Folding Forum

People hate to hear about failures, but I have understood that FAH looks for the most stable protein conformation, indeed the least energy required to be stable.
However, I have heard (indeed I have not read them) which functional proteins may not be the most stable.

I can catalogue this cases as "FAH failures", because FAH can not predict these structures "in vivo" or "ex vivo". These "failures" are very important, since they are pointing that some "mysterious" forces (maybe enzymes) look for this unstable shape.

I ask:
How many of these "failures" have you found?
How unstable are them?
How you can explain these "abnormalities"?

Hello hedley, welcome to the folding forum.

If you read the home page, fah is looking at protein folding, and the protein mis-folding that can cause diseases. I assume these misfolded proteins are the same "failures" to which you refer. I'm rather sure the project isn't so inept as to ONLY look at the most stable configuration. But then I don't work for Stanford, so I'll leave any further comment up to Stanford to make.

hedley wrote:I have understood that FAH looks for the most stable protein conformation, indeed the least energy required to be stable.

I think you have FAH confused with some other protein simulation projects. FAH is not looking for a single conformation. Those sites which try to predict protein shape do.

I agree with 7im. FAH's goal is to understand the process of folding, not just the final conformation. That same process is also involved in creating less stable shapes so it contributes to the scientific understanding of what those shapes are, too.

The folding process is driven by energy. If you want to unfold a protein, you can heat it up (add energy). Many FAH projects are studying the folding process as it approaches a stable shape but other FAH projects have involved the sequences of unfolding. The simulated temperature and the transfer of energy is an integral part of any FAH study.

Send some of those "heat it up" WUs my way! No simulation needed -- getting to 101 today in Seattle, and no A/C!