it in cancer cells. So far, they have confirmed that MB17 strongly prefers to stick to Mdm4 over Mdm2 (about 170 times better, in their experiments). They also found that MB17 works correctly inside living cells, a major milestone for a designed protein. In the mean time, we've created new versions of MB17 that preference Mdm4 even more (about 370 times more than Mdm2), some that pinch-hit and prefer Mdm2 instead of Mdm4 (about 120 times more than Mdm4), and some that like both Mdm4 and Mdm2 equally well. The folks at St. Judes are starting to work with these improved variants as well. This is the first time that the cancer research community has ever had a tool to knock out just Mdm4 while leaving Mdm2 alone, so naturally, the folks at St. Jude's are pretty excited. They are gearing up to test MB17 in real cancer cells so we'll keep our fingers crossed. We'll keep you updated as new developments arise. I'm sorry for the long delays between posts. Things are pretty busy around here. For those of you seeing this thread for the first time, I've re-posted below what I posted previously about this topic:

Project 1:
The first of these interactions involves a protein called p53 and another called Mdm4. p53 is a communication hub in our cells, used to translate information about unwanted DNA mutations into an effective response by the cell. The activity of p53 is modulated by a pair of other proteins, Mdm4 and Mdm2, which act to shut off p53 when all is well. Cancer cells depend on DNA mutations to stay alive and so they find ways to shut off p53, either by reducing the amount available p53 or by expanding the amount of available Mdm4 or Mdm2. that way p53 doesn't rat out mutations that the cancer might need to survive. Scientists have spent a lot of time trying to understand how Mdm4 and Mdm2 work. They do this by shutting off Mdm2 and Mdm4 with drugs. There are even drugs that will shut off just Mdm2. There are no drugs, however, that will shut off just Mdm4. So I'm trying to make one. This is a tricky process since Mdm2 and Mdm4 are very similar, making it hard for proteins to tell them apart.

I aim to use Rosetta@home to design proteins that will attach to Mdm4 while ignoring Mdm2. I hope to provide a research tool to scientists that work on Mdm4, Mdm2 and p53, allowing them to better understand how this critical communication hub works. I hope that this leads to new cancer treatments. So far, I've used Rosetta@home to design 26 proteins that should attach to Mdm4 but not Mdm2. Many of the designed proteins do stick to Mdm4, but unfortunately, they also stick to Mdm2. I am working on a third round of design using a new approach that I hope will work. For more info about the proteins involved in this project, please visit the links below:

Hello,

My name is Sarel Fleishman and I've been a postdoc in the Baker lab for the past two years. My project deals with structure prediction and design of protein-protein interfaces and you may have read a few messages from me on CAPRI and structure prediction. Now, I'm very excited to tell you that with minirosetta v1.40 we can do design work using the massive computational power of Rosetta @ Home.

A few words on protein-interface design. The primary challenge in this field is to be able to take a protein target and to design another protein that would bind to it in a specific way. Nature provides us with hundreds of thousands of examples of such protein-binding events. Such events are used for the amplification of signals within and between our cells in processes related to growth and development as well as for recognition, e.g., in the immune system. When such signals go awry, protein interactions become the center of events for uncontrolled cell growth, or cancer. Many pathogenic bacteria and viruses hijack molecular recognition processes to promote their growth and proliferation causing sickness and endangering lives.

These processes being so central to both health and disease it is hardly surprising that being able to manipulate them computationally is a major ongoing goal of molecular biology. Being able to target a protein and bind to it would open the way to novel therapies for a large number of diseases.

We have selected a small number of protein targets for which we want to design protein binders. As an example, one such target that I have been working on is cholera toxin. This protein is a crucial component of the process by which the cholera bacterium causes cells in the gut to excrete large amounts of water, which causes death from dehydration (see the following wiki page for more details: http://en.wikipedia.org/wiki/Cholera). We have developed a computational strategy that allows us to design proteins to bind to the cholera toxin and disable it.

We are now in the process of testing this and similar design methodologies on a number of other targets. But expanding the number of targets we quickly realized that we need a lot more computational resources to adequately address this problem. This is why we have turned to Rosetta @ Home and to you for your help in this exciting project.

