Proteins are dynamic molecular machines, undergoing motions on a wide range of time scales. Although there is considerable evidence both from theory and experiment that many enzymes are inherently flexible, fundamental questions about the relationship between protein dynamics and enzyme catalysis remain unanswered. Are protein motions coupled to the chemical transformation, or are they involved primarily in controlling the flux of substrate, products, or cofactors? What role do protein motion play in progression from the preorganized ground state structure to an active site configuration that facilitates the chemical reaction? What is the time scale of active site conformational changes required for catalysis? How is the energy landscape of the enzyme modulated during the catalytic cycle and how is it shaped during evolution? Are there species-related differences in protein dynamics and available conformational substates that might potentially be exploited for development of highly selective drugs that better discriminate between enzymes from humans and pathogens? These issues will be addressed using state-of-the-art NMR methods and multi-conformer room temperature X-ray crystallography to elucidate the dynamic properties of an exceptionally well- characterized enzyme, dihydrofolate reductase (DHFR). DHFR is the target for anti-folate drugs such as the anticancer agent methotrexate and the antibacterials trimethoprim and iclaprim. The proposed research will lead to new understanding of the intrinsic molecular dynamics of this important enzyme and how its motions are modulated by interaction with substrate, cofactor, and products at various stages in the catalytic cycle. It will also provide novel insights into the role of evolution in shaping the energy landscapes of E. coli and human DHFR and will advance our understanding of the relationship between protein dynamics and catalytic function.

Public Health Relevance

The proposed research will address the role of protein motions in controlling the catalytic function of the enzyme dihydrofolate reductase. This enzyme is of major clinical importance as a target for anticancer agents, anti-infectives, and anti-malaril drugs. The research will provide novel information on species-related differences in protein structure and dynamics that might potentially be exploited for development of highly selective drugs that better discriminate between enzymes from humans and pathogens to decrease undesirable side effects.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Macromolecular Structure and Function E Study Section (MSFE)
Program Officer
Wehrle, Janna P
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Scripps Research Institute
La Jolla
United States
Zip Code
Oyen, David; Fenwick, R Bryn; Aoto, Phillip C et al. (2017) Defining the Structural Basis for Allosteric Product Release from E. coli Dihydrofolate Reductase Using NMR Relaxation Dispersion. J Am Chem Soc 139:11233-11240
Fenwick, R Bryn; Dyson, H Jane (2016) Classic Analysis of Biopolymer Dynamics Is Model Free. Biophys J 110:3-6
Aoto, Phillip C; Martin, Bryan T; Wright, Peter E (2016) NMR Characterization of Information Flow and Allosteric Communities in the MAP Kinase p38?. Sci Rep 6:28655
Fenwick, R Bryn; Oyen, David; Wright, Peter E (2016) Multi-probe relaxation dispersion measurements increase sensitivity to protein dynamics. Phys Chem Chem Phys 18:5789-98
Oyen, David; Fenwick, R Bryn; Stanfield, Robyn L et al. (2015) Cofactor-Mediated Conformational Dynamics Promote Product Release From Escherichia coli Dihydrofolate Reductase via an Allosteric Pathway. J Am Chem Soc 137:9459-68
Tuttle, Lisa M; Dyson, H Jane; Wright, Peter E (2014) Side chain conformational averaging in human dihydrofolate reductase. Biochemistry 53:1134-45
Aoto, Phillip C; Fenwick, R Bryn; Kroon, Gerard J A et al. (2014) Accurate scoring of non-uniform sampling schemes for quantitative NMR. J Magn Reson 246:31-5
Fenwick, R Bryn; van den Bedem, Henry; Fraser, James S et al. (2014) Integrated description of protein dynamics from room-temperature X-ray crystallography and NMR. Proc Natl Acad Sci U S A 111:E445-54
Boehr, David D; Schnell, Jason R; McElheny, Dan et al. (2013) A distal mutation perturbs dynamic amino acid networks in dihydrofolate reductase. Biochemistry 52:4605-19
van den Bedem, Henry; Bhabha, Gira; Yang, Kun et al. (2013) Automated identification of functional dynamic contact networks from X-ray crystallography. Nat Methods 10:896-902

Showing the most recent 10 out of 20 publications