Large Domain Fluctuations on 50-ns Timescale Enable Catalytic Activity in Phosphoglycerate Kinase

• Published in: Biophysical journal Vol. 99; no. 7; pp. 2309 - 2317
• Main Authors: Inoue, R., Biehl, R., Rosenkranz, T., Fitter, J., Monkenbusch, M., Radulescu, A., Farago, B., Richter, D.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 06.10.2010; Biophysical Society; The Biophysical Society
• Subjects: Biocatalysis; Biophysics; Construction; Crystal structure; Diffusion; Displacement; Dynamics; Echo surveys; Enzymes; Fluctuation; Kinases; Kinetics; Models, Molecular; Neutron Diffraction; Phosphoglycerate Kinase - chemistry; Phosphoglycerate Kinase - metabolism; Phosphorylation; Protein; Protein Structure, Secondary; Protein Structure, Tertiary; Proteins; Saccharomyces cerevisiae - enzymology; Scattering, Small Angle; Spectroscopy; Spectrum analysis; Structure-Activity Relationship; Time Factors
• ISSN: 0006-3495; 1542-0086
• DOI: 10.1016/j.bpj.2010.08.017

Large-scale domain motions of enzymes are often essential for their biological function. Phosphoglycerate kinase has a wide open domain structure with a hinge near the active center between the two domains. Applying neutron spin echo spectroscopy and small-angle neutron scattering we have investigated the internal domain dynamics. Structural analysis reveals that the holoprotein in solution seems to be more compact compared to the crystal structure but would not allow the functionally important phosphoryl transfer between the substrates if the protein were static. Brownian large-scale domain fluctuation dynamics on a timescale of 50 ns was revealed by neutron spin echo spectroscopy. The dynamics observed was compared to the displacement patterns of low-frequency normal modes. The displacements along the normal-mode coordinates describe our experimental results reasonably well. In particular, the domain movements facilitate a close encounter of the key residues in the active center to build the active configuration. The observed dynamics shows that the protein has the flexibility to allow fluctuations and displacements that seem to enable the function of the protein. Moreover, the presence of the substrates increases the rigidity, which is deduced from a faster dynamics with smaller amplitude.