Photoinduced isomerization sampling of retinal in bacteriorhodopsin

Spin-Coupled Electron Densities of Iron-Sulfur Cluster Imaged by In Situ Serial Laue Diffraction

Iron-sulfur clusters are inorganic cofactors found in many proteins involved in fundamental biological processes. The prokaryotic DNA repair photolyase PhrB carries a four-iron-four-sulfur cluster ([4Fe4S]) in addition to the catalytic flavin adenine dinucleotide (FAD) and a second cofactor ribolumazine. Our recent study suggested that the [4Fe4S] cluster functions as an electron cache to coordinate two interdependent photoreactions of the FAD and ribolumazine. Here we report the crystallography observations of light-induced responses in PhrB using the cryo-trapping method and in situ serial Laue diffraction at room temperature. We capture strong signals that depict electron density changes arising from quantized electronic movements in the [4Fe4S] cluster. Our data reveal the mixed valence layers of the [4Fe4S] cluster due to spin coupling and their dynamic responses to light-induced redox changes. The quantum effects imaged by decomposition of electron density changes have shed light on the emerging roles of metal clusters in proteins.

Deconvolution of dynamic heterogeneity in protein structure

Heterogeneity is intrinsic to the dynamic process of a chemical reaction. As reactants are converted to products via intermediates, the nature and extent of heterogeneity vary temporally throughout the duration of the reaction and spatially across the molecular ensemble. The goal of many biophysical techniques, including crystallography and spectroscopy, is to establish a reaction trajectory that follows an experimentally provoked dynamic process. It is essential to properly analyze and resolve heterogeneity inevitably embedded in experimental datasets. We have developed a deconvolution technique based on singular value decomposition (SVD), which we have rigorously practiced in diverse research projects. In this review, we recapitulate the motivation and challenges in addressing the heterogeneity problem and lay out the mathematical foundation of our methodology that enables isolation of chemically sensible structural signals. We also present a few case studies to demonstrate the concept and outcome of the SVD-based deconvolution. Finally, we highlight a few recent studies with mechanistic insights made possible by heterogeneity deconvolution.

Multiple retinal isomerizations during the early phase of the bestrhodopsin photoreaction

Bestrhodopsins constitute a class of light-regulated pentameric ion channels that consist of one or two rhodopsins in tandem fused with bestrophin ion channel domains. Here, we report on the isomerization dynamics in the rhodopsin tandem domains of Phaeocystis antarctica bestrhodopsin, which binds all-trans retinal Schiff-base (RSB) absorbing at 661 nm and, upon illumination, converts to the meta-stable P540 state with an unusual 11-cis RSB. The primary photoproduct P682 corresponds to a mixture of highly distorted 11-cis and 13-cis RSB directly formed from the excited state in 1.4 ps. P673 evolves from P682 in 500 ps and contains highly distorted 13-cis RSB, indicating that the 11-cis fraction in P682 converts to 13-cis. Next, P673 establishes an equilibrium with P595 in 1.2 µs, during which RSB converts to 11-cis and then further proceeds to P560 in 48 µs and P540 in 1.0 ms while remaining 11-cis. Hence, extensive isomeric switching occurs on the early ground state potential energy surface (PES) on the hundreds of ps to µs timescale before finally settling on a metastable 11-cis photoproduct. We propose that P682 and P673 are trapped high up on the ground-state PES after passing through either of two closely located conical intersections that result in 11-cis and 13-cis RSB. Co-rotation of C11=C12 and C13=C14 bonds results in a constricted conformational landscape that allows thermal switching between 11-cis and 13-cis species of highly strained RSB chromophores. Protein relaxation may release RSB strain, allowing it to evolve to a stable 11-cis isomeric configuration in microseconds.

Dynamic interplays between three redox cofactors in a DNA photolyase revealed by spectral decomposition

DNA repair catalyzed by photolyases is accomplished by a light-dependent electron transfer event from a fully reduced flavin adenine dinucleotide to a DNA lesion site. Prokaryotic DNA photolyase, PhrB, possesses a ribolumazine cofactor and a four-iron-four-sulfur cluster in addition to the catalytic flavin, but their functional roles are poorly understood. Here, we employ time-resolved absorption spectroscopy to probe light-induced responses in both solution and single crystals of PhrB. We jointly analyze a large collection of light-induced difference spectra from the wild-type and mutant PhrB obtained under different light and redox conditions. By applying singular value decomposition to 159 time series, we dissect light-induced spectral changes and examine the dynamic interplay between three cofactors. Our findings suggest that these cofactors form an interdependent redox network to coordinate light-induced redox responses. We propose that the ribolumazine cofactor serves as a photoprotective pigment under intense light or prolonged illumination, while the iron-sulfur cluster acts as a transient electron cache to maintain balance between two otherwise independent photoreactions of the flavin and ribolumazine.

Spin-Coupled Electron Densities of Iron-Sulfur Cluster Imaged by In Situ Serial Laue Diffraction

Iron-sulfur clusters are inorganic cofactors found in many proteins involved in fundamental biological processes including DNA processing. The prokaryotic DNA repair enzyme PhrB, a member of the protein family of cryptochromes and photolyases, carries a four-iron-four-sulfur cluster [4Fe4S] in addition to the catalytic cofactor flavin adenine dinucleotide (FAD) and a second pigment 6,7-dimethyl-8-ribityllumazine (DMRL). The light-induced redox reactions of this multi-cofactor protein complex were recently shown as two interdependent photoreductions of FAD and DMRL mediated by the [4Fe4S] cluster functioning as an electron cache to hold a fine balance of electrons. Here, we apply the more traditional temperature-scan cryo-trapping technique in protein crystallography and the newly developed technology of in situ serial Laue diffraction at room temperature. These diffraction methods in dynamic crystallography enable us to capture strong signals of electron density changes in the [4Fe4S] cluster that depict quantized electronic movements. The mixed valence layers of the [4Fe4S] cluster due to spin coupling and their dynamic responses to light illumination are observed directly in our difference maps between its redox states. These direct observations of the quantum effects in a protein bound iron-sulfur cluster have thus opened a window into the mechanistic understanding of metal clusters in biological systems.