need to change temperature for folding - not everything lives at 37oC

3 replies [Last post]
aloraine
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Joined: 02/11/2012

On the main mfold Web page, there is this sentence:

"The folding temperature is fixed at 37C. You may still fold with the older version 2.3 RNA parameters, which allow the temperature to be varied."

Does this mean that future (and presumably better) versions of mfold will not permit folding at other temperatures?

Where do I find the 2.3 version of mfold that would allow me to try folding RNAs at different temperatures?

Best wishes,

Ann Loraine

atlanticnetusa
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Joined: 05/26/2012
I will assume that you are

I will assume that you are talking about enzymes found in the normal human body. Enzymes function best at an optimal temperature (in our case, around 37 degrees celsius) because of the inherent tradeoff between reaction rates and protein stability. Remembering your elementary kinetics, the rate of an endothermic reaction (i.e. one that needs energy to function) is directly proportional to the temperature. Since by all means enzymes are biological catalysts, they follow this rule of thumb. However, remembering your biochemistry, higher temperatures lead to protein denaturization, wherein the activity of the enzyme becomes zero due to changes in the protein folding. Thus, in the case of human enzymes, we can expect to see optimal activity at body temp, low activity at lower temperatures, and no activity at very high temperatures.
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zukerm
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Joined: 11/12/2010
I apologize for the inability

I apologize for the inability to alter temperature for RNA folding using the more up to date free energies. There are newer parameters that allow the user to change temperature for RNA folding. They will be implemented after further testing is done. A word of caution is needed. Folding RNA from organisms that live at very high temperatures using the version 2.3 energies at the indicated temperature yields nonsense. That is, the RNA does not fold at that temperature. It is already melted. I expect the same behavior with the newer free energies.

Please feel free to remind us in June 2012 if the updates have not yet been made.

admin
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Joined: 09/23/2010
The older version is on this

The older version is on this page. I'll make some minor edits to avoid any further confusion.