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The increasing integration of renewable energy requires a good model of the existing power distribution infrastructure, represented by its admittance matrix. However, a reliable estimate may either be missing or quickly become obsolete, as distribution grids are continuously modified. In this work, we propose a method for estimating the admittance matrix from voltage and current measurements. By focusing on μPMU measurements and partially observed networks, we show that voltage collinearity and noisy samples of all electric variables are the main challenges for accurate identification. Moreover, the accuracy of maximum likelihood estimation is often insufficient in real-world scenarios. To overcome this problem, we develop a flexible Bayesian framework that allows one to exploit different forms of prior knowledge about individual line parameters, as well as network-wide characteristics such as the sparsity of the interconnections. Most importantly, we show how to use maximum likelihood estimates for tuning relevant hyperparameters, hence making the identification procedure self-contained. We also discuss numerical aspects of the maximum a posteriori estimate computation. Realistic simulations conducted on benchmark electrical systems demonstrate that, compared to other algorithms, our method can achieve significantly greater accuracy than previously developed methods. ISSN:1949-3053 ISSN:1949-3061

Bacteriophytochromes (BphPs) are photoreceptors that regulate a wide range of biological mechanisms via red light–absorbing (Pr)–to–far-red light–absorbing (Pfr) reversible photoconversion. The structural dynamics underlying Pfr-to-Pr photoconversion in a liquid solution phase are not well understood. We used time-resolved x-ray solution scattering (TRXSS) to capture light-induced structural transitions in the bathy BphP photosensory module of Pseudomonas aeruginosa . Kinetic analysis of the TRXSS data identifies three distinct structural species, which are attributed to lumi-F, meta-F, and Pr, connected by time constants of 95 μs and 21 ms. Structural analysis based on molecular dynamics simulations shows that the light activation of PaBphP accompanies quaternary structural rearrangements from an “II”-framed close form of the Pfr state to an “O”-framed open form of the Pr state in terms of the helical backbones. This study provides mechanistic insights into how modular signaling proteins such as BphPs transmit structural signals over long distances and regulate their downstream biological responses.

This paper presents a method for jointly estimating the state, input, and parameters of linear systems in an online fashion. The method is specially designed for measurements that are corrupted with non-Gaussian noise or outliers, which are commonly found in engineering applications. In particular, it combines recursive, alternating, and iteratively-reweighted least squares into a single, one-step algorithm, which solves the estimation problem online and benefits from the robustness of least-deviation regression methods. The convergence of the iterative method is formally guaranteed. Numerical experiments show the good performance of the estimation algorithm in presence of outliers and in comparison to state-of-the-art methods., Comment: 6 pages, 2 figures

Phasor Based Control is a novel approach to controlling Distributed Energy Resources that aims at relieving various constraints that arise in the distribution grid. It is a two-layer control system with a supervisory control that coordinates distributed controllers to reach voltage phasor targets. The distributed controllers use local synchrophasor measurements and operate as feedback controllers. This control method is currently under development with several algorithms being under consideration for both the central and ditributed components. In this paper, we present the experimental setup that was prepared to prototype a hardware implementation and validate the control method in Hardware-In-the-Loop.

Electrochemical energy storage is critical for a range of applications spanning electrified transportation and grid energy storage, and there is a need to further improve both the active management and diagnostic capability of current battery management systems. Lithium-based battery chemistries have been favored for their high energy and power densities but require precise management to prevent premature degradation and failure. This work presents an efficient power converter (based on a switched-inductor ladder topology), instrumentation, and an embedded control platform that can provide both active balancing and real-time diagnostic capability through electrochemical impedance spectroscopy (EIS). A digital proportional-integral controller enforces sinusoidal reference signals from a direct digital synthesizer, enabling the power converter to perturb the cells and extract their impedance. Cell-level diagnostics allow for noninvasive measurement of physical electrochemical battery properties that can be used to assess the state of charge and state of health of a battery. A ladder converter prototype was implemented on a printed circuit board to perform EIS on two Panasonic 18650 cells in series. Experimental results showed balancing converter efficiency of 95%, and the accuracy of the prototype was validated through comparison to a state-of-the-art commercial benchtop system.

This paper introduces two tools-the Effective Impedance State Estimator (EISE), and the Real Time Effective Impedance Estimator (RTEIE). The EISE is novel in that it is an entirely data-driven state estimator, and does not require a network model. Thus, the EISE is well suited for applications in which an accurate network model is not available. Instead of using a network impedance model, the EISE uses an effective impedance network model that is learned online by the RTEIE. The RTEIE recursively estimates the effective impedance network model using phasor measurement unit (PMU) measurements. The mathematical reasoning for using an effective impedance model, rather than a full network impedance model, is given. The recursive estimation framework allows the RTEIE to take the entire history of phasor measurements into account to produce a model estimate, while still adjusting to changes in the network impedance due to external factors such as topology changes and temperature. The merits of the RTEIE and EISE are demonstrated by comparing the accuracy of the EISE with a conventional state estimator on a toy network.

