Modeling difference x-ray scattering observations from an integral membrane protein within a detergent micelle.

Time-resolved x-ray solution scattering (TR-XSS) is a sub-field of structural biology, which observes secondary structural changes in proteins as they evolve along their functional pathways. While the number of distinct conformational states and their rise and decay can be extracted directly from TR-XSS experimental data recorded from light-sensitive systems, structural modeling is more challenging. This step often builds from complementary structural information, including secondary structural changes extracted from crystallographic studies or molecular dynamics simulations. When working with integral membrane proteins, another challenge arises because x-ray scattering from the protein and the surrounding detergent micelle interfere and these effects should be considered during structural modeling. Here, we utilize molecular dynamics simulations to explicitly incorporate the x-ray scattering cross term between a membrane protein and its surrounding detergent micelle when modeling TR-XSS data from photoactivated samples of detergent solubilized bacteriorhodopsin. This analysis provides theoretical foundations in support of our earlier approach to structural modeling that did not explicitly incorporate this cross term and improves agreement between experimental data and theoretical predictions at lower x-ray scattering angles.

Deciphering Photochemical Reaction Pathways of Aqueous Tetrachloroauric Acid by X-ray Transient Absorption Spectroscopy.

Photolysis reaction pathways of [Au(III)Cl4]- in aqueous solution have been investigated by time-resolved X-ray absorption spectroscopy. Ultraviolet excitation directly breaks the Au-Cl bond in [Au(III)Cl4]- to form [Au(II)Cl3]- that becomes highly reactive within 79 ps. Disproportionation of [Au(II)Cl3]- generates [Au(I)Cl2]-, which is stable for ≤10 µs. In contrast, intense near-infrared lasers photolyze water to generate hydrated electrons, which then reduce [Au(III)Cl4]- to [Au(II)Cl3]- at 5 ns. Hydrated electrons further induce a chain reaction from [Au(II)Cl3]- to [Au(0)Cl]- by successively removing one Cl-. The zero-valency Au anions quickly polymerize and condense to form Au nanoparticles, which become the dominating product after 400 s. Our results reveal that the condensation of zero-valency Au starts with dimerization of gold clusters coordinated with chloride ions rather than direct condensation of pristine Au atoms.

Photoactivation of triosmium dodecacarbonyl at 400 nm probed with time-resolved X-ray liquidography.

The photoactivation mechanism of Os3(CO)12 at 400 nm is examined with time-resolved X-ray liquidography. The data reveal two pathways: the vibrational relaxation following an internal conversion to the electronic ground state and the ligand dissociation to form Os3(CO)11 with a ligand vacancy at the axial position.

Tracking the ATP-binding response in adenylate kinase in real time.

The biological function of proteins is critically dependent on dynamics inherent to the native structure. Such structural dynamics obey a predefined order and temporal timing to execute the specific reaction. Determination of the cooperativity of key structural rearrangements requires monitoring protein reactions in real time. In this work, we used time-resolved x-ray solution scattering (TR-XSS) to visualize structural changes in the Escherichia coli adenylate kinase (AdK) enzyme upon laser-induced activation of a protected ATP substrate. A 4.3-ms transient intermediate showed partial closing of both the ATP- and AMP-binding domains, which indicates a cooperative closing mechanism. The ATP-binding domain also showed local unfolding and breaking of an Arg131-Asp146 salt bridge. Nuclear magnetic resonance spectroscopy data identified similar unfolding in an Arg131Ala AdK mutant, which refolded in a closed, substrate-binding conformation. The observed structural dynamics agree with a "cracking mechanism" proposed to underlie global structural transformation, such as allostery, in proteins.

Instrument-model refinement in normalized reciprocal-vector space for X-ray Laue diffraction.

A simple yet efficient instrument-model refinement method for X-ray diffraction data is presented and discussed. The method is based on least-squares minimization of differences between respective normalized (i.e. unit length) reciprocal vectors computed for adjacent frames. The approach was primarily designed to work with synchrotron X-ray Laue diffraction data collected for small-molecule single-crystal samples. The method has been shown to work well on both simulated and experimental data. Tests performed on simulated data sets for small-molecule and protein crystals confirmed the validity of the proposed instrument-model refinement approach. Finally, examination of data sets collected at both BioCARS 14-ID-B (Advanced Photon Source) and ID09 (European Synchrotron Radiation Facility) beamlines indicated that the approach is capable of retrieving goniometer parameters (e.g. detector distance or primary X-ray beam centre) reliably, even when their initial estimates are rather inaccurate.

Evidence for laser-induced homogeneous oriented ice nucleation revealed via pulsed x-ray diffraction.

