Laurent Guérin

Protein Structural Dynamics of Photoactive Yellow Protein in Solution Revealed by Pump–Probe X-ray Solution Scattering

Photoreceptor proteins play crucial roles in receiving light stimuli that give rise to the responses required for biological function. However, structural characterization of conformational transition of the photoreceptors has been elusive in their native aqueous environment, even for a prototype photoreceptor, photoactive yellow protein (PYP). We employ pump-probe X-ray solution scattering to probe the structural changes that occur during the photocycle of PYP in a wide time range from 3.16 μs to 300 ms. By the analysis of both kinetics and structures of the intermediates, the structural progression of the protein in the solution phase is vividly visualized. We identify four structurally distinct intermediates and their associated five time constants and reconstructed the molecular shapes of the four intermediates from time-independent, species-associated difference scattering curves. The reconstructed structures of the intermediates show the large conformational changes such as the protrusion of N-terminus, which is restricted in the crystalline phase due to the crystal contact and thus could not be clearly observed by X-ray crystallography. The protrusion of the N-terminus and the protein volume gradually increase with the progress of the photocycle and becomes maximal in the final intermediate, which is proposed to be the signaling state. The data not only reveal that a common kinetic mechanism is applicable to both the crystalline and the solution phases, but also provide direct evidence for how the sample environment influences structural dynamics and the reaction rates of the PYP photocycle.

Developing 100 ps-resolved X-ray structural analysis capabilities on beamline NW14A at the Photon Factory Advanced Ring

NW14A is a newly constructed undulator beamline for 100 ps time-resolved X-ray experiments at the Photon Factory Advanced Ring. This beamline was designed to conduct a wide variety of time-resolved X-ray measurements, such as time-resolved diffraction, scattering and X-ray absorption fine structure. Its versatility is allowed by various instruments, including two undulators, three diffractometers, two pulse laser systems and an X-ray chopper. The potential for the detection of structural changes on the 100 ps time scale at NW14A is demonstrated by two examples of photo-induced structural changes in an organic crystal and photodissociation in solution.

Growth anomalies in Pecten maximus from coastal waters (Bay of Brest, France): relationship with diatom blooms

The aim of this study was to characterize the daily shell growth of Pecten maximus from early 1998 to late spring 1999 in the Bay of Brest with a careful qualitative and quantitative description of the pelagic primary production. Our results, in accordance with previous studies, demonstrate that there are episodic declines in the growth rate. Concurrent events of low growth rate and large bottom-concentrations of algae following diatom blooms (Cerataulina pelagica or Rhizosolenia delicatula), suggests that this high concentration of phytoplankton on the bottom layer may affect food intake or respiratory activity of the scallops by gill clogging or oxygen depletion. In this study, silicic acid or phosphorus are inferred to be limiting factors responsible for the collapse of the spring bloom. Further, we suggest that, in an N-enriched ecosystem, Si or P-limitation and the changing sinking velocities of phytoplankton, could affect the biology of benthic suspension-feeders.

Structural dynamics of photoinduced molecular switching in the solid state.

Fast and ultra-fast time-resolved diffraction is a fantastic tool for directly observing the structural dynamics of a material rearrangement during the transformation induced by an ultra-short laser pulse. The paper illustrates this ability using the dynamics of photoinduced molecular switching in the solid state probed by 100 ps X-ray diffraction. This structural information is crucial for establishing the physical foundations of how to direct macroscopic photoswitching in materials. A key feature is that dynamics follow a complex pathway from molecular to material scales through a sequence of processes. Not only is the pathway indirect, the nature of the dynamical processes along the pathway depends on the timescale. This dictates which types of degrees of freedom are involved in the subsequent dynamics or kinetics and which are frozen or statistically averaged. We present a recent investigation of the structural dynamics in multifunctional spin-crossover materials, which are prototypes of molecular bistability in the solid state. The time-resolved X-ray diffraction results show that the dynamics span from subpicosecond molecular photoswitching followed by volume expansion (on a nanosecond timescale) and additional thermoswitching (on a microsecond timescale).

100 Picosecond Diffraction Catches Structural Transients of Laser‐Pulse Triggered Switching in a Spin‐Crossover Crystal

We study by 100 picosecond X-ray diffraction the photo-switching dynamics of single crystal of the orthorhombic polymorph of the spin-crossover complex [(TPA)Fe(TCC)]PF(6), in which TPA = tris(2-pyridyl methyl)amine, TCC(2-) = 3,4,5,6-Cl(4)-Catecholate(2-). In the frame of the emerging field of dynamical structural science, this is made possible by using optical pump/X-ray probe techniques, which allow following in real time structural reorganization at intra- and intermolecular levels associated with the change of spin state in the crystal. We use here the time structure of the synchrotron radiation generating 100 picosecond X-ray pulses, coupled to 100 fs laser excitation. This study has revealed a rich variety of structural reorganizations, associated with the different steps of the dynamical process. Three consecutive regimes are evidenced in the time domain: 1) local molecular photo-switching with structural reorganization at constant volume, 2) volume relaxation with inhomogeneous distribution of local temperatures, 3) homogenization of the crystal in the transient state 100 µs after laser excitation. These findings are fundamentally different from those of conventional diffraction studies of long-lived photoinduced high spin states. The time-resolution used here with picosecond X-ray diffraction probes different physical quantities on their intrinsic time-scale, shedding new light on the successive processes driving macroscopic switching in a functionalized material. These results pave the way for structural studies away from equilibrium and represent a first step toward femtosecond crystallography.

