Domain Fluctuations Enable Catalytic Activity in Phosphoglycerate Kinase?

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The biological function of enzymes is often related to large-scale domain movements. The configuration changes are observed by methods like x-ray crystallography, which give a static image of the protein structure in the crystal confinement. The question is, if these configuration changes are due to the substrate binding or if they are also related to the crystal packing which favors specific configurations. The structure of a protein in solution can deviate from the crystal structure but the protein has also the ability to fluctuate between different configurations. Are these fluctuations important for protein function?Phosphoglycerate kinase (PGK) has a widely open domain structure with a hinge near to the active center between the two domains. The hypothesis of a substrate-induced configuration change, was first proposed by Banks et al. based on the comparison of crystal structures.We have recently investigated the domain dynamics of PGK (1). Structural analysis by small angle neutron scattering revealed that the structure of the holoprotein in solution is more compact as compared to the crystal structure, but would not allow the functionally important phosphoryl transfer between the substrates, if the protein would be static. Brownian large scale domain fluctuations on a timescale of 50 ns was revealed by neutron spin echo spectroscopy. 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 function. The presence of the substrates increases the rigidity, which is deduced from a faster dynamics with smaller amplitude.(1) in press: Inoue et al., Large Domain Fluctuations on 50-ns Timescale Enable Catalytic Activity in Phosphoglycerate Kinase, Biophysical Journal (2010), doi:10.1016/j.bpj.2010.08.017