Whither Enzymology in the Twenty First Century?

Abstract

This “grand challenge” article marks the creation of a new specialty section shared between Frontiers in Chemistry and Frontiers in Molecular Biology that is dedicated to enzymology and protein chemistry. My aim in this article is to provide a personal perspective on the challenges and opportunities for field of enzymology and the directions in which it could and should move in the coming years. I hope this will challenge the reader to think more deeply about this discipline and its broader impact on science. But before gazing into the future, it is worthwhile briefly reviewing how our field has evolved until now, as it is this perspective that frames our outlook. Whither Enzymology? was the title of a symposium held in 1990 to honor the late Jeremy Knowles on the occasion of his Sixtieth birthday (Raines, 2008). Knowles was in the vanguard of a pioneering group of enzymologists who first employed the tools of physical organic chemistry to study enzyme reactions. In the 1970's his group was the first to determine the full set of elementary rate constants defining the free energy profile for an enzyme-catalyzed reaction—that of triose phosphate isomerase (Albery and Knowles, 1976). This information, put together with the crystal structure for this enzyme, allowed us to understand enzyme catalysis with the kind of precision previously only possible for simple organic molecules. Subsequently, his lab was among the first to use site-specific mutagenesis to make precisely defined changes to enzyme active sites, which combined with detailed measurements of their effect on catalysis, allowed the relationships between enzyme structure and mechanism to be elucidated. Studies such as these blew away the “fluffy clouds” obscuring the view of earlier generations of enzymologists, revealing enzymes to be exquisitely evolved, highly complex and incredibly efficient organic catalysts, but nevertheless subject to, and understood through, the basic principles of chemistry—in Knowles' words: “not different, just better” (Knowles, 1991). This view has shaped enzymology for the past 25 years, and by extension our view of cellular biology. It directly underpins the burgeoning discipline of synthetic biology, a field that involves tinkering with enzymes on a scale unimaginable in Knowles' era. The tools available to enzymologists have advanced immeasurably in the last 25 years, resulting in a paradigm shift in our approach to studying them. Not least, much of the drudgery (and perhaps also some of the fun!) of obtaining enzymes for study has been removed and the accessibility of enzymes has expanded enormously. The advent of genomic sequencing, combined with cheap, commercially available gene synthesis and protein affinity tags, allows one to select essentially any enzyme for study and produce large quantities of pure protein with minimal effort. What would once have taken many person years to accomplish can now be achieved in a few days. (Although some classes of proteins, e.g., integral membrane proteins still remain challenging to express.) Advances in structural biology mean that determining the 3-D structure of most enzymes, if not trivial, is now routine; indeed, thanks to structural proteomics initiatives, the structure is increasingly the first information to emerge for a new enzyme. Moreover, techniques for studying enzymes have become increasingly powerful: instrumentation more sensitive (for some techniques to the level of single molecules) and data analysis more sophisticated and rapid due to exponential increases in computing power. With such powerful tools and so many enzymes to explore, it seems reasonable some 25+ years on from Knowles' apotheosis, once again to pose the question: whither enzymology? In attempting to answer this question, I propose the three “grand challenges” discussed below. The first two I have chosen because they fundamentally challenge our understanding of enzyme catalysis. The first challenge is to predict enzyme catalytic activity from structure and dynamic information; the second challenge to design enzymes from scratch that approach the activity of naturally evolved enzymes. The third challenges focuses on expanding the frontiers of enzymology by discovering new enzymes that catalyze new reactions.