Mechanistic Roles of Protein Dynamics

1. Quantitative high-resolution single-molecule spectroscopy

High-resolution time-dependent single-molecule spectroscopic techniques have been developed to quantitatively address the functional consequences of structural fluctuations in macromolecules. While we continue to develop new methods to advance the state of the art, the already-developed techniques are being applied to examine:

2. The functional consequences of thermal fluctuations: Adenylate Kinase from Escherichia coli

A quantitative description for important features that characterize structure-function dynamics of a working enzyme has been provided. These features include: (a) molecular motions that facilitate or hamper catalytic events in a biomolecule; (b) a free-energy landscape relating the uptake of different substrates and biochemical reactivity of enzymes; and (c) time scale of structural relaxation following ligand binding and release [PNAS_2007]. In addition to providing further understanding how an enzyme works in general, we hope that careful characterizations of these features will help to create predictive theoretical models.

3. The dynamics of energy coupling in AAA+ motor proteins: NtrC (from Escherichia coli) and NtrC1 (from the thermophile Aquifex aeolicus)

In this project, we study two other fundamental aspects of structure-function dynamics, namely, allosteric regulation and energy coupling. In the former, chemical modification to a certain site of a protein is translated to modified functionality at the distant reactive site. In the latter, binding or hydrolysis of high energy-content molecules such as ATP or ADP is converted to mechanical work. Both have been generally thought as through conformational rearrangements. The molecular mechanisms and their time scale, however, remain largely unknown. In collaboration with Professors Tracy Nixon and Sacha De Carlo, we are investigating these two important processes using as model systems the NtrC protein from E. coli and the NtrC1 protein from the thermophilic A. aeolicus; both proteins interact with the bacterial σ54 factor and regulates the activity of bacterial RNA polymerase (RNAP).

4. Other proteins of interest

Several biological macromolecules of health and technological interest are now under study. Updates coming soon.