Learning from the "Shape" of Proteins: An Introduction to Structural Biochemistry

Norifumi Muraki (Associate Professor, Department of Chemistry)

We acquire a great deal of information from "shapes." When we see a bird flying, even one we have never seen before, we can identify it as a bird, not a butterfly or a bat. A watchmaker determines from its "shape" whether a mechanism will keep time accurately, and a blade sharpener judges the quality of a blade from the "shape" of its edge. The amount of information conveyed by "shapes" is immense, and it is just as important in the world of chemistry.

Structural biochemistry, my area of expertise, is a field of study dedicated to understanding the function of proteins from their "shape." Proteins are macromolecules created by the polymerization of twenty types of amino acids, each with different properties such as hydrophobic, hydrophilic, acidic, basic, and aromatic. Depending on the properties of these constituent amino acids, a protein folds into an energetically stable conformation, forming a specific three-dimensional structure. It is by forming these three-dimensional structures that proteins perform their various functions. By elucidating the three-dimensional structure of a protein, we can understand how it works.

I have intentionally used the term "structural biochemistry" here, rather than the more familiar "structural biology," because my aim is to explain the structure and function of proteins using chemistry. While there are numerous methods for examining protein structures, explaining them through chemistry requires determining the structure at a resolution where individual atoms are distinguishable (atomic resolution). In pursuit of atomic resolution, I conduct my research using X-ray crystallography and cryo-electron microscopy single-particle analysis, a technique that has seen remarkable advancements in recent years.

Here, as an example of research in structural biochemistry, I present the crystal structure of an enzyme called HypX, which I determined (Figure 1). HypX is a carbon monoxide synthase found in some bacteria. The synthesis of carbon monoxide within cells is not at all uncommon and even occurs in human cells. However, all previously known carbon monoxide biosynthesis reactions involved metals, such as iron. Although it was suggested that HypX might also involve a metal, a search for a metal's electron cloud within the obtained electron density map (the electron cloud derived from X-ray crystal structure analysis) yielded no results. Instead, a clear electron density for a small molecule was observed within a cavity formed inside the protein (see magnified view in Figure 1). This electron density matched the structure of coenzyme A. Using coenzyme A as a starting point, we conducted further experiments, including molecular dynamics simulations, and proposed a novel mechanism for carbon monoxide biosynthesis—the first in a biological reaction to not involve a metal, but rather coenzyme A.

Although the research introduced here may not lead to immediate applications, structural biochemistry techniques are applied in various fields, including drug discovery and biocatalyst development. The anti-influenza drug Tamiflu was developed using structure-based drug design (SBDD) (Figure 2). More recently, cryo-electron microscopy single-particle analysis has been used in the development of vaccines for COVID-19.

Structural biochemistry indispensably involves collaboration with experts not only in chemistry but also in life sciences, computational science, medical sciences, pharmacology, and even synchrotron radiation science and microscopy. Furthermore, AI-powered structure prediction and design using tools like AlphaFold2 are becoming more prevalent. While it is a highly specialized field, it is also an open one, and I hope this has sparked your interest.