ObjectiveTo synthesise international evidence for demand, use and outcomes of primary care out-of-hours health services (OOHS).DesignSystematic scoping review.Data sourcesCINAHL; Medline; PsyARTICLES; PsycINFO; SocINDEX; and Embase from 1995 to 2019.Study selectionEnglish language studies in UK or similar international settings, focused on services in or directly impacting primary care.Results105 studies included: 54% from mainland Europe/Republic of Ireland; 37% from UK. Most focused on general practitioner-led out-of-hours cooperatives. Evidence for increasing patient demand over time was weak due to data heterogeneity, infrequent reporting of population denominators and little adjustment for population sociodemographics. There was consistent evidence of higher OOHS use in the evening compared with overnight, at weekends and by certain groups (children aged 65, women, those from socioeconomically deprived areas, with chronic diseases or mental health problems). Contact with OOHS was driven by problems perceived as urgent by patients. Respiratory, musculoskeletal, skin and abdominal symptoms were the most common reasons for contact in adults; fever and gastrointestinal symptoms were the most common in the under-5s. Frequent users of daytime services were also frequent OOHS users; difficulty accessing daytime services was also associated with OOHS use. There is some evidence to suggest that OOHS colocated in emergency departments (ED) can reduce demand in EDs.ConclusionsPolicy changes have impacted on OOHS over the past two decades. While there are generalisable lessons, a lack of comparable data makes it difficult to judge how demand has changed over time. Agreement on collection of OOHS data would allow robust comparisons within and across countries and across new models of care. Future developments in OOHS should also pay more attention to the relationship with daytime primary care and other services.PROSPERO registration numberCRD42015029741.

Phytochromes are red/far-red photoreceptors that are widely distributed in plants and prokaryotes. Ultrafast photoisomerization of a double bond in a biliverdin cofactor or other linear tetrapyrrole drives their photoactivity, but their photodynamics are only partially understood. Multiexponential dynamics were observed in previous ultrafast spectroscopic studies and were attributed to heterogeneous populations of the pigment-protein complex. In this work, two-dimensional photon echo spectroscopy was applied to study dynamics of the bacteriophytochromes RpBphP2 and PaBphP. Two-dimensional photon echo spectroscopy can simultaneously resolve inhomogeneity in ensembles and fast dynamics by correlating pump wavelength with the emitted signal wavelength. The distribution of absorption and emission energies within the same state indicates an ensemble of heterogeneous protein environments that are spectroscopically distinct. However, the lifetimes of the dynamics are uniform across the ensemble, suggesting a homogeneous model involving sequential intermediates for the initial photodynamics of isomerization.

We investigate photocycle excitation of crystalline photoactive yellow protein using femtosecond laser pulses. This work establishes the feasibility and suitable optical excitation conditions to perform femtosecond time resolved X-ray crystallographic measurements using an X-ray free electron laser. Flash photolysis experiments demonstrated photocycle yields of the long-lived ‘pB’ signalling state of PYP of up to 10% with pulse durations of 130, 500 and 850 fs at 450 nm wavelength. The power density dependence of the transient pB concentration depends strongly on the pulse duration primarily because photobleaching is prominent at the GW/mm 2 level.

Background People with multimorbidity experience impaired quality of life, poor health and a burden from treatment. Their care is often disease-focused rather than patient-centred and tailored to their individual needs. Objective To implement and evaluate a patient-centred intervention to improve the management of patients with multimorbidity in general practice. Design Pragmatic, cluster randomised controlled trial with parallel process and economic evaluations. Practices were centrally randomised by a statistician blind to practice identifiers, using a computer-generated algorithm. Setting Thirty-three general practices in three areas of England and Scotland. Participants Practices had at least 4500 patients and two general practitioners (GPs) and used the EMIS (Egton Medical Information Systems) computer system. Patients were aged ≥ 18 years with three or more long-term conditions. Interventions The 3D (Dimensions of health, Depression and Drugs) intervention was designed to offer patients continuity of care with a named GP, replacing separate reviews of each long-term condition with comprehensive reviews every 6 months. These focused on individualising care to address patients’ main problems, attention to quality of life, depression and polypharmacy and on disease control and agreeing treatment plans. Control practices provided usual care. Outcome measures Primary outcome – health-related quality of life (assessed using the EuroQol-5 Dimensions, five-level version) after 15 months. Secondary outcomes – measures of illness burden, treatment burden and patient-centred care. We assessed cost-effectiveness from a NHS and a social care perspective. Results Thirty-three practices (1546 patients) were randomised from May to December 2015 [16 practices (797 patients) to the 3D intervention, 17 practices (749 patients) to usual care]. All participants were included in the primary outcome analysis by imputing missing data. There was no evidence of difference between trial arms in health-related quality of life {adjusted difference in means 0.00 [95% confidence interval (CI) –0.02 to 0.02]; p = 0.93}, illness burden or treatment burden. However, patients reported significant benefits from the 3D intervention in all measures of patient-centred care. Qualitative data suggested that both patients and staff welcomed having more time, continuity of care and the patient-centred approach. The economic analysis found no meaningful differences between the intervention and usual care in either quality-adjusted life-years [(QALYs) adjusted mean QALY difference 0.007, 95% CI –0.009 to 0.023] or costs (adjusted mean difference £126, 95% CI –£739 to £991), with wide uncertainty around point estimates. The cost-effectiveness acceptability curve suggested that the intervention was unlikely to be either more or less cost-effective than usual care. Seventy-eight patients died (46 in the intervention arm and 32 in the usual-care arm), with no evidence of difference between trial arms; no deaths appeared to be associated with the intervention. Limitations In this pragmatic trial, the implementation of the intervention was incomplete: 49% of patients received two 3D reviews over 15 months, whereas 75% received at least one review. Conclusions The 3D approach reflected international consensus about how to improve care for multimorbidity. Although it achieved the aim of providing more patient-centred care, this was not associated with benefits in quality of life, illness burden or treatment burden. The intervention was no more or less cost-effective than usual care. Modifications to the 3D approach might improve its effectiveness. Evaluation is needed based on whole-system change over a longer period of time. Trial registration Current Controlled Trials ISRCTN06180958. Funding This project was funded by the National Institute for Health Research (NIHR) Health Services and Delivery Research programme and will be published in full in Health Services and Delivery Research; Vol. 7, No. 5. See the NIHR Journals Library website for further project information.

