NIH awarded Albert Einstein College of Medicine of Yeshiva University a five-year, $10 million grant to study how the motion of atoms on both extremely small and long time scales contribute to enzyme function. The research aims to elucidate chemical reactions that are both central to life and become dysfunctional in disease states.
It is well known that atomic motion alters the shape of proteins over relatively broad time scales, from milliseconds to seconds. These motion-induced changes thus affect the speed of enzymatic reactions. Until recently, researchers have lacked the tools to study protein motion on a sub-millisecond time scale, according to the University.
Theoretical and experimental techniques developed at Einstein and at Emory University now allow investigators to watch these chemical reactions from picoseconds to milliseconds. These technologies include nanosecond laser spectroscopies and ultrafast microfluidic mixing, which are coupled with innovative computational analyses.
“Some of our findings to date challenge long-held textbook understanding of enzymatic catalysis,” remarks study leader, Robert Callender, Ph.D., professor of biochemistry at Einstein. In the conventional view, an enzyme combines with a substrate to form what is known as the Michaelis complex, ultimately leading to a new molecule, or the product.
“But it turns out to be more complicated than this,” according to Dr. Callender. “If you look at this process more deeply, you see all these different enzyme-substrate conformations, numbering in the thousands, even hundreds of thousands. Our hypothesis is that not all of these conformations are equally active, just a few actually lead to the product. In addition, the protein body of the enzyme functions more as a chemical machine than a simple organic catalyst. This stands classical enzymology on its head.
“The detailed structure of the enzymatic transition state is a powerful target for drug design, and increased knowledge of how enzymes form this state is fundamental for all catalysts and specifically for designing new classes of drugs,” notes Dr. Callender.
The research program is divided into four projects:
• Energy landscapes encoding function in lactate dehydrogenase (LDH) over broad time scales: LDH is an enzyme that catalyzes the conversion of lactate to pyruvate, an important step in energy production in cells.
• Protein dynamic contributions to transition state formation in purine nucleoside phosphorylase (PNP): PNP is an enzyme that helps to degrade nucleotides and nucleic acids and has emerged as a drug target in a variety of diseases including cancer and autoimmune dysfunction.
• Mapping the energy landscape of catalysis in dihydrofolate reductase (DHFR): DHFR is an enzyme needed for synthesizing DNA, RNA, and protein. It is a target for methotrexate and other DHFR inhibitors used in treating diseases including rheumatoid arthritis and cancer.
• Energy landscapes and motional timescales in enzyme catalysis.