The induction of homogeneous and oriented ice nucleation has to date not been achieved. Here, we report induced nucleation of ice from millimeter sized supercooled water drops illuminated by ns-optical laser pulses well below the ionization threshold making use of particular laser beam configurations and polarizations. Employing a 100 ps synchrotron x-ray pulse 100 ns after each laser pulse, an unambiguous correlation was observed between the directions and the symmetry of the laser fields and that of the H-bonding arrays of the induced ice crystals. Moreover, an analysis of the x-ray diffraction data indicates that, in the main, the induced nucleation of ice is homogeneous at temperatures well above the observed and predicted values for supercooled water.

Protein folding from heterogeneous unfolded state revealed by time-resolved X-ray solution scattering.

One of the most challenging tasks in biological science is to understand how a protein folds. In theoretical studies, the hypothesis adopting a funnel-like free-energy landscape has been recognized as a prominent scheme for explaining protein folding in views of both internal energy and conformational heterogeneity of a protein. Despite numerous experimental efforts, however, comprehensively studying protein folding with respect to its global conformational changes in conjunction with the heterogeneity has been elusive. Here we investigate the redox-coupled folding dynamics of equine heart cytochrome c (cyt-c) induced by external electron injection by using time-resolved X-ray solution scattering. A systematic kinetic analysis unveils a kinetic model for its folding with a stretched exponential behavior during the transition toward the folded state. With the aid of the ensemble optimization method combined with molecular dynamics simulations, we found that during the folding the heterogeneously populated ensemble of the unfolded state is converted to a narrowly populated ensemble of folded conformations. These observations obtained from the kinetic and the structural analyses of X-ray scattering data reveal that the folding dynamics of cyt-c accompanies many parallel pathways associated with the heterogeneously populated ensemble of unfolded conformations, resulting in the stretched exponential kinetics at room temperature. This finding provides direct evidence with a view to microscopic protein conformations that the cyt-c folding initiates from a highly heterogeneous unfolded state, passes through still diverse intermediate structures, and reaches structural homogeneity by arriving at the folded state.

Tracking Ca2+ ATPase intermediates in real time by x-ray solution scattering.

Sarco/endoplasmic reticulum Ca2+ ATPase (SERCA) transporters regulate calcium signaling by active calcium ion reuptake to internal stores. Structural transitions associated with transport have been characterized by x-ray crystallography, but critical intermediates involved in the accessibility switch across the membrane are missing. We combined time-resolved x-ray solution scattering (TR-XSS) experiments and molecular dynamics (MD) simulations for real-time tracking of concerted SERCA reaction cycle dynamics in the native membrane. The equilibrium [Ca2]E1 state before laser activation differed in the domain arrangement compared with crystal structures, and following laser-induced release of caged ATP, a 1.5-ms intermediate was formed that showed closure of the cytoplasmic domains typical of E1 states with bound Ca2+ and ATP. A subsequent 13-ms transient state showed a previously unresolved actuator (A) domain arrangement that exposed the ADP-binding site after phosphorylation. Hence, the obtained TR-XSS models determine the relative timing of so-far elusive domain rearrangements in a native environment.

Revealing Hot and Long-Lived Metastable Spin States in the Photoinduced Switching of Solvated Metallogrid Complexes with Femtosecond Optical and X-ray Spectroscopies.

An atomistic understanding of the photoinduced spin-state switching (PSS) within polynuclear systems of d4-d7 transition metal ion complexes is required for their rational integration into light-driven reactions of chemical and biological interest. However, in contrast to mononuclear systems, the multidimensional dynamics of the PSS in solvated molecular arrays have not yet been elucidated due to the expected complications associated with the connectivity between the metal centers and the strong interactions with the surroundings. In this work, the PSS in a solvated triiron(II) metallogrid complex is characterized using transient optical absorption and X-ray emission spectroscopies on the femtosecond time scale. The complementary measurements reveal the photoinduced creation of energy-rich (hot) and long-lived quintet states, whose dynamics differ critically from their mononuclear congeners. This finding opens major prospects for developing novel schemes in solution-phase spin chemistry that are driven by the dynamic PSS process in compact oligometallic arrays.

Demonstration of a picosecond Bragg switch for hard X-rays in a synchrotron-based pump-probe experiment.

A benchmark experiment is reported that demonstrates the shortening of hard X-ray pulses in a synchrotron-based optical pump-X-ray probe measurement. The pulse-shortening device is a photoacoustic Bragg switch that reduces the temporal resolution of an incident X-ray pulse to approximately 7.5 ps. The Bragg switch is employed to monitor propagating sound waves in nanometer thin epitaxial films. From the experimental data, the pulse duration, diffraction efficiency and switching contrast of the device can be inferred. A detailed efficiency analysis shows that the switch can deliver up to 109 photons s-1 in high-repetition-rate synchrotron experiments.

