Protein flexibility: coordinate uncertainties and interpretation of structural differences

Protein flexibility: coordinate uncertainties and interpretation of structural differences.

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 exp...

Characterization and Prediction of Protein Flexibility Based on Structural Alphabets

Motivation. To assist efforts in determining and exploring the functional properties of proteins, it is desirable to characterize and predict protein flexibilities. Results. In this study, the conformational entropy is used as an indicator of the protein flexibility. We first explore whether the conformational change can capture the protein flexibility. The well-defined decoy structures are con...

Differences between CusA and AcrB Crystallisation Highlighted by Protein Flexibility

BACKGROUND Until very recently, AcrB was the only Resistance Nodulation and cell Division transporter for which the structure has been elucidated. Towards a general understanding of this protein family, CusA and AcrB were compared. METHODOLOGY/PRINCIPAL FINDINGS In dodecylmaltoside, AcrB crystallised in many different conditions, while CusA does not. This could be due to the difference in dyn...

Approaching structural flexibility with flexibility

Three-dimensional electron microscopy (3D-EM) is a powerful technology for imaging macromolecular complexes. Through a process known as singleparticle reconstruction, tens of thousands of separate images of a complex of interest are used to arrive at a single resolved structure. Although this method works sufficiently well for rigid macromolecular complexes, conformationally flexible complexes ...

Operational Flexibility Responses to Environmental Uncertainties