Insights into protein flexibility: The relationship between normal modes and conformational change upon protein-protein docking.
Understanding protein interactions has broad implications for the mechanism of recognition, protein design, and assigning putative functions to uncharacterized proteins. Studying protein flexibility is a key component in the challenge of describing protein interactions. In this work, we characterize the observed conformational change for a set of 20 proteins that undergo large conformational change upon association (>2 A Calpha RMSD) and ask what features of the motion are successfully reproduced by the normal modes of the system. We demonstrate that normal modes can be used to identify mobile regions and, in some proteins, to reproduce the direction of conformational change. In 35% of the proteins studied, a single low-frequency normal mode was found that describes well the direction of the observed conformational change. Finally, we find that for a set of 134 proteins from a docking benchmark that the characteristic frequencies of normal modes can be used to predict reliably the extent of observed conformational change. We discuss the implications of the results for the mechanics of protein recognition.
Dobbins
Sara E
SE
Structural Bioinformatics Group, Division of Molecular Biosciences, Imperial College London, London SW7 2AY, United Kingdom.
Lesk
Victor I
VI
Sternberg
Michael J E
MJ
D019295:Computational Biology / Q000379:methods; D030562:Databases, Protein; D004926:Escherichia coli / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000737:chemistry; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D015233:Models, Statistical; D008968:Molecular Conformation; D009991:Oscillometry / Q000379:methods; D033903:Periplasmic Proteins / Q000737:chemistry; D018583:Pliability; D011485:Protein Binding; D011487:Protein Conformation; D025941:Protein Interaction Mapping; D011506:Proteins / Q000737:chemistry
C039076:Eco protein, E coli; D029968:Escherichia coli Proteins; D033903:Periplasmic Proteins; D011506:Proteins