Structural Dynamics of Bismuth Triiodide in Solution Triggered by Photoinduced Ligand-to-Metal Charge Transfer.

Bismuth triiodide, BiI3, is one of the simplest bismuth halides, which have recently attracted considerable attention because of their promising properties. Here, we investigate the structural dynamics of a photoinduced reaction of BiI3 in solution phase using time-resolved X-ray liquidography (TRXL) and density functional theory (DFT) and time-dependent DFT (TDDFT) calculations. The photoreaction was initiated by excitation at 400 nm, which corresponds to the ligand-to-metal charge-transfer transition. The detailed structures and kinetic profiles of all relevant intermediate species from the TRXL data show that the trigonal planar structure of BiI3, which is predicted to be the most stable structure of the lowest excited state by TDDFT calculation, was not observed, and the photoreaction proceeds via two parallel pathways within the time resolution of 100 ps: (i) isomer formation to produce iso-BiI2-I, which relaxes back to the ground-state structure, and (ii) dissociation into BiI2· and I· radicals, which nongeminately recombine to generate ground-state BiI3 and I2.

Light-induced structural changes in a full-length cyanobacterial phytochrome probed by time-resolved X-ray scattering.

Phytochromes are photoreceptor proteins that transmit a light signal from a photosensory region to an output domain. Photoconversion involves protein conformational changes whose nature is not fully understood. Here, we use time-resolved X-ray scattering and optical spectroscopy to study the kinetics of structural changes in a full-length cyanobacterial phytochrome and in a truncated form with no output domain. X-ray and spectroscopic signals on the µs/ms timescale are largely independent of the presence of the output domain. On longer time-scales, large differences between the full-length and truncated proteins indicate the timeframe during which the structural transition is transmitted from the photosensory region to the output domain and represent a large quaternary motion. The suggested independence of the photosensory-region dynamics on the µs/ms timescale defines a time window in which the photoreaction can be characterized (e.g. for optogenetic design) independently of the nature of the engineered output domain.

Solvent-dependent complex reaction pathways of bromoform revealed by time-resolved X-ray solution scattering and X-ray transient absorption spectroscopy.

The photochemical reaction pathways of CHBr3 in solution were unveiled using two complementary X-ray techniques, time-resolved X-ray solution scattering (TRXSS) and X-ray transient absorption spectroscopy, in a wide temporal range from 100 ps to tens of microseconds. By performing comparative measurements in protic (methanol) and aprotic (methylcyclohexane) solvents, we found that the reaction pathways depend significantly on the solvent properties. In methanol, the major photoproducts are CH3OCHBr2 and HBr generated by rapid solvolysis of iso-CHBr2-Br, an isomer of CHBr3. In contrast, in methylcyclohexane, iso-CHBr2-Br returns to CHBr3 without solvolysis. In both solvents, the formation of CHBr2 and Br is a competing reaction channel. From the structural analysis of TRXSS data, we determined the structures of key intermediate species, CH3OCHBr2 and iso-CHBr2-Br in methanol and methylcyclohexane, respectively, which are consistent with the structures from density functional theory calculations.

Tracking the picosecond deactivation dynamics of a photoexcited iron carbene complex by time-resolved X-ray scattering.

Recent years have seen the development of new iron-centered N-heterocyclic carbene (NHC) complexes for solar energy applications. Compared to typical ligand systems, the NHC ligands provide Fe complexes with longer-lived metal-to-ligand charge transfer (MLCT) states. This increased lifetime is ascribed to strong ligand field splitting provided by the NHC ligands that raises the energy levels of the metal centered (MC) states and therefore reduces the deactivation efficiency of MLCT states. Among currently known NHC systems, [Fe(btbip)2]2+ (btbip = 2,6-bis(3-tert-butyl-imidazol-1-ylidene)pyridine) is a unique complex as it exhibits a short-lived MC state with a lifetime on the scale of a few hundreds of picoseconds. Hence, this complex allows for a detailed investigation, using 100 ps X-ray pulses from a synchrotron, of strong ligand field effects on the intermediate MC state in an NHC complex. Here, we use time-resolved wide angle X-ray scattering (TRWAXS) aided by density functional theory (DFT) to investigate the molecular structure, energetics and lifetime of the high-energy MC state in the Fe-NHC complex [Fe(btbip)2]2+ after excitation to the MLCT manifold. We identify it as a 260 ps metal-centered quintet (5MC) state, and we refine the molecular structure of the excited-state complex verifying the DFT results. Using information about the hydrodynamic state of the solvent, we also determine, for the first time, the energy of the 5MC state as 0.75 ± 0.15 eV. Our results demonstrate that due to the increased ligand field strength caused by NHC ligands, upon transition from the ground state to the 5MC state, the metal to ligand bonds extend by unusually large values: by 0.29 Å in the axial and 0.21 Å in the equatorial direction. These results imply that the transition in the photochemical properties from typical Fe complexes to novel NHC compounds is manifested not only in the destabilization of the MC states, but also in structural distortion of these states.

