"As a consequence, their hydrogen bonding partners---some of which are water molecules---also rearrange. Then their hydrogen bonding partners also rearrange, creating a domino effect, where a local modification spreads throughout the molecule and modifies the structure elsewhere, even at quite a distance," Walter said. Water facilitates the process by increasing the number of hydrogen bonds and making the ribozyme behave as an interconnected whole.
Walter and coworkers also found evidence that water is directly involved in catalyzing reactions in the ribozyme's core, another previously unknown role. The research team explored the new roles of water molecules using a combination of computational simulations and a technique called single-molecule fluorescence resonance energy transfer (FRET), which allowed the researchers to directly observe and measure how quickly the ribozyme switched forms and how the rates changed when various parts of the molecule were altered.
The situation in ribozymes contrasts with what happens in protein enzymes, which repel water from their cores and rely on direct contact, rather than a network of hydrogen bonds, to communicate structural changes from one part of the molecule to another.
So far, the researchers have focused on one particular ribozyme, but Walter predicts the findings will apply to other RNAs. If so, those findings should be of great interest to scientists who are learning more all the time about the diverse roles of RNA. Once thought to be only a passive carrier of encoded genetic information, RNA is now known to regulate gene expression and other important cellular proces
Source:University of Michigan