Background: \ud The management of people with multiple chronic conditions challenges health-care systems designed around single conditions. There is international consensus that care for multimorbidity should be patient-centred, focus on quality of life, and promote self-management towards agreed goals. However, there is little evidence about the effectiveness of this approach. Our hypothesis was that the patient-centred, so-called 3D approach (based on dimensions of health, depression, and drugs) for patients with multimorbidity would improve their health-related quality of life, which is the ultimate aim of the 3D intervention.\ud \ud Methods: \ud We did this pragmatic cluster-randomised trial in general practices in England and Scotland. Practices were randomly allocated to continue usual care (17 practices) or to provide 6-monthly comprehensive 3D reviews, incorporating patient-centred strategies that reflected international consensus on best care (16 practices). Randomisation was computer-generated, stratified by area, and minimised by practice deprivation and list size. Adults with three or more chronic conditions were recruited. The primary outcome was quality of life (assessed with EQ-5D-5L) after 15 months' follow-up. Participants were not masked to group assignment, but analysis of outcomes was blinded. We analysed the primary outcome in the intention-to-treat population, with missing data being multiply imputed. This trial is registered as an International Standard Randomised Controlled Trial, number ISRCTN06180958.\ud \ud Findings: \ud Between May 20, 2015, and Dec 31, 2015, we recruited 1546 patients from 33 practices and randomly assigned them to receive the intervention (n=797) or usual care (n=749). In our intention-to-treat analysis, there was no difference between trial groups in the primary outcome of quality of life (adjusted difference in mean EQ-5D-5L 0·00, 95% CI −0·02 to 0·02; p=0·93). 78 patients died, and the deaths were not considered as related to the intervention.\ud \ud Interpretation: \ud To our knowledge, this trial is the largest investigation of the international consensus about optimal management of multimorbidity. The 3D intervention did not improve patients' quality of life.\ud \ud Funding: \ud National Institute for Health Research.

SummaryRpBphP2 and RpBphP3, two tandem bacteriophytochromes from the photosynthetic bacterium Rhodopseudomonas palustris, share high sequence identity but exhibit distinct photoconversion behavior. Unlike the canonical RpBphP2, RpBphP3 photoconverts to an unusual near-red-absorbing (Pnr) state; both are required for synthesis of light-harvesting complexes under low-light conditions. Here we report the crystal structures of the photosensory core modules of RpBphP2 and RpBphP3. Despite different quaternary structures, RpBphP2 and RpBphP3 adopt nearly identical tertiary structures. The RpBphP3 structure reveals tongue-and-groove interactions at the interface between the GAF and PHY domains. A single mutation in the PRxSF motif at the GAF-PHY interface abolishes light-induced formation of the Pnr state in RpBphP3, possibly due to altered structural rigidity of the chromophore-binding pocket. Structural comparisons suggest that long-range signaling involves structural rearrangement of the helical spine at the dimer interface. These structures, together with mutational studies, provide insights into photoconversion and the long-range signaling mechanism in phytochromes.

A personal, historical view is presented of Laue X-ray diffraction and its application to time-resolved studies of dynamic processes, largely in light-sensitive biological systems. In Laue diffraction, a stationary crystal is illuminated by a polychromatic X-ray source. Laue diffraction has inherent complications largely absent in monochromatic diffraction, and consequently fell into disuse for quantitative structure determination. However, the advent of naturally polychromatic, intense, pulsed storage ring X-ray sources in the 1970s led to re-examination at Daresbury and elsewhere of its underlying principles. Laue diffraction has been successfully applied at storage ring sources to time-resolved, pump–probe crystallographic studies, whose exposure time and time resolution were progressively reduced from minutes to seconds, milliseconds, nanoseconds and 100 ps. Most recently, hard X-ray free electron laser sources have been used to generate narrow bandpass Laue diffraction patterns. The femtosecond X-ray pulses from such sources are completely destructive, generate only one diffraction pattern per tiny crystal and have unusual properties. However, they too are being applied to time-resolved crystallography to explore, for example, isomerization and rapid tertiary structural changes on the chemical, femtosecond timescale. This article is part of the theme issue ‘Fifty years of synchrotron science: achievements and opportunities’.

Dynamic behavior of proteins is critical to their function. X-ray crystallography, a powerful yet mostly static technique, faces inherent challenges in acquiring dynamic information despite decades of effort. Dynamic `structural changes' are often indirectly inferred from `structural differences' by comparing related static structures. In contrast, the direct observation of dynamic structural changes requires the initiation of a biochemical reaction or process in a crystal. Both the direct and the indirect approaches share a common challenge in analysis: how to interpret the structural heterogeneity intrinsic to all dynamic processes. This paper presents a real-space approach to this challenge, in which a suite of analytical methods and tools to identify and refine the mixed structural species present in multiple crystallographic data sets have been developed. These methods have been applied to representative scenarios in dynamic crystallography, and reveal structural information that is otherwise difficult to interpret or inaccessible using conventional methods.

Trans-to-cis isomerization, the key reaction in photoactive proteins, usually cannot occur through the standard one-bond-flip mechanism. Owing to spatial constraints imposed by a protein environment, isomerization probably proceeds through a volume-conserving mechanism in which highly choreographed atomic motions are expected, the details of which have not yet been observed directly. Here we employ time-resolved X-ray crystallography to visualize structurally the isomerization of the p-coumaric acid chromophore in photoactive yellow protein with a time resolution of 100 ps and a spatial resolution of 1.6 A. The structure of the earliest intermediate (IT) resembles a highly strained transition state in which the torsion angle is located halfway between the trans- and cis-isomers. The reaction trajectory of IT bifurcates into two structurally distinct cis intermediates via hula-twist and bicycle-pedal pathways. The bifurcating reaction pathways can be controlled by weakening the hydrogen bond between the chromophore and an adjacent residue through E46Q mutation, which switches off the bicycle-pedal pathway. Time-resolved X-ray crystallography on photoactive yellow protein shows the existence of a short-lived, highly distorted intermediate whose reaction trajectory bifurcates along ‘bicycle-pedal’ and ‘hula-twist’ pathways. The bifurcating reaction pathways can be controlled by weakening the hydrogen bond between the chromophore and an adjacent residue, which switches off the bicycle-pedal pathway.

