A protein crystal is a highly ordered, three-dimensional lattice of protein molecules in a repeating pattern. While they share the name “crystal” with substances like salt or sugar, protein crystals are different. The molecules are immense and complex, and the weak bonds holding them together are more delicate than the strong ionic bonds in a salt crystal. This makes protein crystals fragile and soft, with a consistency often compared to jelly.
Their value is informational, not aesthetic. This ordered arrangement is the key to understanding a protein’s three-dimensional structure. Proteins are the microscopic machines that drive countless biological processes, and their specific shape dictates their function. Crystallization allows scientists to use specialized techniques to map this shape at an atomic level, providing a blueprint that is otherwise impossible to see.
The Protein Crystallization Process
Growing a protein crystal is a challenge because proteins are large, irregularly shaped, and delicate molecules that do not easily form an ordered lattice. The process requires creating a supersaturated solution, where the protein concentration is pushed beyond its normal solubility limit to encourage the molecules to assemble into an ordered solid. This is a meticulous process of trial and error, as conditions must be controlled to favor crystal growth over disordered precipitation.
A widely used method is vapor diffusion, using a “hanging drop” or “sitting drop” setup. In the hanging drop technique, a droplet of purified protein and a reagent is suspended over a reservoir with a higher concentration of the same reagent. Water vapor slowly leaves the droplet and moves into the reservoir. This gradual dehydration increases the concentration of the protein and reagent in the drop, pushing it toward the supersaturated state needed for crystals to form.
This process is analogous to salt crystals forming from evaporating saltwater, but it is far more sensitive. Scientists must experiment with numerous factors, including the precipitating agent, pH, and temperature, to find the right recipe for a specific protein. The goal is to find conditions where nucleation—the initial formation of a crystal seed—can occur, followed by slow growth as more protein molecules attach to this lattice.
Analyzing the Crystal with X-Ray Diffraction
Once a protein crystal has been grown, the next step is to determine its atomic structure using a technique called X-ray crystallography. The crystal is mounted and placed into a high-intensity beam of X-rays. Unlike a microscope that provides a direct image, this method works by capturing how X-rays scatter, or diffract, as they pass through the ordered lattice of protein molecules.
The crystal acts like a three-dimensional grating, causing the X-rays to diffract into a complex pattern of spots recorded by a detector. This diffraction pattern is not a direct picture of the protein molecule. Instead, it contains detailed information about the arrangement and spacing of the atoms inside the crystal.
Translating this pattern into a model is a computationally intensive process. Software analyzes the positions and intensities of the thousands of diffraction spots. This analysis solves what is known as the “phase problem” to calculate a three-dimensional electron density map. This map reveals the shape of the electron clouds surrounding the atoms, which a crystallographer interprets to build an atom-by-atom model of the protein’s structure.
The Importance of Protein Structures
Determining the three-dimensional structure of a protein is important for understanding its function in health and disease. Because a protein’s shape dictates its interactions, this knowledge allows researchers to understand biological processes at a molecular level, from how enzymes catalyze reactions to how signals are transmitted between cells.
A primary application is in structure-based drug design. By visualizing the shape of a protein’s active site—the region where it binds other molecules—scientists can design drugs that fit into this site like a key into a lock. This approach allows for creating specific inhibitors that block the function of a protein in a virus or bacterium, leading to more effective treatments with fewer side effects.
Understanding a protein’s structure also provides insight into genetic diseases. Many inherited conditions are caused by mutations that alter an amino acid, causing the protein to misfold and lose its function. By comparing the structure of a healthy protein to its mutated form, scientists can understand the molecular basis of the disease and devise strategies to address it.
Crystallization in Microgravity
For some proteins, growing crystals of sufficient size and quality on Earth is extremely difficult. On the ground, gravity interferes with the crystallization process. It causes convection currents in the solution as denser, protein-depleted liquid sinks, disrupting the uniform environment needed for orderly growth. Gravity also leads to sedimentation, where tiny crystals fall out of solution before they can mature.
To overcome these obstacles, scientists use the microgravity environment of space, such as on the International Space Station (ISS). In the absence of gravity, convection and sedimentation are eliminated. This allows protein molecules to assemble into a crystal lattice with fewer imperfections. As a result, crystals grown in space are often larger and more highly ordered than those grown on Earth.
This improved crystal quality has practical benefits. A more ordered crystal diffracts X-rays more cleanly, yielding higher-resolution data. This allows for the determination of a more accurate protein structure. This approach has been valuable for challenging proteins, including those targeted for new drugs to treat diseases like Duchenne Muscular Dystrophy and various cancers.