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How would you recommend to approach this problem - we have a peptide that has side-chain exposed to the solvent and it is likely that side-chains dynamically occupy many conformations.

However, the backbone is probably less mobile.

How do you calibrate NOE restraints based on the peak intensity in a situation like this?

edit: sorry I was not clear enough the first time - I mean that conformational exchange that is fast on NMR time scale.

Thank you.

asked Mar 08 '10 at 13:35

Evgeny%20Fadeev's gravatar image

Evgeny Fadeev

updated Mar 13 '10 at 18:48

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You might try 2 series of NOE experiments. The first plotting the intensity as a function of the mixing time at a static temperature. The second as a function of temperature (both above and below the previous static value) at say maybe 3 different mixing times. Different conformational states should be apparent if present and with the amount of data available from the experiments, some reasonable restraints might be extracted.


answered Mar 13 '10 at 10:25

bernie%20o%27hare's gravatar image

bernie o'hare

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