Enzymes are the workhorses of biology. Without them, the chemical reactions that make each organism tick would proceed at a snail鈥檚 pace. Yet despite their crucial function, many secrets of how they work are still emerging, and now a computer simulation suggests they may have a hitherto unknown way of gathering energy that can then be used to help speed a reaction on its way.
Enzymes usually acquire the energy needed to catalyse a reaction between two substrates by splitting energy-rich molecules such as adenosine triphosphate (ATP). However, physicist Brice Jaunico of the 脡cole Normale Sup茅rieure in Lyon, France, and colleagues suspected that they may also acquire some energy another way.
They created a computer simulation of the vibrational dynamics of enzymes in which they treated each enzyme as a network of interacting parts. They then explored how energy that is pumped into this system 鈥� through a collision with another molecule, for example 鈥� causes the enzyme to deform and vibrate.
Advertisement
From what we understand of the structure of enzymes, such energy should quickly spread, diffusing as a wave of vibration through the whole structure before draining away into the surrounding environment. Yet in their simulations, Juanico and his team found otherwise. In many enzymes, the energy often remained localised, locked into the vigorous motion of just a few parts of each molecule.
Such localised vibrations are called 鈥渂reathers鈥�, and are known to exist in ordered crystalline materials, where they can keep energy locked up for long periods of time. 鈥淚t was a surprise to find breathers in the complex structures of enzymes,鈥� says Yves-Henri Sanejouand, one of the Lyon team. The researchers suggest that the breathers may lock in energy within an enzyme until it is needed to help catalyse a reaction (Physical Review Letters, ).
The breathers occur in the parts of the enzyme molecules that are most likely to retain their shape. From data on more than 800 enzymes, the team found that these rigid regions also tend to be close to the sites where biologists know specific molecules bind before they react. From this they infer that breathers may help to gather energy from the random collisions of an enzyme with other molecules, and focus it precisely where it can help reactions along. 鈥淭hey may play an important role in enzyme function,鈥� says Juanico.
鈥淟ocalised vibrations may help to gather energy from the random collisions of an enzyme with other molecules, and focus it鈥�
Michel Peyrard, a colleague of the researchers at the 脡cole Normale Sup茅rieure, agrees, but also cautions that the identified link between breathers and catalysis could be less significant than it seems. After all, catalytic sites are more rigid than normal, as they need to have a fixed shape in order to bind to the molecules whose reactions they catalyse.
The researchers hope further simulations and experiments can help to pin down what functional role, if any, breathers might play. 鈥淚t could prove to be a coincidence,鈥� says Sanejouand, 鈥渂ut it might not be.鈥�
