SARS-CoV-2 Mpro responds to oxidation by forming disulfide and NOS/SONOS bonds

The main protease (Mpro) of SARS-CoV-2 is critical for viral function and a key drug target. Mpro is only active when reduced; turnover ceases upon oxidation but is restored by re-reduction. This suggests the system has evolved to survive periods in an oxidative environment, but the mechanism of this protection has not been confirmed. Here, we report a crystal structure of oxidized Mpro showing a disulfide bond between the active site cysteine, C145, and a distal cysteine, C117. Previous work proposed this disulfide provides the mechanism of protection from irreversible oxidation. Mpro forms an obligate homodimer, and the C117-C145 structure shows disruption of interactions bridging the dimer interface, implying a correlation between oxidation and dimerization. We confirm dimer stability is weakened in solution upon oxidation. Finally, we observe the protein's crystallization behavior is linked to its redox state. Oxidized Mpro spontaneously forms a distinct, more loosely packed lattice. Seeding with crystals of this lattice yields a structure with an oxidation pattern incorporating one cysteine-lysine-cysteine (SONOS) and two lysine-cysteine (NOS) bridges. These structures further our understanding of the oxidative regulation of Mpro and the crystallization conditions necessary to study this structurally.

Time-resolved crystallography captures light-driven DNA repair

Photolyase is an enzyme that uses light to catalyze DNA repair. To capture the reaction intermediates involved in the enzyme's catalytic cycle, we conducted a time-resolved crystallography experiment. We found that photolyase traps the excited state of the active cofactor, flavin adenine dinucleotide (FAD), in a highly bent geometry. This excited state performs electron transfer to damaged DNA, inducing repair. We show that the repair reaction, which involves the lysis of two covalent bonds, occurs through a single-bond intermediate. The transformation of the substrate into product crowds the active site and disrupts hydrogen bonds with the enzyme, resulting in stepwise product release, with the 3' thymine ejected first, followed by the 5' base.

Modeling diffuse scattering with simple, physically interpretable models

Diffuse scattering has long been proposed to probe protein dynamics relevant for biological function, and more recently, as a tool to aid structure determination. Despite recent advances in measuring and modeling this signal, the field has not been able to routinely use experimental diffuse scattering for either application. A persistent challenge has been to devise models that are sophisticated enough to robustly reproduce experimental diffuse features but remain readily interpretable from the standpoint of structural biology. This chapter presents eryx, a suite of computational tools to evaluate the primary models of disorder that have been used to analyze protein diffuse scattering. By facilitating comparative modeling, eryx aims to provide insights into the physical origins of this signal and help identify the sources of disorder that are critical for reproducing experimental features. This framework also lays the groundwork for the development of more advanced models that integrate different types of disorder without loss of interpretability.

Melting domain size and recrystallization dynamics of ice revealed by time-resolved x-ray scattering

The phase transition between water and ice is ubiquitous and one of the most important phenomena in nature. Here, we performed time-resolved x-ray scattering experiments capturing the melting and recrystallization dynamics of ice. The ultrafast heating of ice I is induced by an IR laser pulse and probed with an intense x-ray pulse which provided us with direct structural information on different length scales. From the wide-angle x-ray scattering (WAXS) patterns, the molten fraction, as well as the corresponding temperature at each delay, were determined. The small-angle x-ray scattering (SAXS) patterns, together with the information extracted from the WAXS analysis, provided the time-dependent change of the size and the number of liquid domains. The results show partial melting (~13%) and superheating of ice occurring at around 20 ns. After 100 ns, the average size of the liquid domains grows from about 2.5 nm to 4.5 nm by the coalescence of approximately six adjacent domains. Subsequently, we capture the recrystallization of the liquid domains, which occurs on microsecond timescales due to the cooling by heat dissipation and results to a decrease of the average liquid domain size.

Advancing structural biology through breakthroughs in AI

The past century has witnessed an exponential increase in our atomic-level understanding of molecular and cellular mechanisms from a structural perspective, with multiple landmark achievements contributing to the field. This, coupled with recent and continuing breakthroughs in artificial intelligence methods such as AlphaFold2, and enhanced computational power, is enabling our understanding of protein structure and function at unprecedented levels of accuracy and predictivity. Here, we describe some of the major recent advances across these fields, and describe, as these technologies coalesce, the potential to utilise our enhanced knowledge of intricate cellular and molecular systems to discover novel therapeutics to alleviate human suffering.

Liquid-liquid phase separation in supercooled water from ultrafast heating of low-density amorphous ice

Recent experiments continue to find evidence for a liquid-liquid phase transition (LLPT) in supercooled water, which would unify our understanding of the anomalous properties of liquid water and amorphous ice. These experiments are challenging because the proposed LLPT occurs under extreme metastable conditions where the liquid freezes to a crystal on a very short time scale. Here, we analyze models for the LLPT to show that coexistence of distinct high-density and low-density liquid phases may be observed by subjecting low-density amorphous (LDA) ice to ultrafast heating. We then describe experiments in which we heat LDA ice to near the predicted critical point of the LLPT by an ultrafast infrared laser pulse, following which we measure the structure factor using femtosecond x-ray laser pulses. Consistent with our predictions, we observe a LLPT occurring on a time scale < 100 ns and widely separated from ice formation, which begins at times >1 μs.

