THE Operational and design principles of molecular machines

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. We are developing and applying single-molecule tools to address this problem.

Instrumentation and Technology Development

Photon-by-Photon Single-Molecule Analysis is a practice developed by our group that, experimentally, records the arrival time of each detected photon and, theoretically, analyzes the photon time series using data-driven and model-free methods that are statistically robust. The change-point analysis is one such method developed by our group. Additional new methods that are currently under development include trajectory entropy based data analysis and Bayesian inference framework.

Adenylate Kinase (AK)

Adenylate kinase is an ubiquitous enzyme that maintains the energy balance in cells. It has been one of the prototypical model system for studying protein dynamics. Conformational gating and dynamically induced fit are two operational principles observed from our single-molecule experiments. We are currently studying how point mutations may alter the conformational dynamics.

Protein Tyrosine Phosphatase B (PtpB)

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 impacts on the kinetics of conformational changes. We are currently working on further understanding the molecular details of the observations.

Human Insulin Degrading Enzyme (IDE)

The human insulin degrading enzyme digests insulin and the Aβ peptide, and has implications in type-II diabetes and Alzheimer's disease, respectively. We are currently using high-resolution single-molecule spectroscopy to gain a better understanding for the roles in which conformational dynamics may play in the enzyme's activity.

Non-Ribosomal Peptide Synthetases (NRPS)

We are currently using single-molecule methods combined with bulk assays trying to understand how these remarkable molecular assembly lines work.

External collaborators on this topic include: Prof. Jhih-Wei Chu of the National Chiao Tung University, Taiwan; Prof. Wei-Jen Tang of the University of Chicago; Prof. Henning Mootz of the University of Münster, Germany; Prof. Tamiki Komatsuzaki of the Hokkaido University, Japan.