Filming the Birth of Molecules and Accompanying Solvent Rearrangement

Molecules are often born with high energy and large-amplitude vibrations. In solution, a newly formed molecule cools down by transferring energy to the surrounding solvent molecules. The progression of the molecular and solute-solvent cage structure during this fundamental process has been elusive, and spectroscopic data generally do not provide such structural information. Here, we use picosecond X-ray liquidography (solution scattering) to visualize time-dependent structural changes associated with the vibrational relaxation of I(2) molecules in two different solvents, CCl(4) and cyclohexane. The birth and vibrational relaxation of I(2) molecules and the associated rearrangement of solvent molecules are mapped out in the form of a temporally varying interatomic distance distribution. The I-I distance increases up to ~4 Å and returns to the equilibrium distance (2.67 Å) in the ground state, and the first solvation cage expands by ~1.5 Å along the I-I axis and then shrinks back accompanying the structural change of the I(2) molecule.

Direct Observation of Acoustic Oscillations in InAs Nanowires

Time-resolved X-ray diffraction and optical reflectivity are used to directly measure three different acoustic oscillations of InAs nanowires. The oscillations are excited by a femtosecond laser pulse and evolve at three different time scales. We measure the absolute scale of the initial radial expansion of the fundamental breathing eigenmode and determine the frequency by transient optical reflectivity. For the extensional eigenmode we measure the oscillations of the average radial and axial lattice constants and determine the amplitude of oscillations and the average extension. Finally we observe a bending motion of the nanowires. The frequencies of the eigenmodes are in good agreements with predictions made by continuum elasticity theory and we find no difference in the speed of sound between the wurtzite nanowires and cubic bulk crystals, but the measured strain is influenced by the interaction between different modes. The wurtzite crystal structure of the nanowires however has an anisotropic thermal expansion.

Rôle des interactions biotiques sur le devenir du pré-recrutement et la croissance de Pecten maximus (L.) en rade de Brest

Biotic interactions within benthic megafauna were studied from quantitative dredge samples to investigate their role in the persistence of low scallop, Pecten maximus, stocks in the Bay of Brest. The distributions of 148 species of the megafauna and of four age classes of Pecten maximus were sampled. Suspension feeders dominate all megabenthic assemblages within the bay. This domination can be related to Crepidula fornicata spreading in the bay; however, no direct competition for food between scallops and the slipper limpet (introduced species) has been observed. On the other hand, Crepidula spreading leads to major changes in sediment type (silting) in the bay owing to biodeposit production, and silting would be a major factor inducing the decrease in Pecten maximus distribution. Predation would not be limiting. Within 10 years, one may predict a strong decrease in the area colonized by scallops in the bay.Biotic interactions within benthic megafauna were studied from quantitative dredge samples to investigate their role in the persistence of low scallop, Pecten maximus, stocks in the Bay of Brest. The distributions of 148 species of the megafauna and of four age classes of Pecten maximus were sampled. Suspension feeders dominate all megabenthic assemblages within the bay. This domination can be related to Crepidula fornicata spreading in the bay; however, no direct competition for food between scallops and the slipper limpet (introduced species) has been observed. On the other hand, Crepidula spreading leads to major changes in sediment type (silting) in the bay owing to biodeposit production, and silting would be a major factor inducing the decrease in Pecten maximus distribution. Predation would not be limiting. Within 10 years, one may predict a strong decrease in the area colonized by scallops in the bay.

Confined linear molecules inside an aperiodic supramolecular crystal: The sequence of superspace phases in n-hexadecane/urea

High-resolution studies of the host-guest inclusion compound n-hexadecane/urea are reported at atmospheric pressure, using both cold neutrons and x-ray diffraction. This intergrowth crystal presents a misfit parameter, defined by the ratio c(h)/c(g) (c(host)/c(guest)), which is temperature independent and irrational (γ = 0.486 ± 0.002) from 300 to 30 K. Three different structural phases are reported for this aperiodic crystal over this temperature range. The crystallographic superspaces are of rank 4 in phases I and II, whereas phase III is associated with an increase in rank to 5, with a supplementary misfit parameter (δ = 0.058 ± 0.002) that is constant throughout this phase. The superspace group of phase I is hexagonal P6(1)22(00γ) down to T(c1) = 149.5 ± 0.5 K; phase II, which persists down to T(c2) = 127.8 ± 0.5 K is orthorhombic P2(1)2(1)2(1)(00γ), and phase III is orthorhombic P2(1)2(1)2(1)(00γ)(00δ).

Structural investigation of the photoinduced spin transition in the three states molecular system [Fe(2-pic)3]Cl2EtOH

We present the detailed results of the investigation by x-ray diffraction of the photoinduced phase transition in the tris(α-picolylamine)iron(II) chloride–ethanol complex. This system undergoes a two-steps spin transition between a high spin state at room temperature and a low spin state at low temperature. The intermediate phase consists of stripes of high spin and low spin molecules. The x-ray diffraction data evidence the structural rearrangement at the molecular scale accompanying the photoinduced change of electronic state between the low-spin phase and the photo-steady high-spin one, which is similar to the stable one in the high temperature phase. The dynamical mechanism of the transformation is discussed with the observation of a domain nucleation process, associated with the coexistence of the stable and photoinduced phases.