Rational Control of Off-State Heterogeneity in a Photoswitchable Fluorescent Protein Provides Switching Contrast Enhancement

Reversibly photoswitchable fluorescent proteins are essential markers for advanced biological imaging, and optimization of their photophysical properties underlies improved performance and novel applications. Here we establish a link between photoswitching contrast, one of the key parameters that dictate the achievable resolution in nanoscopy applications, and chromophore conformation in the non-fluorescent state of rsEGFP2, a widely employed label in REversible Saturable OpticaL Fluorescence Transitions (RESOLFT) microscopy. Upon illumination, the cis chromophore of rsEGFP2 isomerizes to two distinct off-state conformations, trans1 and trans2, located on either side of the V151 side chain. Reducing or enlarging the side chain at this position (V151A and V151L variants) leads to single off-state conformations that exhibit higher and lower switching contrast, respectively, compared to the rsEGFP2 parent. The combination of structural information obtained by serial femtosecond crystallography with high-level quantum chemical calculations and with spectroscopic and photophysical data determined in vitro suggests that the changes in switching contrast arise from blue- and red-shifts of the absorption bands associated to trans1 and trans2, respectively. Thus, due to elimination of trans2, the V151A variants of rsEGFP2 and its superfolding variant rsFolder2 display a more than two-fold higher switching contrast than their respective parent proteins, both in vitro and in E. coli cells. The application of the rsFolder2-V151A variant is demonstrated in RESOLFT nanoscopy. Our study rationalizes the connection between structural and photophysical chromophore properties and suggests a means to rationally improve fluorescent proteins for nanoscopy applications.

Acoustic Focusing of Protein Crystals for In-Line Monitoring and Up-Concentration during Serial Crystallography

Serial femtosecond crystallography (SFX) has become one of the standard techniques at X-ray free-electron lasers (XFELs) to obtain high-resolution structural information from microcrystals of proteins. Nevertheless, reliable sample delivery is still often limiting data collection, as microcrystals can clog both field- and flow-focusing nozzles despite in-line filters. In this study, we developed acoustic 2D focusing of protein microcrystals in capillaries that enables real-time online characterization of crystal size and shape in the sample delivery line after the in-line filter. We used a piezoelectric actuator to create a standing wave perpendicular to the crystal flow, which focused lysozyme microcrystals into a single line inside a silica capillary so that they can be imaged using a high-speed camera. We characterized the acoustic contrast factor, focus size, and the coaxial flow lines and developed a splitting union that enables up-concentration to at least a factor of five. The focus size, flow rates, and geometry may enable an upper limit of up-concentration as high as 200 fold. The novel feedback and concentration control could be implemented for serial crystallography at synchrotrons with minor modifications. It will also aid the development of improved sample delivery systems that will increase SFX data collection rates at XFELs, with potential applications to many proteins that can only be purified and crystallized in small amounts.

Antiviral activity of natural phenolic compounds in complex at an allosteric site of SARS-CoV-2 papain-like protease

SARS-CoV-2 papain-like protease (PLpro) covers multiple functions. Beside the cysteine-protease activity, facilitating cleavage of the viral polypeptide chain, PLpro has the additional and vital function of removing ubiquitin and ISG15 (Interferon-stimulated gene 15) from host-cell proteins to support coronaviruses in evading the host's innate immune responses. We identified three phenolic compounds bound to PLpro, preventing essential molecular interactions to ISG15 by screening a natural compound library. The compounds identified by X-ray screening and complexed to PLpro demonstrate clear inhibition of PLpro in a deISGylation activity assay. Two compounds exhibit distinct antiviral activity in Vero cell line assays and one inhibited a cytopathic effect in non-cytotoxic concentration ranges. In the context of increasing PLpro mutations in the evolving new variants of SARS-CoV-2, the natural compounds we identified may also reinstate the antiviral immune response processes of the host that are down-regulated in COVID-19 infections.

Following the Crystallization of Amorphous Ice after Ultrafast Laser Heating

Using time-resolved wide-angle X-ray scattering, we investigated the early stages (10 μs–1 ms) of crystallization of supercooled water, obtained by the ultrafast heating of high- and low-density amorphous ice (HDA and LDA) up to a temperature T = 205 K ± 10 K. We have determined that the crystallizing phase is stacking disordered ice (I_sd), with a maximum cubicity of χ = 0.6, in agreement with predictions from molecular dynamics simulations at similar temperatures. However, we note that a growing small portion of hexagonal ice (I_h) was also observed, suggesting that within our timeframe, I_sd starts annealing into I_h. The onset of crystallization, in both amorphous ice, occurs at a similar temperature, but the observed final crystalline fraction in the LDA sample is considerably lower than that in the HDA sample. We attribute this discrepancy to the thickness difference between the two samples.

