RESEARCH

Single-Molecule Protein Dynamics

Proteins are remarkable molecular machines capable of carrying out a wide array of biochemical transformations and biological functions. More often than not, a protein changes its structural configuration to achieve the designated tasks. The central physical chemistry problem is to be able to quantitatively predict the manner by which a protein changes its conformation under the stochastic sway of solvent molecules. A missing key piece of information that hinders a first-principles understanding of the chemical dynamics of a protein is the accurate and precise experimental data for the protein's functional structure dynamics. We continue to develop advanced single-molecule methods and use these new tools to address interesting problems in biochemistry through quantifying the dynamical aspects of the structure–dynamics–function relationship in proteins. Currently, with the technical advances made in our lab, we have been able to achieve a precision and an accuracy of 5 Å and 2–4 Å for distance measurements, respectively, while experimentally following sub-ms protein dynamics using single-molecule FRET (smFRET). Some scientific problems to which we have contributed are:

Biochemical Systems Studied

Nonribosomal Peptide Synthetases (NRPS): Conformation coordinations in multi-module megaenzymes

Nonribosomal peptide synthetases are multi-module enzyme templates for the synthesis of bioactive peptides, and large-amplitude conformational changes occur during peptide synthesis and assembly. Our single-molecule studies have uncovered new metastable structures, and how the spontaneous dynamics of these transient conformations enable the sequential catalysis. Works along this line continue.

Links:
Biochemistry, 53, 7983–7989 (2014);
Nat. Chem. Biol., 13, 1009–1015 (2017);
RSC Chem. Biol., 2, 843–854 (2021);
Nat. Chem., 16, 259–268 (2024).

Adenylate Kinase (AK): Conformational gating and dynamically induced fit

Adenylate kinase is a ubiquitous enzyme that maintains the energy balance in cells. It has been one of the prototypical model systems for studying protein dynamics. Conformational gating and dynamically induced fit are two operational principles observed from our single-molecule experiments. In collaboration with Professor Jhih-Wei Chu, we are currently developing theoretical and computational tools to quantitatively analyze our new smFRET data to shed light on how point mutations may alter protein conformational dynamics.

Links:
Proc. Natl. Acad. Sci. USA, 104, 18055–18060 (2007);
J. Biol. Chem., 284, 3306–3313 (2009).

Protein Tyrosine Phosphatase B (PtpB): Local folding/unfolding and single-molecule compound logic

Protein Tyrosine Phosphatase B from Mycobacterium tuberculosis is a protein that has been implicated in the virulence of tuberculosis. Our single-molecule study revealed that the large-amplitude conformational movements protect the active site from being oxidized and at the same time allow its interactions with substrates. More generally, our work provides the first experimental evidence that local folding/unfolding directly affects the kinetics of conformational changes, and has direct implications in how it might be utilized by M. tuberculosis to perform compound logic operations in manipulating host-cell signaling networks.

Links:
J. Am. Chem. Soc., 132, 4772–4780 (2010);
J. Am. Chem. Soc., 140, 14747–14752 (2018).

Technical Advances Made

Below is a partial list of the lab's technical contributions to the single-molecule community:

Updated: 2026.11.07.