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In earlier work, a team led by U-M's Nils Walter,
associate professor of chemistry, found that modifications made
anywhere on the ribozyme molecule - even far from the site where the
chemical reaction occurs - affect the rates at which the enzyme
changes conformation and catalyzes the reaction. Something similar had
been seen in protein enzymes, but never before in RNA enzymes.
The earlier finding, published in PNAS two years
ago, suggested that information about changes in distant parts of the
ribozyme travels through some sort of network to the core of the
molecule, where chemical reactions take place. The latest work shows
that water molecules trapped inside the ribozyme's core are essential
components of that network.
The network acts like a jostling crowd at a
cocktail party, where hydrogen bonds - weak, electrostatic attractions
between molecules or parts of molecules - take the place of handshakes.
Water molecules trapped in ribozymes can form hydrogen bonds with
other water molecules or with parts of the ribozyme molecule.
"The way we interpret the data is that in ribozymes,
a chemical modification introduced at one place changes the local
structure slightly," Walter said. The building blocks making up the
ribozyme wiggle into different positions and in the process must let
go of some hydrogen bonds and form others, just as partygoers shift
position and engage with other guests.
"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 processes and to act as a sort of sensor -
detecting cellular signals and carrying out appropriate reactions in
response. In fact, there are many more so-called non-protein coding
RNAs in the cell (around 100,000 in humans), which are not translated
into protein, than there are protein coding messenger RNAs (about
25,000), making these vast numbers of RNA molecules central players in
our bodies.
Work is also underway in academic and industrial
labs around the world to engineer RNA for medical purposes. The
engineered molecules, called RNA aptamers, are selected for their
ability to bind to particular proteins involved in certain diseases,
blocking key steps in the disease process.
"It's likely that water helps mediate the binding
between these aptamers and their disease-causing protein targets,
ultimately keeping the protein away from where it can wreak havoc,"
Walter said. "So the fundamental understanding we are gaining of the
role of water in RNA almost certainly will have relevance in the
treatment or prevention of disease." |