Anomalous temperature dependence of the experimental x-ray structure factor of supercooled water

The structural changes of water upon deep supercooling were studied through wide-angle x-ray scattering at SwissFEL. The experimental setup had a momentum transfer range of 4.5 Å^-1, which covered the principal doublet of the x-ray structure factor of water. The oxygen-oxygen structure factor was obtained for temperatures down to 228.5 ± 0.6 K. Similar to previous studies, the second diffraction peak increased strongly in amplitude as the structural change accelerated toward a local tetrahedral structure upon deep supercooling. We also observed an anomalous trend for the second peak position of the oxygen-oxygen structure factor (q₂). We found that q₂ exhibits an unprecedented positive partial derivative with respect to temperature for temperatures below 236 K. Based on Fourier inversion of our experimental data combined with reference data, we propose that the anomalous q₂ shift originates from that a repeat spacing in the tetrahedral network, associated with all peaks in the oxygen-oxygen pair-correlation function, gives rise to a less dense local ordering that resembles that of low-density amorphous ice. The findings are consistent with that liquid water consists of a pentamer-based hydrogen-bonded network with low density upon deep supercooling.

Nonuniform Flow Dynamics Probed by Nanosecond X-Ray Speckle Visibility Spectroscopy

We report observations of nanosecond nonuniform colloidal dynamics in a free flowing liquid jet using ultrafast x-ray speckle visibility spectroscopy. Utilizing a nanosecond double-bunch mode, the Linac Coherent Light Source free electron laser produced pairs of femtosecond coherent hard x-ray pulses. By exploring anisotropy in the visibility of summed speckle patterns which relates to the correlation functions, we evaluate not only the average particle flow rate in a colloidal nanoparticle jet, but also the nonuniform flow field within. The methodology presented here establishes the foundation for the study of nano- and atomic-scale inhomogeneous fluctuations in complex matter using x-ray free electron laser sources.

X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease

The coronavirus disease (COVID-19) caused by SARS-CoV-2 is creating tremendous human suffering. To date, no effective drug is available to directly treat the disease. In a search for a drug against COVID-19, we have performed a high-throughput x-ray crystallographic screen of two repurposing drug libraries against the SARS-CoV-2 main protease (Mpro), which is essential for viral replication. In contrast to commonly applied x-ray fragment screening experiments with molecules of low complexity, our screen tested already-approved drugs and drugs in clinical trials. From the three-dimensional protein structures, we identified 37 compounds that bind to Mpro In subsequent cell-based viral reduction assays, one peptidomimetic and six nonpeptidic compounds showed antiviral activity at nontoxic concentrations. We identified two allosteric binding sites representing attractive targets for drug development against SARS-CoV-2.

Mechanism and dynamics of fatty acid photodecarboxylase

Fatty acid photodecarboxylase (FAP) is a photoenzyme with potential green chemistry applications. By combining static, time-resolved, and cryotrapping spectroscopy and crystallography as well as computation, we characterized Chlorella variabilis FAP reaction intermediates on time scales from subpicoseconds to milliseconds. High-resolution crystal structures from synchrotron and free electron laser x-ray sources highlighted an unusual bent shape of the oxidized flavin chromophore. We demonstrate that decarboxylation occurs directly upon reduction of the excited flavin by the fatty acid substrate. Along with flavin reoxidation by the alkyl radical intermediate, a major fraction of the cleaved carbon dioxide unexpectedly transformed in 100 nanoseconds, most likely into bicarbonate. This reaction is orders of magnitude faster than in solution. Two strictly conserved residues, R451 and C432, are essential for substrate stabilization and functional charge transfer.

Effect of X-ray free-electron laser-induced shockwaves on haemoglobin microcrystals delivered in a liquid jet

X-ray free-electron lasers (XFELs) enable obtaining novel insights in structural biology. The recently available MHz repetition rate XFELs allow full data sets to be collected in shorter time and can also decrease sample consumption. However, the microsecond spacing of MHz XFEL pulses raises new challenges, including possible sample damage induced by shock waves that are launched by preceding pulses in the sample-carrying jet. We explored this matter with an X-ray-pump/X-ray-probe experiment employing haemoglobin microcrystals transported via a liquid jet into the XFEL beam. Diffraction data were collected using a shock-wave-free single-pulse scheme as well as the dual-pulse pump-probe scheme. The latter, relative to the former, reveals significant degradation of crystal hit rate, diffraction resolution and data quality. Crystal structures extracted from the two data sets also differ. Since our pump-probe attributes were chosen to emulate EuXFEL operation at its 4.5 MHz maximum pulse rate, this prompts concern about such data collection.

Experimental observation of the liquid-liquid transition in bulk supercooled water under pressure

We prepared bulk samples of supercooled liquid water under pressure by isochoric heating of high-density amorphous ice to temperatures of 205 ± 10 kelvin, using an infrared femtosecond laser. Because the sample density is preserved during the ultrafast heating, we could estimate an initial internal pressure of 2.5 to 3.5 kilobar in the high-density liquid phase. After heating, the sample expanded rapidly, and we captured the resulting decompression process with femtosecond x-ray laser pulses at different pump-probe delay times. A discontinuous structural change occurred in which low-density liquid domains appeared and grew on time scales between 20 nanoseconds to 3 microseconds, whereas crystallization occurs on time scales of 3 to 50 microseconds. The dynamics of the two processes being separated by more than one order of magnitude provides support for a liquid-liquid transition in bulk supercooled water.

