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Richard Mitnick
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Re: Interesting news about proteome folding:

So, someone tell me, did I miss it? Where is WCG mentioned in the article?
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[Jun 11, 2010 7:41:00 PM]   Link   Report threatening or abusive post: please login first  Go to top 
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Re: Interesting news about proteome folding:

Physicists Help Biologists to Understand Protein Folding

http://www.sciencedaily.com/releases/2010/06/100617132222.htm

Physicists at UC Santa Barbara have created a microscopic device to assist biologists in making very fast molecular measurements that aid the understanding of protein folding. This development may help elucidate biological processes associated with diseases such as Alzheimer's and Parkinson's. Since proteins in the body perform different functions according to their shape, the folding process is considered a key area of study.
[Jun 21, 2010 8:16:07 AM]   Link   Report threatening or abusive post: please login first  Go to top 
sk..
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Re: Interesting news about proteome folding:

The mere existence of chaperone complex's sort of undermines Radford's misfolding work (first post). Proteins often have several relaxed (inert) states, and are often activated to go to work, through many different biochemical means. I wonder if Redfords group assessed for degradation. Single cell organism research is not always a good paradigm for the human body. It is highly unlikely that studying the folding route of one protein in a bug will lead to a cure for Schizophrenia or Parkinsons disease. Most of us have heard miracle break through a bit too often. It seems every science team now tries to justify its research with some sort of vague link to some disease.
Might have been nice if sciencedaily had elaborated on 'device'!
That papers title is, The mechanism of folding of Im7 reveals competition between functional and kinetic evolutionary constraints.
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[Edit 2 times, last edit by skgiven at Jun 21, 2010 10:11:44 AM]
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Re: Interesting news about proteome folding:

Human proteome fully mapped

A research team from ETH Zurich, led by Professor Ruedi Aebersold, and from the Institute for Systems Biology, Seattle, has used mass spectroscopy methods to fully map the human proteome for the first time. The data is being made available to all researchers.


Researchers at the Institute for Systems Biology (IBS) in Seattle and at ETH Zurich from the group led by Professor Ruedi Aebersold have recorded and identified using various mass spectrometry methods, and whose data they have entered into a database as a reference. The researchers describe this as the “Gold Standard Reference for the human proteome”.

The spectra for every protein coded and expressed by the 20,300 human genes has been identified and recorded.

http://www.ethlife.ethz.ch/archive_articles/100921_proteomik_per/index_EN

http://www.ethlife.ethz.ch/archive_articles/1...fr_aebersold_per/index_EN
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[Edit 1 times, last edit by Former Member at Sep 25, 2010 6:27:37 PM]
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littlepeaks
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Re: Interesting news about proteome folding:

Researches are using the supercomputer "Anton" to simulate protein folding. For one of the proteins studied, they performed a 100-microsecond simulation and found the domain folds and unfolds the same way each time. Anton was built solely for the purpose of molecular dynamics simulations of the behavior of large biological molecules. The full article is available in Chemical and Engineering News.

The following image compares protein folding results from X-ray crystallography (blue) and Anton's simulations (red).


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Papa3
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Re: Interesting news about proteome folding:

http://www.sciencedaily.com/releases/2011/01/110110154645.htm

New Method Takes Snapshots of Proteins as They Fold

ScienceDaily (Jan. 10, 2011) — Scientists have invented a way to 'watch' proteins fold -- in less than thousandths of a second -- into the elaborate twisted shapes that determine their function. [...] the scientists demonstrated that the new technique can follow folding and unfolding on a submillisecond time scale. [...] this proof-of-principle experiment stands at the end of a long line of elegant experiments of a similar type, called pump-probe experiments. Other techniques probe the change in protein structure by monitoring the absorption or emission of light--or a similar physical effect. They can provide only global information, such as the rate constant of a folding reaction. "Because we use a chemical rather than a physical probe, we can see what's going on in much greater detail," says Gross. "We can say which part of the structure closes first, which second, and so on." [...] Jiawei Chen, Don L. Rempel, Michael L. Gross. Temperature Jump and Fast Photochemical Oxidation Probe Submillisecond Protein Folding. Journal of the American Chemical Society, 2010; 132 (44): 15502 DOI: 10.1021/ja106518d
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Papa3
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Re: Interesting news about proteome folding:

http://arstechnica.com/science/news/2011/02/x...us-as-it-vaporizes-it.ars

X-ray laser finds structure of a single virus as it vaporizes it

In two Letters in Nature, scientists are reporting that they have been able to reconstruct the structures of biological molecules using femtosecond X-ray pulses. In the first Letter, they imaged nano-crystals of the photosystem I protein, part of the photosynthetic machinery. In the second, they were able to image individual single mimiviruses, part of a family of giant viruses. We seem to be well on the way to single molecule structural imaging. [...] higher energy x-rays and shorter bursts are expected to increase resolution and decrease the size of the sample particles. Plans are already in the works for x-ray lasers 105 times brighter but with pulses lasting less than 10fs.
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Re: Interesting news about proteome folding:

http://www.technologyreview.com/blog/arxiv/26421/

Physicists Discover Quantum Law of Protein Folding

Two researchers in Inner Mongolia have come up with equations that amount to the first universal laws of protein folding. According to MIT's Technology Review, that's the equivalent in biology to something like the thermodynamic laws in physics.

They say quantum mechanics finally explains why protein folding depends on temperature in such a strange way.
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Papa3
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Re: Interesting news about proteome folding:

http://www.sciencecodex.com/polarized_microsc...how_proteins_are_arranged

Polarized microscopy technique shows new details of how proteins are arranged

[...] "Our new technique allows us to measure how components of large protein complexes are arranged in relation to one another," [...] there is a "resolution gap" between the two techniques primarily used to visualize protein complexes. Electron microscopy can reveal the broad outlines of a large protein complex, but it can't show details. X-ray crystallography, meanwhile, can show minute detail but only of a small piece of the complex; it can't say how the individual pieces fit together. To further complicate matters, both techniques require fixed samples – while they can give you an idea of what something looks like at a moment in time, they can't tell you how its pieces might move. [...] After genetically attaching fluorescent markers to individual components of the nuclear pore complex, the scientists replaced the cell's own copy of the gene that encodes the protein with the new form that has the fluorescent tag. Then, they used customized microscopes to measure the orientation of the waves of light the fluorescently tagged proteins emitted. By combining these measurements with known data about the structure of the complex, the scientists can confirm or deny the accuracy of previously suggested models. [...] Eventually, the scientists say their technique could go even further. Because the proteins' fluorescence can be measured while the cells are still alive, it could give scientists new insights into how protein complexes react to varying environmental conditions, and how their configurations change over time. [...]
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Papa3
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Re: Interesting news about proteome folding:

http://www.sciencecodex.com/ornl_invention_unravels_mystery_of_protein_folding

OAK RIDGE, Tenn., Sept. 14, 2011 -- An Oak Ridge National Laboratory invention able to quickly predict three-dimensional structure of protein could have huge implications for drug discovery and human health.

While scientists have long studied protein structure and the mechanism of folding, this marks the first time they are able to computationally predict three-dimensional structure independent of size of the protein. Because the invention also determines possible intermediate states in the protein folding process, it provides a clearer picture and could open doors to designing new medicines for neurodegenerative diseases that are caused by incorrectly folded proteins. [...] Proteins often adopt a three-dimensional structure that allows them to carry out their designated function, but such a structure has provided a computationally challenging task. Using the fundamental insights of the protein structure, dynamics and function, the ORNL invention discloses a unique computational methodology to explore the conformational energy landscape of a protein.

"One of the main advantages of this approach is that it follows the natural intrinsic dynamics of the protein and by promoting the relevant dynamical modes allows rapid exploration of the folding pathway and prediction of the protein structure," Agarwal said. [...]
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