Background To identify, summarise and synthesise the evidence for using interactive digital interventions to support patient self-management of asthma, and determine their impact. Methods Systematic review with meta-analysis. We searched MEDLINE, EMBASE, CINAHL, PsycINFO, ERIC, Cochrane Library, DoPHER, TROPHI, Social Science Citation Index and Science Citation Index. The selection criteria requirement was studies of adults (16 years and over) with asthma, interventions that were interactive digital interventions and the comparator was usual care. Outcomes were change in clinical outcomes, cost effectiveness and patient-reported measures of wellbeing or quality of life. Only Randomised Controlled Trials published in peer-reviewed journals in English were eligible. Potential studies were screened and study characteristics and outcomes were extracted from eligible papers independently by two researchers. Where data allowed, meta-analysis was performed using a random effects model. Results Eight papers describing 5 trials with 593 participants were included, but only three studies were eligible for inclusion for meta-analysis. Of these, two aimed to improve asthma control and the third aimed to reduce the total dose of oral prednisolone without worsening control. Analyses with data from all three studies showed no significant differences and extremely high heterogeneity for both Asthma Quality of Life (AQLQ) (Standardised Mean Difference (SMD) 0.05; 95 % Confidence Interval (CI) 0.32 to −0.22: I2 96.8) and asthma control (SMD 0.21; 95 % CI −0.05 to .42; I2 = 87.4). The removal of the third study reduced heterogeneity and indicated significant improvement for both AQLQ (SMD 0.45; 95 % CI 0.13 to 0.77: I2 = 0.34) and asthma control (SMD 0.54; 95 % CI 0.22 to 0.86: I2 = 0.11). No evidence of harm was identified. Conclusion Digital self-management interventions for adults with asthma show promise, with some evidence of small beneficial effects on asthma control. Overall, the evidence base remains weak due to the lack of large, robust trials. Electronic supplementary material The online version of this article (doi:10.1186/s12890-016-0248-7) contains supplementary material, which is available to authorized users.

Summary Aureochrome1, a signaling photoreceptor from a eukaryotic photosynthetic stramenopile, confers blue-light-regulated DNA binding on the organism. Its topology, in which a C-terminal LOV sensor domain is linked to an N-terminal DNA-binding bZIP effector domain, contrasts with the reverse sensor-effector topology in most other known LOV-photoreceptors. How, then, is signal transmitted in Aureochrome1? The dark- and light-state crystal structures of Aureochrome1 LOV domain (AuLOV) show that its helical N- and C-terminal flanking regions are packed against the external surface of the core β sheet, opposite to the FMN chromophore on the internal surface. Light-induced conformational changes occur in the quaternary structure of the AuLOV dimer and in Phe298 of the Hβ strand in the core. The properties of AuLOV extend the applicability of LOV domains as versatile design modules that permit fusion to effector domains via either the N- or C-termini to confer blue-light sensitivity.

Light is a fundamental signal that regulates important physiological processes such as development and circadian rhythm in living organisms. Phytochromes form a major family of photoreceptors responsible for red light perception in plants, fungi and bacteria. They undergo reversible photoconversion between red-absorbing (Pr) and far-red-absorbing (Pfr) states, thereby ultimately converting a light signal into a distinct biological signal that mediates subsequent cellular responses. Several structures of microbial phytochromes have been determined in their dark-adapted Pr or Pfr states. However, the structural nature of initial photochemical events has not been characterized by crystallography. Here we report the crystal structures of three intermediates in the photoreaction of Pseudomonas aeruginosa bacteriophytochrome (PaBphP). We used cryotrapping crystallography to capture intermediates, and followed structural changes by scanning the temperature at which the photoreaction proceeded. Light-induced conformational changes in PaBphP originate in ring D of the biliverdin (BV) chromophore, and E-to-Z isomerization about the C(15) = C(16) double bond between rings C and D is the initial photochemical event. As the chromophore relaxes, the twist of the C(15) methine bridge about its two dihedral angles is reversed. Structural changes extend further to rings B and A, and to the surrounding protein regions. These data indicate that absorption of a photon by the Pfr state of PaBphP converts a light signal into a structural signal via twisting and untwisting of the methine bridges in the linear tetrapyrrole within the confined protein cavity.

BioCARS, a NIH-supported national user facility for macromolecular time-resolved X-ray crystallography at the Advanced Photon Source (APS), has recently completed commissioning of an upgraded undulator-based beamline optimized for single-shot laser-pump X-ray-probe measurements with time resolution as short as 100 ps. The source consists of two in-line undulators with periods of 23 and 27 mm that together provide high-flux pink-beam capability at 12 keV as well as first-harmonic coverage from 6.8 to 19 keV. A high-heat-load chopper reduces the average power load on downstream components, thereby preserving the surface figure of a Kirkpatrick–Baez mirror system capable of focusing the X-ray beam to a spot size of 90 µm horizontal by 20 µm vertical. A high-speed chopper isolates single X-ray pulses at 1 kHz in both hybrid and 24-bunch modes of the APS storage ring. In hybrid mode each isolated X-ray pulse delivers up to ∼4 × 1010photons to the sample, thereby achieving a time-averaged flux approaching that of fourth-generation X-FEL sources. A new high-power picosecond laser system delivers pulses tunable over the wavelength range 450–2000 nm. These pulses are synchronized to the storage-ring RF clock with long-term stability better than 10 ps RMS. Monochromatic experimental capability with Biosafety Level 3 certification has been retained.