Femtosecond quantification of void evolution during rapid material failure

Understanding high-velocity impact, and the subsequent high strain rate material deformation and potential catastrophic failure, is of critical importance across a range of scientific and engineering disciplines that include astrophysics, materials science, and aerospace engineering. The deformation and failure mechanisms are not thoroughly understood, given the challenges of experimentally quantifying material evolution at extremely short time scales. Here, copper foils are rapidly strained via picosecond laser ablation and probed in situ with femtosecond x-ray free electron (XFEL) pulses. Small-angle x-ray scattering (SAXS) monitors the void distribution evolution, while wide-angle scattering (WAXS) simultaneously determines the strain evolution. The ability to quantifiably characterize the nanoscale during high strain rate failure with ultrafast SAXS, complementing WAXS, represents a broadening in the range of science that can be performed with XFEL. It is shown that ultimate failure occurs via void nucleation, growth, and coalescence, and the data agree well with molecular dynamics simulations.

What are the advantages of ghost imaging? Multiplexing for x-ray and electron imaging

Ghost imaging, Fourier transform spectroscopy, and the newly developed Hadamard transform crystallography are all examples of multiplexing measurement strategies. Multiplexed experiments are performed by measuring multiple points in space, time, or energy simultaneously. This contrasts to the usual method of systematically scanning single points. How do multiplexed measurements work and when they are advantageous? Here we address these questions with a focus on applications involving x-rays or electrons. We present a quantitative framework for analyzing the expected error and radiation dose of different measurement scheme that enables comparison. We conclude that in very specific situations, multiplexing can offer improvements in resolution and signal-to-noise. If the signal has a sparse representation, these advantages become more general and dramatic, and further less radiation can be used to complete a measurement.

Attosecond transient absorption spooktroscopy: a ghost imaging approach to ultrafast absorption spectroscopy

Recently demonstrated isolated attosecond XFEL pulses should allow the probing of ultrafast electron dynamics at X-ray wavelengths. The authors use ghost imaging to enable high-resolution transient absorption spectroscopy at fluctuating XFEL sources.

On-chip crystallization for serial crystallography experiments and on-chip ligand-binding studies

Efficient and reliable sample delivery has remained one of the bottlenecks for serial crystallography experiments. Compared with other methods, fixed-target sample delivery offers the advantage of significantly reduced sample consumption and shorter data collection times owing to higher hit rates. Here, a new method of on-chip crystallization is reported which allows the efficient and reproducible growth of large numbers of protein crystals directly on micro-patterned silicon chips for in-situ serial crystallography experiments. Crystals are grown by sitting-drop vapor diffusion and previously established crystallization conditions can be directly applied. By reducing the number of crystal-handling steps, the method is particularly well suited for sensitive crystal systems. Excessive mother liquor can be efficiently removed from the crystals by blotting, and no sealing of the fixed-target sample holders is required to prevent the crystals from dehydrating. As a consequence, 'naked' crystals are obtained on the chip, resulting in very low background scattering levels and making the crystals highly accessible for external manipulation such as the application of ligand solutions. Serial diffraction experiments carried out at cryogenic temperatures at a synchrotron and at room temperature at an X-ray free-electron laser yielded high-quality X-ray structures of the human membrane protein aquaporin 2 and two new ligand-bound structures of thermolysin and the human kinase DRAK2. The results highlight the applicability of the method for future high-throughput on-chip screening of pharmaceutical compounds.

Simplicity Beneath Complexity: Counting Molecular Electrons Reveals Transients and Kinetics of Photodissociation Reactions

Time-resolved pump-probe gas-phase X-ray scattering signals, extrapolated to zero momentum transfer, provide a measure of the number of electrons in a system, an effect that arises from the coherent addition of elastic scattering from the electrons. This allows to identify reactive transients and determine the chemical reaction kinetics without the need for extensive scattering simulations or complicated inversion of scattering data. We examine the photodissociation reaction of trimethylamine and identify two reaction paths upon excitation to the 3p state at 200 nm: a fast dissociation path out of the 3p state to the dimethyl amine radical (16.6±1.2 %) and a slower dissociation via internal conversion to the 3s state (83.4±1.2 %). The time constants for the two reactions are 640±130 fs and 74±6 ps, respectively. Additionally, it is found that the transient dimethyl amine radical has a N-C bond length of 1.45±0.02 Å and a C-N-C bond angle of 118°±4°.

The Macromolecular Femtosecond Crystallography Instrument at the Linac Coherent Light Source

The Macromolecular Femtosecond Crystallography (MFX) instrument at the Linac Coherent Light Source (LCLS) is the seventh and newest instrument at the world's first hard X-ray free-electron laser. It was designed with a primary focus on structural biology, employing the ultrafast pulses of X-rays from LCLS at atmospheric conditions to overcome radiation damage limitations in biological measurements. It is also capable of performing various time-resolved measurements. The MFX design consists of a versatile base system capable of supporting multiple methods, techniques and experimental endstations. The primary techniques supported are forward scattering and crystallography, with capabilities for various spectroscopic methods and time-resolved measurements. The location of the MFX instrument allows for utilization of multiplexing methods, increasing user access to LCLS by running multiple experiments simultaneously.

Determining Orientations of Optical Transition Dipole Moments Using Ultrafast X-ray Scattering

Identification of the initially prepared, optically active state remains a challenging problem in many studies of ultrafast photoinduced processes. We show that the initially excited electronic state can be determined using the anisotropic component of ultrafast time-resolved X-ray scattering signals. The concept is demonstrated using the time-dependent X-ray scattering of N-methyl morpholine in the gas phase upon excitation by a 200 nm linearly polarized optical pulse. Analysis of the angular dependence of the scattering signal near time zero renders the orientation of the transition dipole moment in the molecular frame and identifies the initially excited state as the 3p _z Rydberg state, thus bypassing the need for further experimental studies to determine the starting point of the photoinduced dynamics and clarifying inconsistent computational results.

