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[email protected]'s First Oncology Results Published in JMB

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Nov 22, 2003
New York City
Per http://folding.stanford.edu/news.html:

1/15/2005 First results from [email protected] cancer project published. We have been studying the p53 tumor surpressor and our first results on p53 have recently been published. To our knowledge, this is the first peer-reviewed results from a distributed computing project related to cancer. Thanks to the continued support of FAH donors, this is will be just the first of many cancer related works that will come from FAH.

The nature of our results can best be described in our paper. However, here's a brief summary of our results. Roughly half of all known cancers result from mutations in p53. Our first work in the cancer area examines the tetramerization domain of p53. We predict how p53 folds and in doing so, we can predict which amino acid mutations would be relevant. When compared with experiments, our predictions have appeared to agree with experiment and give a new interpretation to existing data.

Journal of Molecular Biology
Volume 345, Issue 4 , 28 January 2005, Pages 869-878

Dimerization of the p53 Oligomerization Domain: Identification of a Folding Nucleus by Molecular Dynamics Simulations

Dimerization of the p53 oligomerization domain involves coupled folding and binding of monomers. To examine the dimerization, we have performed molecular dynamics (MD) simulations of dimer folding from the rate-limiting transition state ensemble (TSE). Among 799 putative transition state structures that were selected from a large ensemble of high-temperature unfolding trajectories, 129 were identified as members of the TSE via calculation of a 50% transmission coefficient from at least 20 room-temperature simulations. This study is the first to examine the refolding of a protein dimer using MD simulations in explicit water, revealing a folding nucleus for dimerization. Our atomistic simulations are consistent with experiment and offer insight that was previously unobtainable.

The reason I'm posting this is because, well, many folders are folding in the name of fighting cancer, but I don't see too many posts that talk about the actual [email protected] results on the biology/science end.

FYI, In humans, p53 mutations occur in around half of all cancers.... in a nutshell, p53 is a regulator that (in the case of DNA damage) binds to DNA -> induces Pic1 production -> inhibits CDK -> stops cell from dividing, giving time for the cell to either repair its DNA or trigger cell suicide (apoptosis). p53 has 6 points (2 main) that help it bind to DNA. So if something goes wrong in the p53 folding (or whatever else), then p53 can't bind... no p21 is made... cdks go crazy.. the crazy damaged cells start dividing.. and yeah. p53 is also involved in binding/regulation to/from MDM2.

Since I have access to the scientific journals at work, I'm going to print out their publication at tomorrow and read up on their (our DC?) results.

- Jer
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Apr 22, 2004
New Hampshire
you are right, not a lot of progress gets attention here. If you get regular updates on the projects feel free to quote them here, we all like to see the results of our hard work :)


Jan 3, 2005
San Antonio
Wow. I'm glad to find that there has been progress made with the FAH project. I feel all warm & fuzzy inside to be part of it. :)

I'd also like to see more posts of FAH's progress, as I tend to neglect going on Stanford's site seeing as I don't have much time to be online that much...especially once I finish training.


Mar 2, 2004
Irvine, CA
Seven said:
*skips quotes, clicks on EOC link in favorites*

I'm too lazy to listen to Pande talk.

I'm too bored to listen to him talk. I fold for the cure but I guess I don't have to understand the stuff (I don't) thats why I do what I can. Plus Pande is pretty boring, I remember when someone linked that 60 minute lecture he gave, I turned it off pretty fast because it was kinda dull.