The phototropins are blue-light receptors that base their lightdependent action on the reversible formation of a covalent bond between a flavin mononucleotide (FMN) cofactor and a conserved cysteine in light, oxygen or voltage (LOV) domains. The primary reactions of the Avena sativa phototropin 1 LOV2 domain were investigated by means of time-resolved and lowtemperature fluorescence spectroscopy. Synchroscan streak camera experiments revealed a fluorescence lifetime of 2.2 ns in LOV2. A weak long-lived component with emission intensity from 600 to 650 nm was assigned to phosphorescence from the reactive FMN triplet state. This observation allowed determination of the LOV2 triplet state energy level at physiological temperature at 16600 cm )1 . FMN dissolved in aqueous solution showed pH-dependent fluorescence lifetimes of 2.7 ns at pH 2 and 3.9)4.1 ns at pH 3–8. Here, too, a weak phosphorescence band was observed. The fluorescence quantum yield of LOV2 increased from 0.13 to 0.41 upon cooling the sample from 293 to 77 K. A pronounced phosphorescence emission around 600 nm was observed in the LOV2 domain between 77 and 120 K in the steady-state emission.

The initial output of a time-resolved macromolecular crystallography experiment is a time-dependent series of difference electron density maps that displays the time-dependent changes in underlying structure as a reaction progresses. The goal is to interpret such data in terms of a small number of crystallographically refinable, time-independent structures, each associated with a reaction intermediate; to establish the pathways and rate coefficients by which these intermediates interconvert; and thereby to elucidate a chemical kinetic mechanism. One strategy toward achieving this goal is to use cluster analysis, a statistical method that groups objects based on their similarity. If the difference electron density at a particular voxel in the time-dependent difference electron density (TDED) maps is sensitive to the presence of one and only one intermediate, then its temporal evolution will exactly parallel the concentration profile of that intermediate with time. The rationale is therefore to cluster voxels with respect to the shapes of their TDEDs, so that each group or cluster of voxels corresponds to one structural intermediate. Clusters of voxels whose TDEDs reflect the presence of two or more specific intermediates can also be identified. From such groupings one can then infer the number of intermediates, obtain their time-independent difference density characteristics, and refine the structure of each intermediate. We review the principles of cluster analysis and clustering algorithms in a crystallographic context, and describe the application of the method to simulated and experimental time-resolved crystallographic data for the photocycle of photoactive yellow protein.

Phytochromes are red-light photoreceptor proteins that regulate a variety of responses and cellular processes in plants, bacteria, and fungi. The phytochrome light activation mechanism involves isomerization around the C15═C16 double bond of an open-chain tetrapyrrole chromophore, resulting in a flip of its D-ring. In an important new development, bacteriophytochrome (Bph) has been engineered for use as a fluorescent marker in mammalian tissues. Here we report that an unusual Bph, RpBphP3 from Rhodopseudomonas palustris , denoted P3, is fluorescent. This Bph modulates synthesis of light-harvesting complex in combination with a second Bph exhibiting classical photochemistry, RpBphP2, denoted P2. We identify the factors that determine the fluorescence and isomerization quantum yields through the application of ultrafast spectroscopy to wild-type and mutants of P2 and P3. The excited-state lifetime of the biliverdin chromophore in P3 was significantly longer at 330–500 ps than in P2 and other classical phytochromes and accompanied by a significantly reduced isomerization quantum yield. H/D exchange reduces the rate of decay from the excited state of biliverdin by a factor of 1.4 and increases the isomerization quantum yield. Comparison of the properties of the P2 and P3 variants shows that the quantum yields of fluorescence and isomerization are determined by excited-state deprotonation of biliverdin at the pyrrole rings, in competition with hydrogen-bond rupture between the D-ring and the apoprotein. This work provides a basis for structure-based conversion of Bph into an efficient near-IR fluorescent marker.

Phytochromes are red-light photoreceptors that regulate light responses in plants, fungi, and bacteria via reversible photoconversion between red (Pr) and far-red (Pfr) light-absorbing states. Here we report the crystal structure at 2.9 Å resolution of a bacteriophytochrome from Pseudomonas aeruginosa with an intact, fully photoactive photosensory core domain in its dark-adapted Pfr state. This structure reveals how unusual interdomain interactions, including a knot and an “arm” structure near the chromophore site, bring together the PAS (Per-ARNT-Sim), GAF (cGMP phosphodiesterase/adenyl cyclase/FhlA), and PHY (phytochrome) domains to achieve Pr/Pfr photoconversion. The PAS, GAF, and PHY domains have topologic elements in common and may have a single evolutionary origin. We identify key interactions that stabilize the chromophore in the Pfr state and provide structural and mutational evidence to support the essential role of the PHY domain in efficient Pr/Pfr photoconversion. We also identify a pair of conserved residues that may undergo concerted conformational changes during photoconversion. Modeling of the full-length bacteriophytochrome structure, including its output histidine kinase domain, suggests how local structural changes originating in the photosensory domain modulate interactions between long, cross-domain signaling helices at the dimer interface and are transmitted to the spatially distant effector domain, thereby regulating its histidine kinase activity.