Electron Ghost Imaging

In this Letter we report a demonstration of electron ghost imaging. A digital micromirror device directly modulates the photocathode drive laser to control the transverse distribution of a relativistic electron beam incident on a sample. Correlating the structured illumination pattern to the total sample transmission then retrieves the target image, avoiding the need for a pixelated detector. In our example, we use a compressed sensing framework to improve the reconstruction quality and reduce the number of shots compared to raster scanning a small beam across the target. Compressed electron ghost imaging can reduce both acquisition time and sample damage in experiments for which spatially resolved detectors are unavailable (e.g., spectroscopy) or in which the experimental architecture precludes full frame direct imaging.

Coherent X-rays reveal the influence of cage effects on ultrafast water dynamics

The dynamics of liquid water feature a variety of time scales, ranging from extremely fast ballistic-like thermal motion, to slower molecular diffusion and hydrogen-bond rearrangements. Here, we utilize coherent X-ray pulses to investigate the sub-100 fs equilibrium dynamics of water from ambient conditions down to supercooled temperatures. This novel approach utilizes the inherent capability of X-ray speckle visibility spectroscopy to measure equilibrium intermolecular dynamics with lengthscale selectivity, by measuring oxygen motion in momentum space. The observed decay of the speckle contrast at the first diffraction peak, which reflects tetrahedral coordination, is attributed to motion on a molecular scale within the first 120 fs. Through comparison with molecular dynamics simulations, we conclude that the slowing down upon cooling from 328 K down to 253 K is not due to simple thermal ballistic-like motion, but that cage effects play an important role even on timescales over 25 fs due to hydrogen-bonding.

Intermolecular correlations are necessary to explain diffuse scattering from protein crystals

Conformational changes drive protein function, including catalysis, allostery and signaling. X-ray diffuse scattering from protein crystals has frequently been cited as a probe of these correlated motions, with significant potential to advance our understanding of biological dynamics. However, recent work has challenged this prevailing view, suggesting instead that diffuse scattering primarily originates from rigid-body motions and could therefore be applied to improve structure determination. To investigate the nature of the disorder giving rise to diffuse scattering, and thus the potential applications of this signal, a diverse repertoire of disorder models was assessed for its ability to reproduce the diffuse signal reconstructed from three protein crystals. This comparison revealed that multiple models of intramolecular conformational dynamics, including ensemble models inferred from the Bragg data, could not explain the signal. Models of rigid-body or short-range liquid-like motions, in which dynamics are confined to the biological unit, showed modest agreement with the diffuse maps, but were unable to reproduce experimental features indicative of long-range correlations. Extending a model of liquid-like motions to include disorder across neighboring proteins in the crystal significantly improved agreement with all three systems and highlighted the contribution of intermolecular correlations to the observed signal. These findings anticipate a need to account for intermolecular disorder in order to advance the interpretation of diffuse scattering to either extract biological motions or aid structural inference.

Environmental Calcium Controls Alternate Physical States of the Caulobacter Surface Layer

Surface layers (S-layers) are paracrystalline, proteinaceous structures found in most archaea and many bacteria. Often the outermost cell envelope component, S-layers serve diverse functions including aiding pathogenicity and protecting against predators. We report that the S-layer of Caulobacter crescentus exhibits calcium-mediated structural plasticity, switching irreversibly between an amorphous aggregate state and the crystalline state. This finding invalidates the common assumption that S-layers serve only as static wall-like structures. In vitro, the Caulobacter S-layer protein, RsaA, enters the aggregate state at physiological temperatures and low divalent calcium ion concentrations. At higher concentrations, calcium ions stabilize monomeric RsaA, which can then transition to the two-dimensional crystalline state. Caulobacter requires micromolar concentrations of calcium for normal growth and development. Without an S-layer, Caulobacter is even more sensitive to changes in environmental calcium concentration. Therefore, this structurally dynamic S-layer responds to environmental conditions as an ion sensor and protects Caulobacter from calcium deficiency stress, a unique mechanism of bacterial adaptation. These findings provide a biochemical and physiological basis for RsaA's calcium-binding behavior, which extends far beyond calcium's commonly accepted role in aiding S-layer biogenesis or oligomerization and demonstrates a connection to cellular fitness.

Se-SAD serial femtosecond crystallography datasets from selenobiotinyl-streptavidin

We provide a detailed description of selenobiotinyl-streptavidin (Se-B SA) co-crystal datasets recorded using the Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS) for selenium single-wavelength anomalous diffraction (Se-SAD) structure determination. Se-B SA was chosen as the model system for its high affinity between biotin and streptavidin where the sulfur atom in the biotin molecule (C₁₀H₁₆N₂O₃S) is substituted with selenium. The dataset was collected at three different transmissions (100, 50, and 10%) using a serial sample chamber setup which allows for two sample chambers, a front chamber and a back chamber, to operate simultaneously. Diffraction patterns from Se-B SA were recorded to a resolution of 1.9 Å. The dataset is publicly available through the Coherent X-ray Imaging Data Bank (CXIDB) and also on LCLS compute nodes as a resource for research and algorithm development.

