Protein as a Nano-Spring
RNA degradation is essential for gene regulation, and performed by many different classes of ribo-nucleases. It is a complex process involved in multiple pathways since RNA tends to form numerous orders of structures. A class of ribonuclease is able to carry out highly complex mechanical tasks at the processive and synchronized manner. Rrp44 is a 3’ to 5’ exonuclease that digests RNA strand in single nucleotide increments and also unwinds duplex RNA molecules to continuously digest structural RNA in yeast and human. Recently researchers at the Center for the Physics of Living Cells examined how Rrp44 couple its RNA degradation activity to unwinding (Science, 336, 1726-9, 2012). Using single molecule FRET assay, the researchers discovered a surprising mechanism of elastic coupling between RNA degradation and unwinding. Unwinding occurred in about 4 bp steps, not single base pair steps, even though degradation must occur in single nt steps. To coordinate both degradation and unwinding reactions, protein/RNA complex must accumulate elastic energy during several steps of single nt degradation which is relieved through simultaneous unzipping of several basepairs. Biologically, such a mechanism would allow the enzyme to overcome barriers that are too strong to overcome using energy from one nucleotide hydrolysis alone. Thus the enzyme here functions as a chemo-mechanical machine that converts and combines a series of chemical energy releases from hydrolysis of the RNA chain into an elastic energy reserve for the unwinding reaction. From the viewpoint of proteins as ‘nanomachines’, the data support the notion that proteins can behave like ‘springs’, a component we often see in man-made machines.