Chemical Insights into Enzyme Structure and Function

Justin M Miller ^1* Adam Offenbacher ²

• ¹ Middle Tennessee State University, Murfreesboro, United States
• ² East Carolina University, Greenville, North Carolina, United States

The relationship between molecular or biomolecular structure and function remains an active area of investigation within the life sciences. As fields like biotechnology, drug discovery, or genetic engineering push the boundaries of what is possible, advancing our understanding of molecular processes becomes increasingly important. On the other hand, an array of technologies may not even exist without the knowledge that basic science research in these areas has provided. For example, the COVID-19 vaccines would not exist in the absence of the foundational insights provided by research into mRNA biology, synthesis, and related lipid nanoparticle delivery systems.1-12 Another, often overlooked, example is that of restriction enzymes, which were originally studied by researchers seeking to understand bacterial immune systems.13-14 Indeed, the Nobel Prize in Physiology or Medicine was awarded in 1978 to Werner Arber, Daniel Nathans, and Hamilton O. Smith for their discovery of restriction enzymes, which enabled applications to molecular genetics that set the stage for modern biotechnology as we know it today.15 These examples serve to highlight how basic knowledge of chemical and biochemical processes, gleaned from fundamental studies, can enable and inspire scientific applications that seem to be distant from the original goals of a research project. This special issue makes this point a centerpiece by bringing together cutting-edge research that illuminates the complex interplay between enzyme structure, dynamics, and function, viewed through a distinctly chemical lens.With methods ranging from electron paramagnetic resonance (EPR) spectroscopy to in silico high-throughput screening, this special issue is structured to provide a glimpse into approaches presented with the goal of reflecting the multifaceted nature of model enzymology as a field. We hope that by bridging advanced structural and functional studies with the “classic” methods, such as modeling enzyme activity through the methods of Michaelis and Menten, readers will observe how diverse technical methodologies can converge to deepen our understanding of enzyme-catalyzed processes. This special issue features a blend of research and review articles, showcasing how diverse methodologies drive scientific progress while highlighting the importance of drawing insights from past discoveries to move a field forward. Consider the investigation by Xu and colleagues into the catalase activity of KatG, a heme-dependent enzyme.16 The work illustrates the complexity of enzyme regulation by conformational dynamics. An in-depth examination of the interplay between an “Arg Switch” and the oxidizable “proximal Trp” has revealed how conformationally dynamic structural elements can cooperate to maintain efficient hydrogen peroxide degradation. Their findings highlight how subtle structural features can have profound effects on enzyme function and stability – a theme that resonates throughout this special issue.In contrast, Sosa and colleagues highlight how a knowledge of basic chemical details underlying enzyme function can be leveraged to the pursuit of practical applications through their work on ketoreductases.17 Their work made use of computational tools to test 16 enzymes identified as top hits from a screening library of approximately half a million candidate enzymes. The ideal candidate enzyme would serve as a biocatalyst capable of efficient reaction catalysis and producing the desired enantiomeric excess. Their use of computational tools to identify and characterize enzymes capable of synthesizing optically pure compounds demonstrates how a fundamental understanding of structure-function relationships can be leveraged for industrial applications. Their high-resolution structural studies, combined with computational analysis and site-directed mutagenesis, provide insight into how substrate specificity is achieved at the molecular level.The exploration of bifunctional enzymes by Zhu et al. adds another layer to our understanding of structure-function relationships.18 Their review of glutamine-hydrolyzing synthetases demonstrates how nature has evolved elegant solutions for coordinating multiple catalytic activities within a single protein structure. These enzymes, crucial for various biosynthetic pathways, showcase the sophistication of molecular machinery that enables efficient substrate channeling and coupled reactions. Similarly, a review by Richards and Naismith describing C-nucleoside biosynthesis,19 along with the characterization of dual-specific phosphatases by Imhoff and colleagues,20 provides further emphasis of how diverse analytical techniques can be combined to unravel complex enzymatic mechanisms. These works demonstrate the power of integrating structural, spectroscopic, and chemical biology approaches to understand enzyme function.Looking ahead, several key challenges and opportunities emerge from this collection that point to where enzymology is heading as a field. The dynamic nature of enzymes, including conformational changes and protein dynamics, is recognized as integral to their function, which demands attention to mechanisms of conformational regulation, catalysis, and substrate specificity. The integration of computational and experimental approaches is becoming ever more powerful, enabling both prediction and validation of structure-function relationships. Technological advances—such as advanced structural techniques, sophisticated spectroscopic methods, and powerful computational tools—have unveiled unprecedented insights into enzyme mechanism and function, pushing the boundaries of our understanding. The papers in this special issue document significant progress while highlighting the exciting future directions of enzyme engineering, drug design, and fundamental biological catalysis. Serving as both a milestone and a springboard, this collection emphasizes the critical role of new technologies and approaches in driving forward our understanding of these molecular machines.