Defining the Chemical Space of Nature's Tiny Machines

Enzymes are nature's sophisticated machines. These molecular entities perform the chemical work that keeps cells alive: cutting molecules apart, fusing them together, or reshaping them into new forms. Over billions of years of evolution, enzymes diversified into thousands of specialized workers, each precisely shaped to perform a specific task.

Like machines on an assembly line, each enzyme is programmed to do one job, over and over, with remarkable precision and robustness. At the heart of each enzyme lies an active site, the robotic arm that makes contact with the raw material and performs the actual work. These active sites carry out the basic functions of molecular manufacturing.

Enzymes are enormously useful, in medicine, industry, and environmental applications. But they are complex molecules, difficult to design from scratch and expensive to produce. They are also fragile, often losing their function under conditions of high temperature, acidity, or salinity. In a new ERC-funded research project, Prof. Ehud Gazit of the Shmunis School of Biomedicine and Cancer Research at Tel Aviv University aims to overcome these limitations by designing simple molecular structures that mimic the catalytic activity of enzyme active sites, using inexpensive, safe, and robust building blocks.

From Disease Debris to Functional Structures

For decades, amyloids were viewed primarily as cellular debris - misfolded proteins repeatedly clumping together in repetitive structures in diseases like Alzheimer's and Parkinson's. But this picture has changed dramatically. Scientists now recognize that amyloid-like structures are far more organized, widespread and versatile than previously thought.

These organized molecular assemblies can form not only from proteins, but from many types of metabolites, the building blocks, fuels, waste products and signaling molecules of cellular chemistry. Single amino acids, small peptides, nucleotide bases, and even sugars can stack into the characteristic fibrous structures. Most remarkably, recent research reveals that amyloids, like enzymes, can have active sites that perform catalytic functions - cutting, building, and transforming molecules.
 

"It appears that the amyloid structure is a basic, minimal free energy arrangement, a preferred physical organization of various biomolecules," says Prof. Ehud Gazit. "We've found that these structures can be created from amino acids, metabolites, and even from starch, closing a loop that goes back to the very naming of amyloids 170 years ago."

Mapping the Chemical Space of Molecular Catalysts

In his new ERC-funded project, Gazit plans to systematically test combinations of the major components that form amyloid-like structures with catalytic activity. The goal: to map how different combinations give these molecular machines different capabilities.

"Natural enzymes, despite their enormous diversity, are built according to the same basic design principles," Gazit explains. "We want to know: are there other design concepts for molecular robotic arms that evolution never invented? And can we use these principles to create new, useful catalysts?"

The research could enable the production of inexpensive, environmentally friendly, and safe active substances for many applications. The project focuses on environmental challenges - CO₂ fixation and water purification by breaking down organic pollutants. The metabolite building blocks are ideal for such applications: they are abundant, inexpensive, and because they are natural components of living systems, they are safe for organisms and ecosystems.

The Architecture of Active Sites

The active sites of most enzymes share a common architecture: typically three amino acids forming a pocket that holds a metal ion. The metal ion serves two critical functions. First, because it carries a positive charge, it can attract and grip negatively charged atoms, positioning substrate molecules precisely for the reaction. Second, because metals have a unique ability to shuttle electrons - toggling between different charge states - they can drive chemical transformations that would otherwise require extreme conditions.

Gazit's project will screen all combinations of the 20 amino acids, 4 nucleotide bases, and 9 metal ions found in natural metalloenzymes - close to 100,000 combinations in total.

From Screening to Understanding

Using laboratory robotics and machine vision, the team will screen these combinations for catalytic activity. Structures that show promise will be studied further using X-ray crystallography, a technique that reveals molecular architecture by analyzing how crystals scatter X-ray beams, and computational quantum chemistry methods that model the behavior of electrons during chemical reactions.

"The screening tells us what works," says Gazit. "The structural and computational analysis tells us why it works. That understanding is what allows us to design even better catalysts."

 

Beyond What Evolution Found

The effort to map this vast chemical space could reveal fundamental insights about life and its possibilities. In nature, protein enzymes are structured according to consistent design principles refined over billions of years of evolution. But evolution is a tinkerer, not an engineer. It can only build on what already exists.
 

"Evolution discovered certain solutions and stuck with them," Gazit notes. "Our systematic exploration might reveal alternative design concepts for molecular catalysis that are chemically viable but were never discovered by natural selection - paths not taken."

Such discoveries could also illuminate the origins of life itself. On the young Earth, simple molecules began forming structures with rudimentary functions - structures that eventually developed into the complex machinery of living cells. "Some of these primordial molecules formed right here, and some arrived from other solar systems on meteorites," says Gazit. "Understanding what kinds of catalytic structures can self-assemble from simple building blocks and also providing compartmentalized space gives us a window into how life might have bootstrapped itself."