Tai-Yen Chen

Sub-particle reaction and photocurrent mapping to optimize catalyst-modified photoanodes.

The splitting of water photoelectrochemically into hydrogen and oxygen represents a promising technology for converting solar energy to fuel. The main challenge is to ensure that photogenerated holes efficiently oxidize water, which generally requires modification of the photoanode with an oxygen evolution catalyst (OEC) to increase the photocurrent and reduce the onset potential. However, because excess OEC material can hinder light absorption and decrease photoanode performance, its deposition needs to be carefully controlled—yet it is unclear which semiconductor surface sites give optimal improvement if targeted for OEC deposition, and whether sites catalysing water oxidation also contribute to competing charge-carrier recombination with photogenerated electrons. Surface heterogeneity exacerbates these uncertainties, especially for nanostructured photoanodes benefiting from small charge-carrier transport distances. Here we use super-resolution imaging, operated in a charge-carrier-selective manner and with a spatiotemporal resolution of approximately 30 nanometres and 15 milliseconds, to map both the electron- and hole-driven photoelectrocatalytic activities on single titanium oxide nanorods. We then map, with sub-particle resolution (about 390 nanometres), the photocurrent associated with water oxidation, and find that the most active sites for water oxidation are also the most important sites for charge-carrier recombination. Site-selective deposition of an OEC, guided by the activity maps, improves the overall performance of a given nanorod—even though more improvement in photocurrent efficiency correlates with less reduction in onset potential (and vice versa) at the sub-particle level. Moreover, the optimal catalyst deposition sites for photocurrent enhancement are the lower-activity sites, and for onset potential reduction the optimal sites are the sites with more positive onset potential, contrary to what is obtainable under typical deposition conditions. These findings allow us to suggest an activity-based strategy for rationally engineering catalyst-improved photoelectrodes, which should be widely applicable because our measurements can be performed for many different semiconductor and catalyst materials.

Direct substitution and assisted dissociation pathways for turning off transcription by a MerR-family metalloregulator

Metalloregulators regulate transcription in response to metal ions. Many studies have provided insights into how transcription is activated upon metal binding by MerR-family metalloregulators. In contrast, how transcription is turned off after activation is unclear. Turning off transcription promptly is important, however, as the cells would not want to continue expressing metal resistance genes and thus waste energy after metal stress is relieved. Using single-molecule FRET measurements we studied the dynamic interactions of the copper efflux regulator (CueR), a Cu+-responsive MerR-family metalloregulator, with DNA. Besides quantifying its DNA binding and unbinding kinetics, we discovered that CueR spontaneously flips its binding orientation at the recognition site. CueR also has two different binding modes, corresponding to interactions with specific and nonspecific DNA sequences, which would facilitate recognition localization. Most strikingly, a CueR molecule coming from solution can directly substitute for a DNA-bound CueR or assist the dissociation of the incumbent CueR, both of which are unique examples for any DNA-binding protein. The kinetics of the direct protein substitution and assisted dissociation reactions indicate that these two unique processes can provide efficient pathways to replace a DNA-bound holo-CueR with apo-CueR, thus turning off transcription promptly and facilely.

Concentration- and chromosome-organization-dependent regulator unbinding from DNA for transcription regulation in living cells.

Binding and unbinding of transcription regulators at operator sites constitute a primary mechanism for gene regulation. While many cellular factors are known to regulate their binding, little is known on how cells can modulate their unbinding for regulation. Using nanometer-precision single-molecule tracking, we study the unbinding kinetics from DNA of two metal-sensing transcription regulators in living Escherichia coli cells. We find that they show unusual concentration-dependent unbinding kinetics from chromosomal recognition sites in both their apo and holo forms. Unexpectedly, their unbinding kinetics further varies with the extent of chromosome condensation, and more surprisingly, varies in opposite ways for their apo-repressor versus holo-activator forms. These findings suggest likely broadly relevant mechanisms for facile switching between transcription activation and deactivation in vivo and in coordinating transcription regulation of resistance genes with the cell cycle.

