Folding Forum

About two weeeks before ,I happened to read abstract of one paper on folding path way by REMD simulation.
Unfortunately , I didn't save that paper one my computer. And I can't search it out now.

The following are some hints I can remember:
1.That paper was on PNAS or Protein Science.
2.That paper discussed how a beta-sheet formed .
That sheet was formed by amino acids with long distances from sequence.
For example , head and tail of a protein forms one beta-sheet.
The author proposed one "cache" mechanism to explain the folding path way.
During the folding process, head of the protein formed a helix before tail of the protein was synthesised . After the tail of the protein was synthesised , the helix unfolds and forms sheet with tail .
That intermediate helix was recognised as "cache".
3. most important key words in that article "how head and tail meet"




If you have read that paper, please tell me .


Many thanks for your help!

Welcome to the forums! It should be on this page. Be warned though you'll have to search it out because there are 55 on there, all from F@H.

John Naylor wrote:Welcome to the forums! It should be on .... Be warned though you'll have to search it out because there are 55 on there, all from F@H.

I didn't find it there.
It may not be work of Professor Pande.

One thing you should keep in mind is that REMD is an artificial dynamics, so it can't be trusted to give kinetic information.

VijayPande wrote:One thing you should keep in mind is that REMD is an artificial dynamics, so it can't be trusted to give kinetic information.

Thanks for your advice.

Another problem in folding simulation is most of simulations overestimate protein's melting temperature.
Does this have something to do with the "artificial dynamics" ?
Or it's originated from deficiency of classical force field .

The over-estimation of the melting temperature has to do with the fact that most force fields do not include polarizability and thus are forced to be parameterized for certain conditions (eg certain temperature). One need not go to QM to get this -- force fields like AMOEBA should do just fine. Also note that implicit solvents *could* be parameterized to different temperatures just fine, but nobody has done that yet with any major implicit model (but it's been on our minds).

Hi. We works with proteins like a subject and we starting to interest TEE-REX or REMD wich on gromacs based. Can you help?
What we need to start it? We have gromacs 4 (and 3.3.3) so also we must to install some external modules like tee-rex?! How to get It and to work with it? Have you some tutors?

thanks