Time-resolved crystallography uses the brief, intense X-ray pulses emitted by synchrotron or hard X-ray free electron laser (FEL) sources to probe the time course of structural changes as they occur in the molecules in a crystal, via pump - probe experiments. Synchrotron sources such as BioCARS sector 14 at the Advanced Photon Source, Argonne National Laboratory, can access the time scale from seconds to 100 picoseconds, where the lower limit is set by the duration of a single X-ray pulse. The new FEL sources such as the Linac Coherent Light Source at Stanford extend this limit to femtoseconds. The characteristics of the X-ray pulses emitted by synchrotron and FEL sources are radically different which necessitates new approaches to the pump - probe experiments and data analysis. For both synchrotron and FEL sources, reaction initiation typically requires light-sensitive systems in which reaction can be initiated by a visible laser pulse - but clearly, not all interesting biological systems are light-sensitive. This raises the question: how can sensitivity to light be conferred on otherwise light-inert systems, by optogenetic approaches?Ultrafast time-resolved crystallography will be illustrated by experiments conducted at synchrotron and FEL sources, that probe the structure of short-lived structural intermediates in the photocycle of the naturally-occurring bacterial blue light photoreceptor known as photoactive yellow protein, PYP. The principles that can be used to confer sensitivity to light on light-inert systems are illustrated by the design and characterization of a blue-light-sensitive histidine kinase. Finally I ask: are these principles equally applicable to experiments in the femtosecond time range at FEL sources.This research has been supported by NIH grants GM111072 and EY024363.

International audience; Spin-crossover crystals show multi-step responses to femtosecond light excitation. The local molecular photo-switching from low to high spin states occurs on sub-picosecond timescale. It is followed by additional conversion due to elastic (ns) and thermal (µs) effects. In [Fe(phen)2(NCS)2] crystals discussed herein, the thermal switching can be made unobtrusive for the investigation of cooperative elastic switching. We evidence a cooperative transformation induced by lattice expansion through elastic coupling between molecules in the crystal, where up to 3 molecules are transformed per photon.

Many biological processes depend on detecting and responding to light. The response is often mediated by a structural change in a protein that begins when absorption of a photon causes isomerization of a chromophore bound to the protein. Pande et al. used x-ray pulses emitted by a free electron laser source to conduct time-resolved serial femtosecond crystallography in the time range of 100 fs to 3 ms. This allowed for the real-time tracking of the trans-cis isomerization of the chromophore in photoactive yellow protein and the associated structural changes in the protein.Science, this issue p. 725A variety of organisms have evolved mechanisms to detect and respond to light, in which the response is mediated by protein structural changes after photon absorption. The initial step is often the photoisomerization of a conjugated chromophore. Isomerization occurs on ultrafast time scales and is substantially influenced by the chromophore environment. Here we identify structural changes associated with the earliest steps in the trans-to-cis isomerization of the chromophore in photoactive yellow protein. Femtosecond hard x-ray pulses emitted by the Linac Coherent Light Source were used to conduct time-resolved serial femtosecond crystallography on photoactive yellow protein microcrystals over a time range from 100 femtoseconds to 3 picoseconds to determine the structural dynamics of the photoisomerization reaction.

Bacteriophytochromes RpBphP2 and RpBphP3 from the photosynthetic bacterium Rhodopseudomonas palustris work in tandem to modulate synthesis of the light-harvesting complex LH4 in response to light. Although RpBphP2 and RpBphP3 share the same domain structure with 52% sequence identity, they demonstrate distinct photoconversion behaviors. RpBphP2 exhibits the “classical” phytochrome behavior of reversible photoconversion between red (Pr) and far-red (Pfr) light-absorbing states, whereas RpBphP3 exhibits novel photoconversion between Pr and a near-red (Pnr) light-absorbing states. We have determined the crystal structure at 2.2-Å resolution of the chromophore binding domains of RpBphP3, covalently bound with chromophore biliverdin IXα. By combining structural and sequence analyses with site-directed mutagenesis, we identify key residues that directly modulate the photochemical properties of RpBphP3 and RpBphP2. Remarkably, we identify a region spanning residues 207–212 in RpBphP3, in which a single mutation, L207Y, causes this unusual bacteriophytochrome to revert to the classical phenotype that undergoes reversible photoconversion between the Pr and Pfr states. The reverse mutation, Y193L, in the corresponding region in RpBphP2 significantly diminishes the formation of the Pfr state. We propose that residues 207–212 and the spatially adjacent conserved residues, Asp-216 and Tyr-272, interact with the chromophore and form part of the interface between the chromophore binding domains and the PHY domain that modulates photoconversion.

Two-component signal transduction is the major signaling mechanism that enables bacteria to survive and thrive in complex environmental conditions. The photosynthetic bacterium R. palustris employs two tandem bacteriophytochromes, RpBphP2 and RpBphP3, to perceive red-light signals that regulate the synthesis of light-harvesting complexes under low-light conditions. Both RpBphP2 and RpBphP3 are photosensory histidine kinases coupled to the same response regulator RPA3017. Together, they constitute a two-component system that converts a red-light signal into a biological signal. In this work, the crystal structure of RPA3017 in the unphosphorylated form at 1.9 Å resolution is presented. This structure reveals a tightly associated dimer arrangement that is conserved among phytochrome-related response regulators. The conserved active-site architecture provides structural insight into the phosphotransfer reaction between RpBphP2/RpBphP3 and RPA3017. Based on structural comparisons and homology modeling, how specific recognition between RpBphP2/RpBphP3 and RPA3017 is achieved at the molecular level is further explored.