Transient isomers in the photodissociation of bromoiodomethane.

The photochemistry of halomethanes is fascinating for the complex cascade reactions toward either the parent or newly synthesized molecules. Here, we address the structural rearrangement of photodissociated CH2IBr in methanol and cyclohexane, probed by time-resolved X-ray scattering in liquid solution. Upon selective laser cleavage of the C-I bond, we follow the reaction cascade of the two geminate geometrical isomers, CH2I-Br and CH2Br-I. Both meta-stable isomers decay on different time scales, mediated by solvent interaction, toward the original parent molecule. We observe the internal rearrangement of CH2Br-I to CH2I-Br in cyclohexane by extending the time window up to 3 µs. We track the photoproduct kinetics of CH2Br-I in methanol solution where only one isomer is observed. The effect of the polarity of solvent on the geminate recombination pathways is discussed.

Photochemical Mechanism of an Atypical Algal Phytochrome.

Phytochromes are bilin-containing photoreceptors that are typically sensitive to the red/far-red region of the visible spectrum. Recently, phytochromes from certain eukaryotic algae have become attractive targets for optogenetic applications because of their unique ability to respond to multiple wavelengths of light. Herein, a combination of time-resolved spectroscopy and structural approaches across picosecond to second timescales have been used to map photochemical mechanisms and structural changes in this atypical group of phytochromes. The photochemistry of an orange/far-red light-sensitive algal phytochrome from Dolihomastix tenuilepis has been investigated by using a combination of visible, IR and X-ray scattering probes. The entire photocycle, correlated with accompanying structural changes in the cofactor/protein, are reported. This study identifies a complex photocycle for this atypical phytochrome. It also highlights a need to combine outcomes from a range of biophysical approaches to unravel complex photochemical and macromolecular processes in multi-domain photoreceptor proteins that are the basis of biological light-mediated signalling.

Direct Observation of a Transiently Formed Isomer During Iodoform Photolysis in Solution by Time-Resolved X-ray Liquidography.

Photolysis of iodoform (CHI3) in solution has been extensively studied, but its reaction mechanism remains elusive. In particular, iso-iodoform (iso-CHI2-I) is formed as a product of the photolysis reaction, but its detailed structure is not known, and whether it is a major intermediate species has been controversial. Here, by using time-resolved X-ray liquidography, we determined the reaction mechanism of CHI3 photodissociation in cyclohexane as well as the structure of iso-CHI2-I. Both iso-CHI2-I and CHI2 radical were found to be formed within 100 ps with a branching ratio of 40:60. Iodine radicals (I), formed during the course of CHI3 photolysis, recombine nongeminately with either CHI2 or I. Based on our structural analysis, the I-I distance and the C-I-I angle of iso-CHI2-I were determined to be 2.922 ± 0.004 Å and 133.9 ± 0.8°, respectively.

Tuning and Tracking of Coherent Shear Waves in Molecular Films.

We have determined the time-dependent displacement fields in molecular sub-micrometer thin films as response to femtosecond and picosecond laser pulse heating by time-resolved X-ray diffraction. This method allows a direct absolute determination of the molecular displacements induced by electron-phonon interactions, which are crucial for, for example, charge transport in organic electronic devices. We demonstrate that two different modes of coherent shear motion can be photoexcited in a thin film of organic molecules by careful tuning of the laser penetration depth relative to the thickness of the film. The measured response of the organic film to impulse heating is explained by a thermoelastic model and reveals the spatially resolved displacement in the film. Thereby, information about the profile of the energy deposition in the film as well as about the mechanical interaction with the substrate material is obtained.

Light-induced structural changes in a monomeric bacteriophytochrome.

Phytochromes sense red light in plants and various microorganism. Light absorption causes structural changes within the protein, which alter its biochemical activity. Bacterial phytochromes are dimeric proteins, but the functional relevance of this arrangement remains unclear. Here, we use time-resolved X-ray scattering to reveal the solution structural change of a monomeric variant of the photosensory core module of the phytochrome from Deinococcus radiodurans. The data reveal two motions, a bend and a twist of the PHY domain with respect to the chromophore-binding domains. Infrared spectroscopy shows the refolding of the PHY tongue. We conclude that a monomer of the phytochrome photosensory core is sufficient to perform the light-induced structural changes. This implies that allosteric cooperation with the other monomer is not needed for structural activation. The dimeric arrangement may instead be intrinsic to the biochemical output domains of bacterial phytochromes.