NMR spectroscopists have developed a method to observe the initial encounter between two proteins before they form a stable complex

Structural NMR spectroscopy has the advantage that it focuses on biomolecules in solution, not frozen in a crystal. However, observing fleeting interactions between molecules in solution requires extremely sophisticated methods. NMR spectroscopists have now developed tools that let them watch the transient encounter between two proteins before a well-defined complex is formed. 

Marius Clore’s team at the National Institutes of Health in Bethesda, Maryland, US, investigated the formation of a complex between a protein called HPr and the N-terminal domain of a bacterial enzyme called enzyme I (EIN). The researchers introduced metal ions at three different, well-defined locations in HPr, and studied the effect of those ions on the NMR spectra of EIN. Previous NMR studies from the same lab had described the stereospecific complex between these two proteins but failed to detect intermediates en route to complex formation. Intermediates appear to involve no more than 10 per cent of the total protein in the sample at any time during complex formation. 

Using the known NMR data of the stable complex to exclude any signals arising from that source, the researchers could calculate a three-dimensional map of the most likely locations of HPr on the surface of the EIN molecule before the two proteins become a stable complex. From these non-specific locations, said the researchers, HPr will eventually find its way ’into a narrow energy funnel that leads directly to the stereospecific complex.’

One biologist contacted by Chemistry World questioned the applicability of the technique, but NMR expert Jochen Balbach from the University of Halle, Germany, was more enthusiastic: ’The concept of encounter complexes during protein-protein association has been discussed for more than 15 years, but high resolution structural data were very difficult to get,’ he said. Clore’s work shows ’various encounter complexes in structural terms, dominated by long-range but non-specific electrostatic interactions. This confirms encounter complexes as key players,’ said Balbach.

Michael Gross

NMR and the 3D world of proteins

Nuclear magnetic resonance spectroscopy is solving the 3D structure of previously inaccessible protein structures, thanks to recent advances in the field. David Bradley reports.

Angling for core proteins in bacterial cells

Bacterium core enzymes have been easily identified, isolated and released