FR Folding@Home Project Update - Folding of Proteins in Nanotube Confinement

Journal of the American Chemical Society ^ | 02/07/2006 | Stanford University

[texas booster]

From a paper in the Journal of the American Chemical Society concerning nanotubes:

The folding of proteins in confined spaces is a ubiquitous theme in biological and biomaterial applications, including folding in chaperones and pores, nanotube-based drug delivery, and cotranslational folding of nascent peptides in the ribosomal exit tunnel. The role of confinement on peptide conformational equilibrium has thus gained much interest in recent years, and a natural first hypothesis to investigate is the role of confinement alone in protein conformational preferences.

...

Still, there exists a growing body of evidence to suggest that molecular water plays a role in the conformational preferences and assembly of biomolecular systems. For example, it has been suggested that the addition of crowding agents or chemical denaturants destabilizes proteins by affecting the structure of water. Moreover, the character of water in confined environments is expected to differ significantly from that in bulk.

...

What role does water play in the stability of confined proteins? To address this question, we have simulated a well-characterized 23-residue helical peptide inside six fully solvated single-walled CNTs with diameters ranging from 15 to 35 Å. For each tube modeled, 1000 independent molecular dynamics trajectories were started from the fully helical and extended states (Figures 1 and 2a). Simulations were performed on the Folding@Home distributed computing network as described previously using the AMBER- 99 helix-coil force field and the TIP3P water model in the NVT ensemble at the approximate midpoint temperature of 305 K (89F). With individual trajectories on the 100-300 ns time scale and an aggregate time exceeding 2.5 ms, our extensive sampling allows us to extract equilibrium thermodynamic data.

(Please click on the above link for the full paper on Nanotube Confinement Denatures Protein Helices)

[texas booster]

We have had the Free Republic folding team for about 2 1/2 years now, and have grown dramatically in the last year. This is some of the folding work in which we may have participated.

Talk of nanotubes to deliver medicines may be the future, but there is a lot of hard work learning how to make it happen. How to pack the medicine inside the tube, how a protein may fold inside a tube and the effect of water molecules on such a small scale will all need to be examined before an effective delivery system utilizing nanotubes can be implemented.

To those not familiar with the Folding@Home distributed project please read on. We are here to help you get started!

[texas booster]

We have reached #57 on the list of teams worldwide, FReepers are in the Top 1,000 of all folders and we are stomping the bejebers out of the DUmmies and Daily Kos.

A year ago we were just beginning to expand. Now we have about 170 regular contributors with nearly 1,050 computers using F@H as their screensaver.

Folding@Home makes a real difference in basic research into such diseases as Alheimer's, Parkinson's and BSE.

All it takes is a little free time to download the core, which runs in the background. Safe, clean and effective!

[Incorrigible]

w00t!

[texas booster]

We have reached #57 on the list of teams worldwide, FReepers are in the Top 1,000 of all folders and we are stomping the bejebers out of the DUmmies and Daily Kos.

A year ago we were just beginning to expand. Now we have about 170 regular contributors with nearly 1,050 computers using F@H as their screensaver.

Folding@Home makes a real difference in basic research into such diseases as Alheimer's, Parkinson's and BSE.

All it takes is a little free time to download the core, which runs in the background. Safe, clean and effective!

[texas booster]

We have reached #57 on the list of teams worldwide, FReepers are in the Top 1,000 of all folders and we are stomping the bejebers out of the DUmmies and Daily Kos.

A year ago we were just beginning to expand. Now we have about 170 regular contributors with nearly 1,050 computers using F@H as their screensaver.

Folding@Home makes a real difference in basic research into such diseases as Alheimer's, Parkinson's and BSE.

All it takes is a little free time to download the core, which runs in the background. Safe, clean and effective!

[texas booster]

As always, please ping me in you want on or off the list!

[Clara Lou]

Woo hoo! My computers are due to complete 3 units today! [Of course, that means it may be a while before any more are completed.]

[Drango]

Proud to b foldin' 4 the "Gipper"

[texas booster]

If you have ever folded a p2061, p2066, p2067, p2071, p2074, p2076, p2094, p2097 or a p2098 assignment then you participated in this work.

One day we will have nanotube delivery of medicines and genetics. This is the hard work plowing new ground that needs to be done.

[texas booster]

Folding@Home FAQ for new users:

What is Folding@Home? A Stanford University project to find out how proteins fold.

Why it's important: Proteins folding wrong causes all kinds of diseases, like Alzheimer's, Parkinson's, and forms of cancer. Folding@Home uses novel computational methods and large scale distributed computing, to simulate timescales thousands to millions of times longer than previously achieved. Through Folding@home, scientists now have the horsepower to study the mechanics of protein folding. With its ability to share the workload among hundred of thousands of computers economically, Folding@home can help scientists understand how proteins snap, or don't, into their predestined shapes - and may help to explain the origins of diseases such as Alzheimer's and apparently unrelated diseases. We're fueling research that could end all that.