Dynamic Multibody Protein Interactions Suggest Versatile Pathways for Copper Trafficking

As part of intracellular copper trafficking pathways, the human copper chaperone Hah1 delivers Cu(+) to the Wilsons Disease Protein (WDP) via weak and dynamic protein-protein interactions. WDP contains six homologous metal binding domains (MBDs) connected by flexible linkers, and these MBDs all can receive Cu(+) from Hah1. The functional roles of the MBD multiplicity in Cu(+) trafficking are not well understood. Building on our previous study of the dynamic interactions between Hah1 and the isolated fourth MBD of WDP, here we study how Hah1 interacts with MBD34, a double-domain WDP construct, using single-molecule fluorescence resonance energy transfer (smFRET) combined with vesicle trapping. By alternating the positions of the smFRET donor and acceptor, we systematically probed Hah1-MBD3, Hah1-MBD4, and MBD3-MBD4 interaction dynamics within the multidomain system. We found that the two interconverting interaction geometries were conserved in both intermolecular Hah1-MBD and intramolecular MBD-MBD interactions. The Hah1-MBD interactions within MBD34 are stabilized by an order of magnitude relative to the isolated single-MBDs, and thermodynamic and kinetic evidence suggest that Hah1 can interact with both MBDs simultaneously. The enhanced interaction stability of Hah1 with the multi-MBD system, the dynamic intramolecular MBD-MBD interactions, and the ability of Hah1 to interact with multiple MBDs simultaneously suggest an efficient and versatile mechanism for the Hah1-to-WDP pathway to transport Cu(+).

Size-dependent ultrafast magnetization dynamics in iron oxide (Fe3O4) nanocrystals.

Optically induced ultrafast demagnetization and its recovery in superparamagnetic colloidal iron oxide (Fe3O4) nanocrystals have been investigated via time-resolved Faraday rotation measurements. Optical excitation with near-infrared laser pulse resulted in ultrafast demagnetization in approximately 100 fs via the destruction of ferrimagnetic ordering. The degree of demagnetization increased with the excitation density, and the complete demagnetization reached at approximately 10% excitation density. The magnetization recovered on two time scales, several picoseconds and hundreds of picoseconds, which can be associated with the initial reestablishment of the ferrimagnetic ordering and the electronic relaxation back to the ground state, respectively. The amplitude of the slower recovery component increased with the size of the nanocrystals, suggesting the size-dependent ferrimagnetic ordering throughout the volume of the nanocrystal.

Time-resolved study of surface spin effect on spin-lattice relaxation in Fe3O4 nanocrystals.

The role of surface spins in the relaxation of magnetization in optically excited Fe(3)O(4) nanocrystals has been investigated via time-resolved Faraday rotation measurements. The time scale of the magnetization recovery following the optically induced demagnetization increased from 250 to 350 ps as the size of the nanocrystals increased from 5 to 15 nm. From analysis of the data with a simple model relating the spin-lattice relaxation rate to the average spin-orbit coupling strength of the interior and surface spins, we estimated the relative efficiency of surface in spin-lattice relaxation with respect to the interior spins. Our analysis indicates that, in Fe(3)O(4) nanocrystals passivated with oleic acid, the surface is 3 times more efficient in spin-lattice relaxation than the interior.

Metalloregulator CueR biases RNA polymerase’s kinetic sampling of dead-end or open complex to repress or activate transcription

Significance MerR-family regulators act on suboptimal promoters to control the transcriptions of genes that help bacteria defend against a diverse set of metals and drugs. How they modulate RNA polymerase (RNAP) activity to control transcription initiation remains unclear, however. Here we show that CueR—a Cu+-responsive MerR-family metalloregulator—biases the kinetic sampling of RNAP binding events that lead to two noninterconverting states: a dead-end complex to repress or an open complex to activate transcription, constituting a branched pathway distinct from the linear pathway prevalent for transcription initiation at optimal promoters. This mechanistic insight contributes new fundamental knowledge to bacterial transcription regulation, and may help develop antibiotics that target this regulation mechanism to compromise bacterial defenses. Metalloregulators respond to metal ions to regulate transcription of metal homeostasis genes. MerR-family metalloregulators act on σ70-dependent suboptimal promoters and operate via a unique DNA distortion mechanism in which both the apo and holo forms of the regulators bind tightly to their operator sequence, distorting DNA structure and leading to transcription repression or activation, respectively. It remains unclear how these metalloregulator−DNA interactions are coupled dynamically to RNA polymerase (RNAP) interactions with DNA for transcription regulation. Using single-molecule FRET, we study how the copper efflux regulator (CueR)—a Cu+-responsive MerR-family metalloregulator—modulates RNAP interactions with CueR’s cognate suboptimal promoter PcopA, and how RNAP affects CueR−PcopA interactions. We find that RNAP can form two noninterconverting complexes at PcopA in the absence of nucleotides: a dead-end complex and an open complex, constituting a branched interaction pathway that is distinct from the linear pathway prevalent for transcription initiation at optimal promoters. Capitalizing on this branched pathway, CueR operates via a “biased sampling” instead of “dynamic equilibrium shifting” mechanism in regulating transcription initiation; it modulates RNAP’s binding–unbinding kinetics, without allowing interconversions between the dead-end and open complexes. Instead, the apo-repressor form reinforces the dominance of the dead-end complex to repress transcription, and the holo-activator form shifts the interactions toward the open complex to activate transcription. RNAP, in turn, locks CueR binding at PcopA into its specific binding mode, likely helping amplify the differences between apo- and holo-CueR in imposing DNA structural changes. Therefore, RNAP and CueR work synergistically in regulating transcription.

