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Stanford's goal: to understand protein folding, protein aggregation, and related diseases.



What are proteins and why do they "fold"? Proteins are biology's workhorses -- its "nanomachines." Before proteins can carry out their biochemical function, they remarkably assemble themselves, or "fold." The process of protein folding, while critical and fundamental to virtually all of biology, remains a mystery. Moreover, perhaps not surprisingly, when proteins do not fold correctly (i.e. "misfold"), there can be serious effects, including many well known diseases, such as Alzheimer's, Mad Cow (BSE), CJD, ALS, and Parkinson's disease.

What does Folding@Home do? Folding@Home is a distributed computing project which studies protein folding, misfolding, aggregation, and related diseases. Stanford uses novel computational methods and large scale distributed computing, to simulate timescales thousands to millions of times longer than previously achieved. This has allowed us to simulate folding for the first time, and to now direct Stanford's approach to examine folding related disease.



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Folding/Chrome to Reveal the Secrets Behind the Type II Diabetes
King_N
[H]ard|Folding Administrator


Posts: 102
Points: 2,813,787
Work Units: 6,596

Posted: Thu Jul 24, 2014 03:33 am
Quote:
by Huang

In the past couple of years, Xuhui Huangs group at HKUST
(http://compbio.ust.hk/) has performed large-scale molecular dynamics
simulations at Folding@Home (Project 2974-2975) to investigate the
mis-folding of the hIAPP (human islet amyloid polypeptide, also called
amylin).

Like other misfolding peptides, hIAPP is generally unstructured in
water solution but adopts an alpha-helix structure when binds to the
cellular membrane. Around 95% of patients with Type II diabetes
exhibit large deposits of misfolded hIAPP (beta-sheet fibrils). The
aggregation of this peptide is suggested to induce apoptotic
cell-death in insulin-producing &#946;-cells that may further cause the
development of the type II diabetes. Using Markov state models
constructed from many molecular dynamics simulations, we have
identified the metastable conformational states of the hIAPP monomer
and the dynamics of transitioning between them. We show that even
though the overall structure of the hIAPP peptide lacks a dominant
folded structure, there exist a large number of reasonably populated
metastable conformational states. Among them, a few states containing
substantial amounts of &#946;-hairpin secondary structure and extended
hydrophobic surfaces may further induce the nucleation of hIAPP
aggregation and eventually form the fibrils. These results were
published at Qin, Bowman, and Huang, J. Am. Chem. Soc., 135 (43),
1609216101, (2013) (http://pubs.acs.org/doi/full/10.1021/ja403147m).



Full Article: here.
Update on drug design successes with Folding@home
King_N
[H]ard|Folding Administrator


Posts: 102
Points: 2,813,787
Work Units: 6,596

Posted: Sat Jun 28, 2014 08:53 am
Vijay gave a brief talk on drug design successes with Folding@home.

Quote:
by Vijay Pande

In the Stanford Big Data conference in 2014, I gave a talk which gives an update on our drug design efforts, summarizing a bit on how FAH works to design drugs and were we are in some areas (but not all alas, its only a 12 minute talk, so I had to be pretty brief).



Link to video here.
Stanford Webinar
King_N
[H]ard|Folding Administrator


Posts: 102
Points: 2,813,787
Work Units: 6,596

Posted: Mon May 26, 2014 03:11 am
Stanford is holding a "Webinar".

Quote:
by Vijay Pande

Please join us on June 3rd for a webinar presented by Vijay Pande, Professor of Chemistry, Structural Biology, and Computer Science at Stanford University and the founder of the Folding@Home project. Professor Pande will give a brief introduction to Folding@home and successes in the project so far. He will also discuss plans to greatly enhance Folding@home capabilities through new initiatives.


The webinar is scheduled to take place on June 3rd at 9am, it requires registration at the link below.

Registration Link

Progress on connecting computation with experiment
King_N
[H]ard|Folding Administrator


Posts: 102
Points: 2,813,787
Work Units: 6,596

Posted: Mon Apr 28, 2014 09:34 pm
Stanford has made progress with their experiment to capture millisecond events through Folding@Home and Markov state models.

Quote:
By Greg Bowman


Many biologically relevant conformational changes occur on milliseconds and slower timescales. Furthermore, many experimental techniques are only sensitive to milliseconds and slower timescales. Therefore, our ability to reliably capture millisecond timescale events through the use of Folding@home and Markov state models opens up a host of exciting possibilities.


Full Article: here.
Recent FAH work on cancer: A brief overview
King_N
[H]ard|Folding Administrator


Posts: 102
Points: 2,813,787
Work Units: 6,596

Posted: Thu Mar 27, 2014 03:20 am
New F@H team member Ms. Jingcheng Wu discusses recent F@H work.

Quote:
Part I

Cancer affects the general population in an extensive and intensive way. It accounts for 1 out of 4 deaths in the US.1 The global annual cancer cases are expected to rise to 22 million within the next two decades.2 Existing drugs used in chemotherapy on the market are not only ineffective 97% of the time,3,4 but also cause severe damage to the body as a whole due to the drugs high toxicity. We are all too familiar with the frightening adverse effects of chemotherapy such as hair-loss, holes in intestine, swelling of the body, feeling sick and tired, abnormal bleeding, to name a few. Many cancer patients choose death over going through the agony of chemotherapy by refusing the treatments.

The reason behind the severe toxicity of anti-cancer drugs lies in their low selectivity. Aiming at killing cancer cells, the drugs also massively destroy normal cells and impede the growth of new healthy cells. Thus come the tragic sufferings very often seen in the oncology wards. The current cancer drugs attempt to cure the patients while kill them at the same time. The solution, then, lies in finding a new way of targeting cancer cells with minimal harm to normal cells.


Full Article here.



Quote:
Part II

C-src is short for c-src tyrosine kinase. Kinase is a type of enzyme that removes a part (phosphate group) of the molecule (ATP) that is required for every energy-expending process in the body, and attaches it to a specific amino acid (tyrosine, threonine or serine) of a protein (substrate). C-src belongs to a family of kinases called the Src tyrosine kinase.

C-src stimulates the pathways that induce cell growth, generate new blood vessels, prevent cell suicide, and give cells ability to migrate1,2 all necessary to give rise to proliferation of invasive cancer cells. When there is a mutation to the gene that encodes c-src, mutant c-srcs produced could mimic the functions of the normal signal transduction c-srcs.3 When there is over or mis-expression of the said gene, too many normal c-srcs would be produced. In both cases, it is like stepping on a gas pedal of a car. Once the aforementioned abnormality is coupled with the loss of tumor suppressor gene functions,4 it is like additional loss of the brake of a car, and the car takes off and wreaks havoc.


Full Article: here.
  • Stickies: 0
  • News Articles: 157
  • Pages: 32
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