Time-resolved ultraviolet-visible spectroscopy was used to characterize the photocycle transitions in single crystals of wild-type and the E-46Q mutant of photoactive yellow protein (PYP) with microsecond time resolution. The results were compared with the results of similar measurements on aqueous solutions of these two variants of PYP, with and without the components present in the mother liquor of crystals. The experimental data were analyzed with global and target analysis. Distinct differences in the reaction path of a PYP molecule are observed between these conditions when it progresses through its photocycle. In the crystalline state i), much faster relaxation of the late blue-shifted photocycle intermediate back to the ground state is observed; ii), this intermediate in crystalline PYP absorbs at 380 nm, rather than at 350-360 nm in solution; and iii), for various intermediates of this photocycle the forward reaction through the photocycle directly competes with a branching reaction that leads directly to the ground state. Significantly, with these altered characteristics, the spectroscopic data on PYP are fully consistent with the structural data obtained for this photoreceptor protein with time-resolved x-ray diffraction analysis, particularly for wild-type PYP. © 2006 by the Biophysical Society.

The flavin-binding BLUF domain of AppA represents a new class of blue light photoreceptors that are present in a number of bacterial and algal species. The dark state X-ray structure of this domain was determined at 2.3 A resolution. The domain demonstrates a new function for the common ferredoxin-like fold; two long alpha-helices flank the flavin, which is bound with its isoalloxazine ring perpendicular to a five-stranded beta-sheet. The hydrogen bond network and the overall protein topology of the BLUF domain (but not its sequence) bear some resemblance to LOV domains, a subset of PAS domains widely involved in signaling. Nearly all residues conserved in BLUF domains surround the flavin chromophore, many of which are involved in an intricate hydrogen bond network. Photoactivation may induce a rearrangement in this network via reorientation of the Gln63 side chain to form a new hydrogen bond to the flavin O4 position. This shift would also break a hydrogen bond to the Trp104 side chain, which may be critical in induction of global structural change in AppA.

We use time-resolved crystallography to observe the structural progression of a bacterial blue light photoreceptor throughout its photocycle. Data were collected from 10 ns to 100 ms after photoactivation of the E46Q mutant of photoactive yellow protein. Refinement of transient chromophore conformations shows that the spectroscopically distinct intermediates are formed via progressive disruption of the hydrogen bond network to the chromophore. Although structural change occurs within a few nanoseconds on and around the chromophore, it takes milliseconds for a distinct pattern of tertiary structural change to fully progress through the entire molecule, thus generating the putative signaling state. Remarkably, the coupling between the chromophore conformation and the tertiary structure of this small protein is not tight: there are leads and lags between changes in the conformation of the chromophore and the protein tertiary structure.

Light-induced structural changes in the bacterial reaction center were studied by a time-resolved crystallographic experiment. Crystals of protein from Blastochloris viridis (formerly Rhodopseudomonas viridis ) were reconstituted with ubiquinone and analyzed by monochromatic and Laue diffraction, in the dark and 3 ms after illuminating the crystal with a pulsed laser (630 nm, 3 mJ/pulse, 7 ns duration). Refinement of monochromatic data shows that ubiquinone binds only in the “proximal” Q B binding site. No significant structural difference was observed between the light and dark datasets; in particular, no quinone motion was detected. This result may be reconciled with previous studies by postulating equilibration of the “distal” and “proximal” binding sites upon extended dark adaption, and in which movement of ubiquinone is not the conformational gate for the first electron transfer between Q A and Q B .

Photoactive yellow protein (E-PYP) is a blue light photoreceptor, implicated in a negative phototactic response in Ectothiorhodospira halophila , that also serves as a model for the Per–Arnt–Sim superfamily of signaling molecules. Because no biological signaling partner for E-PYP has been identified, it has not been possible to correlate any of its photocycle intermediates with a relevant signaling state. However, the PYP domain (Ppr-PYP) from the sensor histidine kinase Ppr in Rhodospirillum centenum , which regulates the catalytic activity of Ppr by blue light absorption, may allow such issues to be addressed. Here we report the crystal structure of Ppr-PYP at 2 Å resolution. This domain has the same absorption spectrum and similar photocycle kinetics as full length Ppr, but a blue-shifted absorbance and considerably slower photocycle than E-PYP. Although the overall fold of Ppr-PYP resembles that of E-PYP, a novel conformation of the β4–β5 loop results in inaccessibility of Met-100, thought to catalyze chromophore reisomerization, to the chromophore. This conformation also exposes a highly conserved molecular surface that could interact with downstream signaling partners. Other structural differences in the α3–α4 and β4–β5 loops are consistent with these regions playing significant roles in the control of photocycle dynamics and, by comparison to other sensory Per–Arnt–Sim domains, in signal transduction. Because of its direct linkage to a measurable biological output, Ppr-PYP serves as an excellent system for understanding how changes in photocycle dynamics affect signaling by PYPs.

The spin crossover compound [FeIIH2L2-Me][PF6]2 presents a two-step phase transition. In the intermediate phase, a spin state concentration wave (SSCW) appears resulting from a symmetry breaking (cell doubling) associated with a long-range order of alternating high and low spin molecular states. By combining time-resolved optical and X-ray diffraction measurements on a single crystal, we study how such a system responds to femtosecond laser excitation and we follow in real time the erasing and rewriting of the SSCW.