Quantifying Multistate Cytoplasmic Molecular Diffusion in Bacterial Cells via Inverse Transform of Confined Displacement Distribution

Single-molecule tracking (SMT) of fluorescently tagged cytoplasmic proteins can provide valuable information on the underlying biological processes in living cells via subsequent analysis of the displacement distributions; however, the confinement effect originated from the small size of a bacterial cell skews the protein’s displacement distribution and complicates the quantification of the intrinsic diffusive behaviors. Using the inverse transformation method, we convert the skewed displacement distribution (for both 2D and 3D imaging conditions) back to that in free space for systems containing one or multiple (non)interconverting Brownian diffusion states, from which we can reliably extract the number of diffusion states as well as their intrinsic diffusion coefficients and respective fractional populations. We further demonstrate a successful application to experimental SMT data of a transcription factor in living E. coli cells. This work allows a direct quantitative connection between cytoplasmic SMT data with diffusion theory for analyzing molecular diffusive behavior in live bacteria.

Adaptor protein mediates dynamic pump assembly for bacterial metal efflux

Significance Multicomponent efflux pumps confer clinically relevant drug resistance in Gram-negative bacteria. These pumps, once assembled to function, traverse the periplasm linking inner and outer membranes tightly. However, little is known on how these pumps can operate efficiently without compromising periplasmic plasticity. We show here that in Escherichia coli, the tripartite complex CusCBA for Cu+ and Ag+ efflux exists as a dynamic structure and shifts toward the assembled form in response to metal stress. Unexpectedly, the periplasmic adaptor protein CusB is a key metal-sensing protein that mediates the complex assembly. This adaptor protein-mediated dynamic pump assembly allows the bacterial cell for efficient efflux on cellular demand while still maintaining periplasmic plasticity; it can be broadly relevant to other multicomponent efflux systems. Multicomponent efflux complexes constitute a primary mechanism for Gram-negative bacteria to expel toxic molecules for survival. As these complexes traverse the periplasm and link inner and outer membranes, it remains unclear how they operate efficiently without compromising periplasmic plasticity. Combining single-molecule superresolution imaging and genetic engineering, we study in living Escherichia coli cells the tripartite efflux complex CusCBA of the resistance–nodulation–division family that is essential for bacterial resistance to drugs and toxic metals. We find that CusCBA complexes are dynamic structures and shift toward the assembled form in response to metal stress. Unexpectedly, the periplasmic adaptor protein CusB is a key metal-sensing element that drives the assembly of the efflux complex ahead of the transcription activation of the cus operon for defending against metals. This adaptor protein-mediated dynamic pump assembly allows the bacterial cell for efficient efflux upon cellular demand while still maintaining periplasmic plasticity; this could be broadly relevant to other multicomponent efflux systems.

Single-molecule dynamics of the molecular chaperone trigger factor in living cells

In bacteria, trigger factor (TF) is the molecular chaperone that interacts with the ribosome to assist the folding of nascent polypeptides. Studies in vitro have provided insights into the function and mechanism of TF. Much is to be elucidated, however, about how TF functions in vivo. Here, we use single‐molecule tracking, in combination with genetic manipulations, to study the dynamics and function of TF in living E. coli cells. We find that TF, besides interacting with the 70S ribosome, may also bind to ribosomal subunits and form TF‐polypeptide complexes that may include DnaK/DnaJ proteins. The TF‐70S ribosome interactions are highly dynamic inside cells, with an average residence time of ∼0.2 s. Our results confirm that the signal recognition particle weakens TFs interaction with the 70S ribosome, and further identify that this weakening mainly results from a change in TFs binding to the 70S ribosome, rather than its unbinding. Moreover, using photoconvertible bimolecular fluorescence complementation, we selectively probe TF2 dimers in the cell and show that TF2 does not bind to the 70S ribosome but is involved in the post‐translational interactions with polypeptides. These findings contribute to the fundamental understanding of molecular chaperones in assisting protein folding in living cells.