How should molecule flexibility affect NOE distance restraint calibration?

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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 Fadeev
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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.

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answered Mar 13 '10 at 10:25

bernie o'hare
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noesy ×26
calibration ×10
distance-restraint ×5
dynamics ×4

Asked: Mar 08 '10 at 13:35

Seen: 8,014 times

Last updated: Mar 13 '10 at 18:48

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