The simulations that you will see in protein interface design will be quite different from one another. In each case we tailor the design strategy to the particular protein target, stressing, for instance, the formation of interactions with a specific key region on the protein surface. In general, though, the simulations will involve docking steps, where the protein binder moves with respect to the target and design, where amino acid residues on the surface of the protein binder change in order to better attach to the target. Promising protein designs are synthesized in our lab and tested for binding to the target protein.

I am working on this project with my colleagues Eva and Jacob, and for each target that we test using Rosetta @ Home we will provide background material on the target and why we selected it on this thread.

These design simulations tend to use more memory than many prediction runs (typically at most 800Mb). We will test different ways of reducing this memory load so that our simulations could run on all participating computers in the Rosetta @ Home project, but initially we will only run these simulations on computers that can handle this memory restriction. Please report any problems that you might have with this simulation.

Thank you very much for participating in this project! I'm looking forward to getting feedback and results from you.

Awesome news :)

Does IPD = Institute for Protein Design?

[quote]To all of our wonderful Rosetta@Home contributors,

Here is an update about the p53-Mdm4 project: Using Rosetta@Home, we identified a set of 14 proteins that could be modified to stick to Mdm4 while ignoring Mdm4. We synthesized these proteins, tested them, and identified one that sticks to Mdm4 about 75 times better than it sticks to Mdm2. We sent this protein, called Mdm4 Binder 17 (MB17) to St. Jude's Childrens Research Hospital so the cancer experts could test it in cancer cells. So far, they have confirmed that MB17 strongly prefers to stick to Mdm4 over Mdm2 (about 170 times better, in their experiments). They also found that MB17 works correctly inside living cells, a major milestone for a designed protein. In the mean time, we've created new versions of MB17 that preference Mdm4 even more (about 370 times more than Mdm2), some that pinch-hit and prefer Mdm2 instead of Mdm4 (about 120 times more than Mdm4), and some that like both Mdm4 and Mdm2 equally well. The folks at St. Judes are starting to work with these improved variants as well. This is the first time that the cancer research community has ever had a tool to knock out just Mdm4 while leaving Mdm2 alone, so naturally, the folks at St. Jude's are pretty excited. They are gearing up to test MB17 in real cancer cells so we'll keep our fingers crossed. We'll keep you updated as new developments arise. I'm sorry for the long delays between posts. Things are pretty busy around here. For those of you seeing this thread for the first time, I've re-posted below what I posted previously about this topic:

Project 1:
The first of these interactions involves a protein called p53 and another called Mdm4. p53 is a communication hub in our cells, used to translate information about unwanted DNA mutations into an effective response by the cell. The activity of p53 is modulated by a pair of other proteins, Mdm4 and Mdm2, which act to shut off p53 when all is well. Cancer cells depend on DNA mutations to stay alive and so they find ways to shut off p53, either by reducing the amount available p53 or by expanding the amount of available Mdm4 or Mdm2. that way p53 doesn't rat out mutations that the cancer might need to survive. Scientists have spent a lot of time trying to understand how Mdm4 and Mdm2 work. They do this by shutting off Mdm2 and Mdm4 with drugs. There are even drugs that will shut off just Mdm2. There are no drugs, however, that will shut off just Mdm4. So I'm trying to make one. This is a tricky process since Mdm2 and Mdm4 are very similar, making it hard for proteins to tell them apart.

I aim to use Rosetta@home to design proteins that will attach to Mdm4 while ignoring Mdm2. I hope to provide a research tool to scientists that work on Mdm4, Mdm2 and p53, allowing them to better understand how this critical communication hub works. I hope that this leads to new cancer treatments. So far, I've used Rosetta@home to design 26 proteins that should attach to Mdm4 but not Mdm2. Many of the designed proteins do stick to Mdm4, but unfortunately, they also stick to Mdm2. I am working on a third round of design using a new approach that I hope will work. For more info about the proteins involved in this project, please visit the links below:

The top MB17 variants bind Mdm4 (Mdmx) or Mdm2 tightly enough to yank them out of human cells

Will this article be useful in rosetta's calculations methods?