Protein flexibility: coordinate uncertainties and interpretation of structural differences.

Area of Science:

• Structural Biology
• Biophysics
• Crystallography

Background:

• Interpreting protein conformational movements from X-ray crystallography data is challenging.
• Distinguishing genuine functional motions from experimental noise requires objective criteria.
• Previous interpretations of protein coordinate changes may be influenced by unaddressed uncertainties.

Purpose of the Study:

• To establish objective uncertainty thresholds for interpreting protein conformational changes.
• To develop and apply novel methods for classifying and describing protein motions.
• To investigate the impact of crystallization on protein structures.

Main Methods:

• Calculation of distance difference matrices (DDMs) from 1014 pairs of independently determined protein structures.
• Introduction and application of contact distance difference matrices (CDDMs).
• Development and use of a novel simple rotation algorithm for structural analysis.

Main Results:

• Uncertainty thresholds were derived from DDMs, revealing that some functional motions are barely above these thresholds.
• The new methods allow for a more meaningful classification of protein motions into rigid-fragment motions and nonrigid deformations.
• Half of identical molecules within the same crystallographic cell showed coordinate differences comparable to functional movements.

Conclusions:

• Uncertainty thresholds provide objective criteria to differentiate true conformational changes from noise in protein crystallography.
• The applied methods enable a more refined description and classification of protein dynamics.
• Crystallization itself may induce significant protein conformational changes comparable to functional ones.