Structure of photosystem II and substrate binding at room temperature

Light-induced oxidation of water by photosystem II (PS II) in plants, algae and cyanobacteria has generated most of the dioxygen in the atmosphere. PS II, a membrane-bound multi-subunit pigment protein complex, couples the one-electron photochemistry at the reaction centre with the four-electron redox chemistry of water oxidation at the Mn₄CaO₅ cluster in the oxygen-evolving complex (OEC). Under illumination, the OEC cycles through five intermediate S-states (S₀ to S₄), in which S₁ is the dark-stable state and S₃ is the last semi-stable state before O-O bond formation and O₂ evolution. A detailed understanding of the O-O bond formation mechanism remains a challenge, and will require elucidation of both the structures of the OEC in the different S-states and the binding of the two substrate waters to the catalytic site. Here we report the use of femtosecond pulses from an X-ray free electron laser (XFEL) to obtain damage-free, room temperature structures of dark-adapted (S₁), two-flash illuminated (2F; S₃-enriched), and ammonia-bound two-flash illuminated (2F-NH₃; S₃-enriched) PS II. Although the recent 1.95 Å resolution structure of PS II at cryogenic temperature using an XFEL provided a damage-free view of the S₁ state, measurements at room temperature are required to study the structural landscape of proteins under functional conditions, and also for in situ advancement of the S-states. To investigate the water-binding site(s), ammonia, a water analogue, has been used as a marker, as it binds to the Mn₄CaO₅ cluster in the S₂ and S₃ states. Since the ammonia-bound OEC is active, the ammonia-binding Mn site is not a substrate water site. This approach, together with a comparison of the native dark and 2F states, is used to discriminate between proposed O-O bond formation mechanisms.

Angular correlations of photons from solution diffraction at a free-electron laser encode molecular structure

During X-ray exposure of a molecular solution, photons scattered from the same molecule are correlated. If molecular motion is insignificant during exposure, then differences in momentum transfer between correlated photons are direct measurements of the molecular structure. In conventional small- and wide-angle solution scattering, photon correlations are ignored. This report presents advances in a new biomolecular structural analysis technique, correlated X-ray scattering (CXS), which uses angular intensity correlations to recover hidden structural details from molecules in solution. Due to its intense rapid pulses, an X-ray free electron laser (XFEL) is an excellent tool for CXS experiments. A protocol is outlined for analysis of a CXS data set comprising a total of half a million X-ray exposures of solutions of small gold nanoparticles recorded at the Spring-8 Ångström Compact XFEL facility (SACLA). From the scattered intensities and their correlations, two populations of nanoparticle domains within the solution are distinguished: small twinned, and large probably non-twinned domains. It is shown analytically how, in a solution measurement, twinning information is only accessible via intensity correlations, demonstrating how CXS reveals atomic-level information from a disordered solution of like molecules.

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

As molecular dynamics (MD) simulations continue to evolve into powerful computational tools for studying complex biomolecular systems, the necessity of flexible and easy-to-use software tools for the analysis of these simulations is growing. We have developed MDTraj, a modern, lightweight, and fast software package for analyzing MD simulations. MDTraj reads and writes trajectory data in a wide variety of commonly used formats. It provides a large number of trajectory analysis capabilities including minimal root-mean-square-deviation calculations, secondary structure assignment, and the extraction of common order parameters. The package has a strong focus on interoperability with the wider scientific Python ecosystem, bridging the gap between MD data and the rapidly growing collection of industry-standard statistical analysis and visualization tools in Python. MDTraj is a powerful and user-friendly software package that simplifies the analysis of MD data and connects these datasets with the modern interactive data science software ecosystem in Python.

OnDA: online data analysis and feedback for serial X-ray imaging

This article describes the software package OnDA: online data analysis and feedback for serial X-ray imaging.

This article describes a free and open-source data analysis utility designed for fast online feedback during serial X-ray diffraction and scattering experiments: OnDA (online data analysis). Three complete real-time monitors for common types of serial X-ray imaging experiments are presented. These monitors are capable of providing the essential information required for quick decision making in the face of extreme rates of data collection. In addition, a set of modules, functions and algorithms that allow developers to modify the provided monitors or develop new ones are provided. The emphasis here is on simple, modular and scalable code that is based on open-source libraries and protocols. OnDA monitors have already proven to be invaluable tools in several experiments, especially for scoring and monitoring of diffraction data during serial crystallography experiments at both free-electron laser and synchrotron facilities. It is felt that in the future the kind of fast feedback that OnDA monitors provide will help researchers to deal with the expected very high throughput data flow at next-generation facilities such as the European X-ray free-electron laser.

