Random coil index

Random coil index (RCI) predicts protein flexibility by calculating an inverse weighted average of backbone secondary chemical shifts and predicting values of model-free order parameters as well as per-residue RMSD of NMR and molecular dynamics ensembles from this parameter.

[1] Even though chemical shifts of rigid residues may adopt random coil values as a result of comparable contributions of shielding and deshielding effects (e.g. from torsion angles, hydrogen bonds, ring currents, etc.

), combining the chemical shifts from multiple nuclei into a single parameter allows one to decrease the influence of these flexibility false positives.

13C, 15 N and 1H secondary chemical shifts are then scaled to account for the characteristic resonance frequencies of these nuclei and to provide numeric consistency among different parts of the protocol.

The last step of the protocol involves smoothing the initial set of RCI values by three-point averaging.

Examples of correlation between RCI and other methods of measuring motional amplitudes in proteins. NMR RMSD - root mean square fluctuations of atomic coordinates in NMR ensembles, MD RMSD - root mean square fluctuations of atomic coordinates in MD ensembles, S2 - model-free order parameter, RCI - random coil index, B-factor - temperature factor of X-ray structures; RCI->NMR RMSD - root mean square fluctuations of atomic coordinates in NMR ensembles predicted from RCI, RCI->MD RMSD - root mean square fluctuations of atomic coordinates in MD ensembles predicted from RCI, RCI->S2 - model-free order parameter predicted from RCI, RCI->B-factor - temperature factor of X-ray structures predicted from RCI.