Opening new avenues for advancing nanotechnologies in the medical field and beyond, researchers have successfully replicated and analyzed two natural processes to enhance the timing of molecular communication and functions.
Living organisms have various ways of perceiving and responding to time, such as detecting light and sound in mere microseconds or reacting through pre-defined physiological mechanisms tied to daily sleep cycles, monthly menstrual rhythms, or seasonal shifts.
This capacity to respond across different timeframes is facilitated by molecular switches or nanomachines that operate as precise molecular timers, designed to activate and deactivate according to environmental cues and time.
In a recent study, scientists from Université de Montréal have adeptly recreated and validated two unique mechanisms that can control both the activation and deactivation speeds of nanomachines in living organisms across various timescales.
Their research appears in the Journal of the American Chemical Society. This significant discovery proposes that engineers can leverage natural mechanisms to enhance nanomedicine and other technologies, while also shedding light on the evolution of life.
The door analogy
Biomolecular switches or nanomachines, primarily composed of proteins or nucleic acids, are fundamental components of life’s machinery. They execute thousands of essential roles, including facilitating chemical reactions, transporting molecules, storing energy, and allowing for movement and growth.
But how have these switches evolved to activate over differing timescales? This intriguing question has captivated chemists for decades, and since the groundbreaking studies by Monod-Wyman-Changeux and Koshland-Nemethy-Filmer in the 1960s, two primary mechanisms have generally been accepted as governing biomolecular switch activation.
“Using the analogy of a door helps illustrate these two mechanisms,” explained Alexis Vallée-Bélisle, a chemistry professor at UdeM and lead researcher of the study.
“The closed door symbolizes the inactive state of the switch or nanomachine, while the open door signifies its active state. The interactions between the switch and its activator—be it light or another molecule—determine the type of activation mechanism in play.”
“In the induced-fit mechanism, the activating molecule, likened to a person, turns the handle of the closed door, supplying the energy to open it quickly,” Vallée-Bélisle clarified. “In contrast, the conformational selection mechanism requires the activating molecule to wait for the door to naturally open before it can interact and block it when in the open position.”
While both mechanisms have been observed in numerous proteins, it’s only recently that researchers identified their potential for engineering more effective nanosystems.
Creating a nanodoor with DNA
To uncover the workings behind these two mechanisms, the researchers constructed a simple molecular “door” using DNA. Although DNA is primarily recognized for encoding the genetic instructions of living things, several bioengineers have begun utilizing its straightforward chemistry to create nanoscale objects.
“DNA is a highly flexible and programmable molecule compared to proteins,” stated Dominic Lauzon, an associate researcher in chemistry at UdeM and co-author of the study. “It’s like the building blocks of chemistry that enable us to design whatever we envision at the nanoscale.”
A thousand times faster
Using DNA, the UdeM team developed a 5-nanometer-wide “door” that can be controlled via both mechanisms using a common activating molecule. This setup allowed the researchers to directly compare the two switching mechanisms, testing their design principles and programmability.
The “door handle” (induced-fit) switch activates and deactivates a thousand times faster since the activating molecule supplies the energy necessary for quick opening. On the other hand, the slower switch without a handle (conformational selection) can be tuned to open at much slower rates by simply enhancing the strength of the interactions keeping the door closed.
“We discovered that we can program the activation rates of switches from hours down to seconds just by designing molecular handles,” said Carl Prévost-Tremblay, a graduate biochemistry student and lead author.
“We also believe this capability to control the activation rates of switches and nanomachines could have numerous applications in nanotechnology where specific timing of chemical events is crucial.”
A step towards new drug delivery technology
One area that would gain significantly from developing nanosystems with adjustable activation and deactivation rates is nanomedicine, which focuses on designing drug delivery systems with customizable drug release rates.
This approach could reduce how frequently patients need to take medication, ensuring the drug concentration in their bodies remains at the optimal level throughout treatment.
To demonstrate the high programmability of both mechanisms, the team created and assessed a carrier for an antimalarial drug that can release medication at any designated rate.
“By creating a molecular handle, we developed a carrier that enables quick and immediate drug release with the simple addition of an activating molecule,” said Achille Vigneault, a master’s student in biomedical engineering and co-author of the study. “Additionally, without a handle, we engineered a carrier that offers a slow, continuous drug release following its activation.”
The results also clarify the distinct evolutionary roles and advantages of these two signaling mechanisms, illustrating why certain proteins have developed to activate via one mechanism over the other, according to the researchers.
“For instance, cell receptors needing rapid activation to detect light or odors likely benefit from a fast induced-fit mechanism,” Vallée-Bélisle noted, “while processes that take weeks, such as protease inhibition, are better suited to the slower conformational selection mechanism.”
About this research
“Programming the kinetics of chemical communication: induced fit vs conformational selection,” authored by Carl Prévost-Tremblay, Achille Vigneault, Dominic Lauzon, and Alexis Vallée-Bélisle, was published on December 19, 2024, in the Journal of the American Chemical Society. This work was supported by the National Sciences and Engineering Research Council of Canada, the Canada Research Chairs program, Les Fonds de recherche du Québec — Nature et technologies, and the PROTEO network.
