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]

I have read through a couple of PS3 threads and it looks like Stanford will have to wait until Sony releases an upgrade to the system, probably before the European release in March. Still, the Pande Group has released the following videos of the PS3 GUI on this FAQ page.

http://www.stanford.edu/group/pandegroup/folding/FAQ-PS3.html

Long forum post whining about not having the Cure@PS3 available. At least Stanford understands what an NDA means.

http://forum.folding-community.org/ftopic16624-0-asc-0.html

[texas booster]

Just want to correct some info I gave.

There is a big boost in performance when one adds an ATI X1900 series card into an older computer. The difference can be seen and felt in general computing and especially in gaming.

When one adds an ATI X1900 series to a new state of the art system there is still a speed gain, but it is not as noticeable. The overall speed of the system as compared to the additional speed of the fast video will not be as great a difference.

If you have a very fast dual core system running Linux, drop in and try the F@H SMP cores.

If you have an older system and do not want to replace the entire system, getting a new ATI card makes a lot of sense and will provide the most bang for your buck. Providing that your power supply can handle it.

These rules apply to general upgrades as well as to F@H upgrades. Personally, my next major upgrade will the an ATI card, since it meets the needs of our general computing needs.

I did decide on ATI over NVidia (which I generally prefer) due to potentially greater F@H points.

[houeto]

My shameless self-promotion for this thread:

Yup, and a chance for me to say thatnks once again.

I check my "Egonometer" every day!

[Mount Athos]

My folding power more than doubled with the dual core upgrade.
Not doing bad for only having a single machine.
Be nice to see what happens when I upgrade to an ATI video card in a few months.
I have to take it down for a few days starting tomorrow.

[contrarian]

Hi folks, Contrarian joined the folders (Freepers)about 19:00 today. Please put me on any ping list so I can keep up with whats happening...

[Drango]

Welcome and may the borg be with you.

[mouser]

My power company sees fit to provide power here at the house most of the time

Don't feel bad my power went out because of an ice storm and was out for a week. Talk about playing hob with your standing on top 20. Not to mention my lifestyle.

[cerberus]

I am running Vista on an AMD machine with a dual core processor. Which version should I download?

[texas booster]

I would try the F@H dual core SMP kernal. It creates a ton of points and completes work units in just a day or so.

If you want to see the client working, go to Youtube and search for “F@H”. The SMP client does deliver pretty pictures but it does a LOT of work.

I’ll FReepmail you a link and instructions. On Vista you have to be administrator. Sometimes I have had to click on “Run as Administrator” tab in one of the Program menus.