Tinkering with the clockwork of life

Living organisms monitor time and respond to it in multiple ways in extremely well-timed ways. On the one hand, for example, they are able to detect and react to light and sound in a few microseconds while, on the other hand, the detection of certain signals causes physiological responses programmed over a much longer time scale. We can think here of the signals that trigger the daily sleep cycle, the monthly menstrual cycle or responses to seasonal changes.

This ability to respond at different time scales is made possible by molecular switches – or nanomachines – that act as timers programmed for functions to turn on and off in response to the environment and time.

In a study published in the Journal of the American Chemical Society On December 19, scientists from the University of Montreal successfully recreated and validated two distinct biochemical mechanisms for programming the activation and deactivation rates of nanomachines in living organisms over several time scales.

Their results could harness these natural processes to improve nanomedicine and other technologies while helping to explain the evolution of life.

The door analogy

Biomolecular switches or nanomachines, generally composed of proteins or nucleic acids, are the cogs in the machinery of life. They perform thousands of key functions, including chemical reactions, transporting molecules, storing energy, and facilitating movement and growth.

But how did these switches evolve to activate on different time scales? This question has fascinated biochemists for a long time. Following the pioneering Monod-Wyman-Changeux and Koshland-Nemethy-Filmer models developed in the 1960s, two distinct mechanisms have been proposed to explain how the activation of biomolecular switches occurs.

“The analogy of a door is practical to illustrate these two mechanisms,” says Alexis Vallée-Bélisle, professor of chemistry at UdeM and principal investigator of this study. The closed door represents the inactive structure of the switch or nanomachine, while the open door represents its active structure. The big difference between these two mechanisms is the presence of a handle on the door! In the mechanism of conformational selection, the activator molecule must wait for the gate to open spontaneously before grasping it in its open form. In contrast, in the induced adjustment mechanism, the activator molecule interacts with the handle and its interaction forces the door to open.

Building a “nanogate” with DNA

To unravel the mystery of these mechanisms, researchers recreated a simple molecular “gate” using DNA. Although primarily known for its role in genetic coding, DNA is also harnessed by bioengineers to make nanoscale objects thanks to its programmable and versatile chemistry.

“Compared to proteins, DNA is like LEGO blocks that allow us to build what we imagine at the nanoscale,” says Dominic Lauzon, associate researcher and co-author of the study.

Using this approach, the researchers designed a five-nanometer gate that can be opened from the two distinct biochemical mechanisms, allowing them to directly compare their effectiveness and how to program them. For example, the induced adjustment mechanism – thanks to the handle – allows the door to open and close up to 1000 times faster than the conformational selection mechanism, i.e. minutes versus days.

The research team also showed that these mechanisms can be used to program nanotechnology systems in various fields, notably for the controlled release of drugs. Thus, “by designing a molecular handle, we have created a nanomachine allowing rapid and immediate release of a drug by the simple addition of an activator molecule,” indicates Achille Vigneault, master’s student in biomedical engineering at UdeM and co-author. of the study. And in the absence of a handle, we also designed a programmable nanomachine offering a slower and continuous release of the drug after its activation.

These results demystify the distinct evolutionary roles and advantages of the two signaling mechanisms and explain why certain proteins have evolved to be activated by one mechanism rather than another, the researchers said.

“Let’s take the cellular receptors that make it possible to detect light or perceive odors: they probably benefit from a rapid induced adjustment mechanism,” emphasizes Alexis Vallée-Bélisle. In contrast, processes that extend over several hours, such as daily cycles, should benefit from the slower mechanism of conformational selection.”