How does it work?: You download a safe, tested program (see link below) that is certified by Stanford University. It gets work from Stanford, runs calculations using your spare computer power, and sends the results back to the University.

Is it safe? Yes! Folding@Home rarely effects computer performance in any way and won't compromise your privacy in any way. It only uses the computing power you aren't using so it doesn't slow down other programs.

How do I get started folding for Team FreeRepublic?:
1.) Download the folding program from Stanford University's folding download page (Folding@home Client Download). Type in your desired username.
2.) Type in 36120 for the team number. THIS IS VERY IMPORTANT - if you get the number wrong, you won't be folding for team FreeRepublic!
3.) The third question asks, "Launch automatically at machine startup, installing this as a service?" - We recommend you answer YES. Otherwise you will have to manually start the program after every reboot.

How can my computer help? Even if they were given exclusive access to all of the world's supercomputers, Stanford still wouldn't have as much processing power as they get from the supercluster of people's desktop systems Folding@home relies on. Modern supercomputers are essentially a cluster of hundreds of processors linked by fast networking. But Stanford needed the power of hundreds of thousands of processors, not just hundreds.

There's no reason to not get involved! It's free, easy, and you can know you're helping every minute without lifting a finger.

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List of Relevant Folding Links
Why Fold - Watch This !!

Another Folding Clip

Folding@home Client Download

FreeRepublic.com Folder Stats

Extreme Overclockers Stats for FreeRepublic

Another Stats Page

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Competition (Not!!) Dummies ..Daily Kos

Dummie Folding Threads #7 #8 #9#10#11 #12

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Other Useful Stuff - Links

How much are those work units worth? And what are they?
All Projects Listed
Point Summary for Workunits

Stat Image Generator

Fahmon Third Party Monitoring Software

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Past FreeRepublic Folding threads

#1 #2 #3 #4 #5 #6 #7 #8 #9 #10 #11 #12 #13 #14 #15 #16 #17 #17 #18 #19 #20#21#22 #23 #24 #25 #26 #27 #28

[E.G.C.]

BTTT

[texas booster]

Another completed project, that provided results that we now build upon. How the molecules G5, C6, A7 and A8 fold into itself yet remain active was the object of many years of folding.

The GNRA hairpin is a small secondary structural unit of RNA that contains what some have called an "unusually stable" tetraloop region bridging the two strands that form this helical hairpin. We have previously characterized short-timescale loop dynamics and thermal unfolding of the hairpin and have since undertaking numerous related studies in silico including: unfolding at a biologically relevant temperature, direct folding, evaluation of the equilibrium thermodynamics of this RNA hairpin via replica exchange stochastic dynamics, and calculations of the folding probabilities for a small ensemble of structures (Pfold), which allow us to examine the transition state for the folding event.

This series of projects is now complete, and is the launching point for the new 340-385 series which uses much more sophisticated algorithms to maximize the accuracy obtained and to examine the role of water molecules and ions in the folding and unfolding processes.

[Paladin2]

At #57, the climb is steep.

[LonePalm]

According to my spreadsheet we will pass the following teams:

AoA Forum: 1/30/07
MozillaZine: 4/3/07
Linux: 4/9/07
Team 2ch: 6/27/07

Unfortunately we get passed by Team xtremesystems.org on 9/27/07.

The good news is that these dates are heavily weighted against us because it covers Christmas-New Year's week when many of Klutz_dohanger's servers are down.

Garde la Foi, mes amis! Nous nous sommes les sauveurs de la République! Maintenant et Toujours!
(Keep the Faith, my friends! We are the saviors of the Republic! Now and Forever!)
LonePalm, le Républicain du verre cassé (The Broken Glass Republican)

[processing please hold]

Thanks for the new thread.

My head hurts, I gotta get me some aspirins. :(

[texas booster]

xstremesystems.org had a contest to get to the 10 million mark. They are a high powered team with a lot of systems. Now their top folders are moving back to the World Computing Grid. We will be OK in the long run.

There are only 56 teams for us to pass, and most have been around a very long time. Our point totals will continue to increase and keep us competitive.

If anyone has upgraded a system this Christmas, or gotten an ATI X-series video card let us know so we can track your increase in points and maximize your production.

Egon's tool will make following your F@H points much easier. FReepmail Egon for the links to start.

[brityank]

Thanks, texas booster, for letting me help. my little WinME is running ~15k a year to the pot.

I've also found that if I shut down F@H before I reboot (updates, etc.) then I don't lose the points generated up to then. Power fails -- bye-bye!

Happy New Year, All.

[Route66]

Please Join the FR Team Bump

[texas booster]

Shutting down the 4.0 GUI version will save a check point in the log so that you can take off from where you last folded.

In case of a system shutdown I would think that you would only lose the points since the last check point, not the results from the entire fold. Let me look into that.

See if you can set the GUI to save a check point every 5 minutes or so.

[Coleus]

you don't even know it is there, just sign up and put in the FR code and your off, helping science and humanity.