Protein flexibility: coordinate uncertainties and interpretation of structural differences.

ABSTRACT: Valid interpretations of conformational movements in protein structures determined by X-ray crystallography require that the movement magnitudes exceed their uncertainty threshold. Here, it is shown that such thresholds can be obtained from the distance difference matrices (DDMs) of 1014 pairs of independently determined structures of bovine ribonuclease A and sperm whale myoglobin, with no explanations provided for reportedly minor coordinate differences. The smallest magnitudes of reportedly functional motions are just above these thresholds. Uncertainty thresholds can provide objective criteria that distinguish between true conformational changes and apparent 'noise', showing that some previous interpretations of protein coordinate changes attributed to external conditions or mutations

SUBMITTER: Rashin AA 

PROVIDER: S-EPMC2777169 | biostudies-literature | 2009 Nov

REPOSITORIES: biostudies-literature