Femtosecond photodissociation dynamics of 1,4-diiodobenzene by gas-phase X-ray scattering and photoelectron spectroscopy

We present a multifaceted investigation into the initial photodissociation dynamics of 1,4-diiodobenzene (DIB) following absorption of 267 nm radiation. We combine ultrafast time-resolved photoelectron spectroscopy and X-ray scattering experiments performed at the Linac Coherent Light Source (LCLS) to study the initial electronic excitation and subsequent rotational alignment, and interpret the experiments in light of Complete Active Space Self-Consistent Field (CASSCF) calculations of the excited electronic landscape. The initially excited state is found to be a bound ¹B₁ surface, which undergoes ultrafast population transfer to a nearby state in 35 ± 10 fs. The internal conversion most likely leads to one or more singlet repulsive surfaces that initiate the dissociation. This initial study is an essential and prerequisite component of a comprehensive study of the complete photodissociation pathway(s) of DIB at 267 nm. Assignment of the initially excited electronic state as a bound state identifies the mechanism as predissociative, and measurement of its lifetime establishes the time between excitation and initiation of dissociation, which is crucial for direct comparison of photoelectron and scattering experiments.

Imaging Molecular Motion: Femtosecond X-Ray Scattering of an Electrocyclic Chemical Reaction

Structural rearrangements within single molecules occur on ultrafast time scales. Many aspects of molecular dynamics, such as the energy flow through excited states, have been studied using spectroscopic techniques, yet the goal to watch molecules evolve their geometrical structure in real time remains challenging. By mapping nuclear motions using femtosecond x-ray pulses, we have created real-space representations of the evolving dynamics during a well-known chemical reaction and show a series of time-sorted structural snapshots produced by ultrafast time-resolved hard x-ray scattering. A computational analysis optimally matches the series of scattering patterns produced by the x rays to a multitude of potential reaction paths. In so doing, we have made a critical step toward the goal of viewing chemical reactions on femtosecond time scales, opening a new direction in studies of ultrafast chemical reactions in the gas phase.

Observation of correlated X-ray scattering at atomic resolution

Tools to study disordered systems with local structural order, such as proteins in solution, remain limited. Such understanding is essential for e.g. rational drug design. Correlated X-ray scattering (CXS) has recently attracted new interest as a way to leverage next-generation light sources to study such disordered matter. The CXS experiment measures angular correlations of the intensity caused by the scattering of X-rays from an ensemble of identical particles, with disordered orientation and position. Averaging over 15 496 snapshot images obtained by exposing a sample of silver nanoparticles in solution to a micro-focused synchrotron radiation beam, we report on experimental efforts to obtain CXS signal from an ensemble in three dimensions. A correlation function was measured at wide angles corresponding to atomic resolution that matches theoretical predictions. These preliminary results suggest that other CXS experiments on disordered ensembles—such as proteins in solution—may be feasible in the future.

Probing the origins of two-state folding

Many protein systems fold in a two-state manner. Random models, however, rarely display two-state kinetics and thus such behavior should not be accepted as a default. While theories for the prevalence of two-state kinetics have been presented, none sufficiently explain the breadth of experimental observations. A model, making minimal assumptions, is introduced that suggests two-state behavior is likely for any system with an overwhelmingly populated native state. We show two-state folding is a natural consequence of such two-state thermodynamics, and is strengthened by increasing the population of the native state. Further, the model exhibits hub-like behavior, with slow interconversions between unfolded states. Despite this, the unfolded state equilibrates quickly relative to the folding time. This apparent paradox is readily understood through this model. Finally, our results compare favorable with measurements of folding rates as a function of chain length and Keq, providing new insight into these relations.

Toward structural femtosecond chemical dynamics: imaging chemistry in space and time

We aim to observe a chemical reaction in real time using gas-phase X-ray diffraction. In our initial experiment at the Linac Coherent Light Source (LCLS), we investigated the model system 1,3-cyclohexadiene (CHD) at very low vapor pressures. This reaction serves as a benchmark for numerous transformations in organic synthesis and natural product biology. Excitation of CHD by an ultraviolet optical pulse initiates an electrocyclic reaction that transforms the closed ring system into the open-chain structure of 1,3,5-hexatriene. We describe technical points of the experimental method and present first results. We also outline an approach to analyze the data involving nonlinear least-square optimization routines that match the experimental observations with predicted diffraction patterns calculated from trajectories for nonadiabatic vibronic wave packets.

Inferring the rate-length law of protein folding

We investigate the rate-length scaling law of protein folding, a key undetermined scaling law in the analytical theory of protein folding. Available data yield statistically significant evidence for the existence of a rate-length law capable of predicting folding times to within about two orders of magnitude (over 9 decades of variation). Unambiguous determination of the functional form of such a law could provide key mechanistic insight into folding. Four proposed laws from literature (power law, exponential, and two stretched exponentials) are tested against one another, and it is found that the power law best explains the data by a modest margin. We conclude that more data is necessary to unequivocally infer the rate-length law. Such data could be obtained through a small number of protein folding experiments on large protein domains.

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

OpenMM is a software toolkit for performing molecular simulations on a range of high performance computing architectures. It is based on a layered architecture: the lower layers function as a reusable library that can be invoked by any application, while the upper layers form a complete environment for running molecular simulations. The library API hides all hardware-specific dependencies and optimizations from the users and developers of simulation programs: they can be run without modification on any hardware on which the API has been implemented. The current implementations of OpenMM include support for graphics processing units using the OpenCL and CUDA frameworks. In addition, OpenMM was designed to be extensible, so new hardware architectures can be accommodated and new functionality (e.g., energy terms and integrators) can be easily added.