Multimorbidity is a growing issue and poses a major challenge to health care systems around the world. Multimorbidity is related to ageing but many studies have now shown that it is also socially patterned, being more common and occurring at an earlier age in areas of high socioeconomic deprivation. There is lack of research on patients with multimorbidity, and thus guidelines are based on single-conditions. Polypharmacy is common in multimorbidity, increasing drug-disease and drug-drug interactions. Multimorbid patients need holistic care, but secondary care services are highly specialised and thus are often duplicative and fragmented and thus increase treatment burden in multimorbid patients. The cost of care is high in multimorbidity, due to high rates of primary and secondary care consultations and unplanned hospital admissions. The combination of mental and physical conditions increases complexity of care, and costs. Mental-physical multimorbidity is especially common in deprived areas. General practitioners and primary care teams have a key role in managing patients with multimorbidity, using a patient-centred generalist approach. Consultation length and continuity of care may need to be substantially enhanced in order to enable such patients. This will require a radical change in how health care systems are organised and funded in order to effectively meet the challenges of multimorbidity. Publisher PDF

X-ray radiation damage of lysozyme single crystals by an intense monochromatic beam from the Advanced Photon Source is studied at cryogenic temperatures between 40 K and 150 K. The results confirm that primary radiation damage is both linearly dependent on the X-ray dose and independent of temperature. The upper limit for the primary radiation damage observed in our previous study [Teng & Moffat (2000), J. Synchrotron Rad. 7, 313–317] holds over the wider temperature range of this study. The X-ray diffraction quality of the data acquired at 40 K is superior to those at 100 K, apparently due to temperature dependence of secondary and tertiary radiation damage and to reduced thermal motion.

Serial femtosecond crystallography using ultrashort pulses from x-ray free electron lasers (XFELs) enables studies of the light-triggered dynamics of biomolecules. We used microcrystals of photoactive yellow protein (a bacterial blue light photoreceptor) as a model system and obtained high-resolution, time-resolved difference electron density maps of excellent quality with strong features; these allowed the determination of structures of reaction intermediates to a resolution of 1.6 angstroms. Our results open the way to the study of reversible and nonreversible biological reactions on time scales as short as femtoseconds under conditions that maximize the extent of reaction initiation throughout the crystal.

Time-resolved X-ray crystallography and solution scattering have been successfully conducted on proteins on time-scales down to around 100 ps, set by the duration of the hard X-ray pulses emitted by synchrotron sources. The advent of hard X-ray free-electron lasers (FELs), which emit extremely intense, very brief, coherent X-ray pulses, opens the exciting possibility of time-resolved experiments with femtosecond time resolution on macromolecular structure, in both single crystals and solution. The X-ray pulses emitted by an FEL differ greatly in many properties from those emitted by a synchrotron, in ways that at first glance make time-resolved measurements of X-ray scattering with the required accuracy extremely challenging. This opens up several questions which I consider in this brief overview. Are there likely to be chemically and biologically interesting structural changes to be revealed on the femtosecond time-scale? How shall time-resolved experiments best be designed and conducted to exploit the properties of FELs and overcome challenges that they pose? To date, fast time-resolved reactions have been initiated by a brief laser pulse, which obviously requires that the system under study be light-sensitive. Although this is true for proteins of the visual system and for signalling photoreceptors, it is not naturally the case for most interesting biological systems. To generate more biological targets for time-resolved study, can this limitation be overcome by optogenetic, chemical or other means?

Reply to 'Contradictions in X-ray structures of intermediates in the photocycle of photoactive yellow protein'

Phototropin, a major blue-light receptor for phototropism in seed plants, exhibits blue-light-dependent autophosphorylation and contains two light, oxygen, or voltage (LOV) domains and a serine/threonine kinase domain. The LOV domains share homology with the PER-ARNT-SIM (PAS) superfamily, a diverse group of sensor proteins. Each LOV domain noncovalently binds a single FMN molecule and exhibits reversible photochemistry in vitro when expressed separately or in tandem. We have determined the crystal structure of the LOV2 domain from the phototropin segment of the chimeric fern photoreceptor phy3 to 2.7-Å resolution. The structure constitutes an FMN-binding fold that reveals how the flavin cofactor is embedded in the protein. The single LOV2 cysteine residue is located 4.2 Å from flavin atom C(4a), consistent with a model in which absorption of blue light induces formation of a covalent cysteinyl-C(4a) adduct. Residues that interact with FMN in the phototropin segment of the chimeric fern photoreceptor (phy3) LOV2 are conserved in LOV domains from phototropin of other plant species and from three proteins involved in the regulation of circadian rhythms in Arabidopsis and Neurospora . This conservation suggests that these domains exhibit the same overall fold and share a common mechanism for flavin binding and light-induced signaling.

X-ray radiation damage of a lysozyme single crystal by an intense monochromatic beam from a third-generation radiation source at the Advanced Photon Source has been studied. The results show that primary radiation damage is linearly dependent on the X-ray dose even when the crystal is at cryogenic temperatures. The existence of an upper limit for the primary radiation damage was observed. Above the threshold of approximately 1 x 10(7) Gy, excessive damage of the crystal develops which is interpreted as the onset of secondary and/or tertiary radiation damage. This upper limit of X-ray dose is compared with Henderson's limit [Henderson (1990). Proc. R. Soc. London, B241, 6-8], and its implication for the amount of useful X-ray diffraction data that can be obtained for crystals of a given scattering power is also discussed.

Wavelength normalization is an essential part of processing of Laue X-ray diffraction data and is critically important for deriving accurate structure-factor amplitudes. The results of wavelength normalization for Laue data obtained in nanosecond time-resolved experiments at the ID09 beamline at the European Synchrotron Radiation Facility, Grenoble, France, are presented. Several wiggler and undulator insertion devices with complex spectra were used. The results show that even in the most challenging cases, such as wiggler/undulator tandems or single-line undulators, accurate wavelength normalization does not require unusually redundant Laue data and can be accomplished using typical Laue data sets. Single-line undulator spectra derived from Laue data compare well with the measured incident X-ray spectra. Successful wavelength normalization of the undulator data was also confirmed by the observed signal in nanosecond time-resolved experiments. Single-line undulators, which are attractive for time-resolved experiments due to their high peak intensity and low polychromatic background, are compared with wigglers, based on data obtained on the same crystal.