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Research: protein dynamics, allostery, NMR spectroscopy, thymidylate synthase, protein biophyics

Professor of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy

Joint Appointment in Biochemistry and Biophysics

(PhD – PhD – UC Berkeley)

Accepting Rotation Students


Structural Biophysics and Protein NMR Spectroscopy

Nearly all biological processes are driven by the same fundamental event: protein conformational changes. The mechanics that govern how proteins “morph” their three-dimensional structures into alternative conformations need to be understood in order to understand the biochemical basis of protein function. Our research is aimed at atomic resolution characterizations of the structural and dynamic properties of proteins and their interactions with other proteins, ligands, and small molecule drugs. Towards this goal, we are making extensive use of heteronuclear NMR spectroscopy and other experimental and theoretical tools. NMR spectroscopy is ideal for our studies, as hundreds – even thousands – of structural and motional “spin probes” are uniformly distributed throughout any given protein. We have a general interest in the role of dynamics in protein function and allostery.

Research Projects

Enzyme Dynamics and Allostery – Thymidylate Synthase

We are particularly interested in how protein dynamics facilitates enzyme catalysis and allosteric communication. To maximize our understanding of these phenomena, we study multiple systems with the idea that different proteins may use different strategies for achieving catalysis and/or allostery. Most recently, we have been studying the 62 kD dimeric enzyme thymidylate synthase (or “TS”). This enzyme is metabolically critical, performing conversion of uridine monophosphate to thymidine monophosphate that is needed for DNA replication. TS is more complex than many of the enzymes studied to date by NMR, as it has a multi-state reaction coordinate linking substrates and products. This affords an opportunity to track how the dynamics throughout TS change as the enzyme populates different intermediate steps in catalysis. In addition to this interesting reaction mechanism, TS is known to be “half the sites reactive”, meaning that catalytic activity in one subunit imparts non-reactivity to the other subunit. This is essentially a form of high negative cooperativity. We are using novel NMR approaches to study cooperative effects that traverse the dimer interface. In summary, TS is a fascinating, large enzyme that it interesting from both the perspective of catalysis and allostery.

Insights into allosteric mechanisms: CheY and PDZ domains

Allostery and the role of dynamics can also be studied in smaller, even monomeric proteins. This is highlighted by comparing the different strategies of two small allosteric proteins: Chemotaxis protein Y (CheY), and the third PDZ domain from PSD-95 (PDZ3). CheY, a so-called response regulator receiver domain, is the master regulatory switch for reversing the direction of the E. coli flagellum, and it undergoes a classical allosteric conformational change upon phosphorylation of an aspartate side chain. NMR studies from our lab and others indicate these proteins dynamically switch between inactive and active conformations on the microsecond-millisecond timescale, but that the actual switching mechanism involves additional states yet to be characterized (see McDonald et al., Structure, 2012, 20, 1363). In contrast to CheY, PDZ3 exhibits allosteric behavior utilizing a different kind of dynamics. From analysis of methyl spin relaxation rates, PDZ3 modulates its binding affinity to its interacting protein using an auxiliary helix, which controls the overall level of side-chain dynamics on the picosecond-nanosecond timescale. This alters the overall entropy change upon binding PDZ3’s interacting protein and is an example of “dynamic allostery”.

Dynamics of small molecule (or drug) binding

Many proteins serve as drug receptors. In such cases the dynamics may contribute to drug binding affinity or residence times, both of which are important metrics for efficacious drugs. From our NMR studies on dihydrofolate reductase (DHFR), we have observed that conformational dynamics can correlate with inhibitor dissociation rates, and we have even observed “dynamic ligands” that rapidly switch their conformations while bound to the protein. We remain interested in this general area.

NMR and other methods

How do we characterize protein dynamics? Our preferred method is heteronuclear NMR spectroscopy, which is uniquely suited to study both structure and dynamics in proteins and other biological macromolecules. A major advantage of NMR is that spectroscopic probes are distributed uniformly throughout the biomolecule, such as NH or CH atom pairs, providing large amounts of molecular information. To gain information on protein dynamics, NMR spin relaxation is highly sensitive to molecular motion over a range of timescales. We look at the relaxation properties of 15N, 13C, 1H, and 2H spins located throughout the protein scaffold, and interpret these in terms of amplitudes and timescales of individual bond vectors. Slower motions on the microsecond-millisecond timescale can be detected to yield site-specific kinetic, thermodynamic, and structural information on the switching between discrete conformational states. In many cases, these NMR-relaxation dynamics are used to complement other structural data from X-ray crystallography, or thermodynamic and kinetic biophysical measurements using methods such as fluorescence spectroscopy, calorimetry, amide hydrogen exchange, and molecular dynamics simulations.

REPRESENTATIVE PUBLICATIONS PubMed (click for Full Publication List)

Lee Receives NIH Grant for Collaboration with Singleton

Lab Contact:

Lab Rooms: 4109 Marsico Hall

Lab Phone: 919-966-7821


Picture of Andrew Lee PhD Joint Professor of Biochemistry and Biophysics and Pharmacy
  • Phone Number

    919-966-7821 (Office Phone)

  • Address

    Lineberger Cancer Cnter

    450 West Drive, A. Lee lab

    CB# 7295

    Chapel Hill, NC 27599-7295