To milliseconds and beyond: challenges in the simulation of protein folding

Quantitatively accurate all-atom molecular dynamics (MD) simulations of protein folding have long been considered a holy grail of computational biology. Due to the large system sizes and long timescales involved, such a pursuit was for many years computationally intractable. Further, sufficiently accurate forcefields needed to be developed in order to realistically model folding. This decade, however, saw the first reports of folding simulations describing kinetics on the order of milliseconds, placing many proteins firmly within reach of these methods. Progress in sampling and forcefield accuracy, however, presents a new challenge: how to turn huge MD datasets into scientific understanding. Here, we review recent progress in MD simulation techniques and show how the vast datasets generated by such techniques present new challenges for analysis. We critically discuss the state of the art, including reaction coordinate and Markov state model (MSM) methods, and provide a perspective for the future.

Eigenvalues of the homogeneous finite linear one step master equation: applications to downhill folding

Motivated by the observed time scales in protein systems said to fold "downhill," we have studied the finite, linear master equation, with uniform rates forward and backward as a model of the downhill process. By solving for the system eigenvalues, we prove the claim that in situations where there is no free energy barrier a transition between single- and multi-exponential kinetics occurs at sufficient bias (towards the native state). Consequences for protein folding, especially the downhill folding scenario, are briefly discussed.

A simple model predicts experimental folding rates and a hub-like topology

A simple model is presented that describes general features of protein folding, in good agreement with experimental results and detailed all-atom simulations. Starting from microscopic physics, and with no free parameters, this model predicts that protein folding occurs remarkably quickly because native-like states are kinetic hubs. A hub-like network arises naturally out of microscopic physical concerns, specifically the kinetic longevity of native contacts during a search of globular conformations. The model predicts folding times scaling as τ(f) ~ e(ξN) in the number of residues, but because the model shows ξ is small, the folding times are much faster than Levinthal's approximation. Importantly, the folding time scale is found to be small due to the topology and structure of the network. We show explicitly how our model agrees with generic experimental features of the folding process, including the scaling of τ(f) with N, two-state thermodynamics, a sharp peak in C(V), and native-state fluctuations.

Markov state model reveals folding and functional dynamics in ultra-long MD trajectories

Two strategies have been recently employed to push molecular simulation to long, biologically relevant time scales: projection-based analysis of results from specialized hardware producing a small number of ultralong trajectories and the statistical interpretation of massive parallel sampling performed with Markov state models (MSMs). Here, we assess the MSM as an analysis method by constructing a Markov model from ultralong trajectories, specifically two previously reported 100 μs trajectories of the FiP35 WW domain (Shaw, D. E. Science 2010, 330, 341-346). We find that the MSM approach yields novel insights. It discovers new statistically significant folding pathways, in which either beta-hairpin of the WW domain can form first. The rates of this process approach experimental values in a direct quantitative comparison (time scales of 5.0 μs and 100 ns), within a factor of ∼2. Finally, the hub-like topology of the MSM and identification of a holo conformation predicts how WW domains may function through a conformational selection mechanism.

MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond Scale

Markov State Models provide a framework for understanding the fundamental states and rates in the conformational dynamics of biomolecules. We describe an improved protocol for constructing Markov State Models from molecular dynamics simulations. The new protocol includes advances in clustering, data preparation, and model estimation; these improvements lead to significant increases in model accuracy, as assessed by the ability to recapitulate equilibrium and kinetic properties of reference systems. A high-performance implementation of this protocol, provided in MSMBuilder2, is validated on dynamics ranging from picoseconds to milliseconds.

How will you need me, how will you read me, when I'm 64 (or more!)?: volume computed tomographic scanning and information overload in the emergency department

Computed tomographic (CT) scanning technology now employs up to 320 detector rows of 0.5-mm width and allows rapid acquisition of isotropic volume datasets over the entire body. Data from a single CT acquisition can be reconstructed into image series that would formerly have required multiple acquisitions. Small isotropic voxels permit scan parameters to be general while reconstruction algorithms remain specific to anatomy. While this results in more efficient operation in the Emergency Department, it necessitates new ways of displaying, interpreting, and archiving the information. Critical decisions include how much of the patient to scan and how to time contrast injections when imaging multiple organs. These choices must be made in light of dose considerations to the patient and the general population of patients. The technical basis of high-density CT scanning is discussed, including detector configurations and reconstruction techniques. Volumetric scanning in the Emergency Department can improve patient care but requires a change of technical habits.

Quantification of the layer of hydration of a supported lipid bilayer

Dual polarization interferometry (DPI) and quartz-crystal microgravimetry (QCM-D) were used to investigate the adsorption of DOPC vesicles to a solid hydrophilic surface. The layer of hydration formed between a self-assembled DOPC bilayer and a silica solid support was probed in assemblies constructed using H(2)O and D(2)O buffers. We used QCM-D to measure the mass of the bilayer, including the mass contribution of the coupled solvent that resides between the membrane-solid interface. The mass of only the DOPC in the bilayer was resolved using DPI. By comparing these two measurements, and also accounting for the bulk phase effects on mass, we have been able to determine the mass of water below the bilayer. The thickness of this hydration layer, calculated by relating its mass to the density of the layer, was determined to be 10.46 A +/- 0.15 A for trapped D(2)O and 10.21 A +/- 0.40 A for trapped H(2)O, in agreement with measurements obtained by other methods. This work establishes the feasibility of concurrently using DPI and QCM-D to gauge the extent of hydration in thin films.