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Radiation damage represents a fundamental limit in the determination of protein structures via macromolecular crystallography (MX) at third-generation synchrotron sources. Over the past decade, improvements in both source and detector technology have led to MX experiments being performed with smaller and smaller crystals (on the order of a few microns), often using microfocus beams. Under these conditions, photoelectrons (PEs), the primary agents of radiation-damage in MX, may escape the diffraction volume prior to depositing all of their energy. The impact of PE escape is more significant at higher beam energies (&gt, 20 keV) as the electron inelastic mean free path (IMFP) is longer, allowing the electrons to deposit their energy over a larger area, extending further from their point of origin. Software such as RADDOSE-3D has been used extensively to predict the dose (energy absorbed per unit mass) that a crystal will absorb under a given set of experimental parameters and is an important component in planning a successful MX experiment. At the time this study was undertaken, dose predictions made using RADDOSE-3D were spatially-resolved, but did not yet account for the propagation of PEs through the diffraction volume. Hence, in the case of microfocus crystallography, it is anticipated that deviations may occur between the predicted and actual dose absorbed due to the influence of PEs. To explore this effect, we conducted a series of simulations of the dose absorbed by micron-sized crystals during microfocus MX experiments. Our simulations spanned beam and crystal sizes ranging from 1&mu, m to 5&mu, m for beam energies between 9 keV and 30 keV. Our simulations were spatially and temporarily resolved and accounted for the escape of PEs from the diffraction volume. The spatially-resolved dose maps produced by these simulations were used to predict the rate of intensity loss in a Bragg spot, a key metric for tracking global radiation damage. Our results were compared to predictions obtained using a recent version of RADDOSE-3D that did not account for PE escape, the predicted crystal lifetimes are shown to differ significantly for the smallest crystals and for high-energy beams, when PE escape is included in the simulations.

This article focuses on the challenges of hit finding and data reduction in serial crystallography (SX). An effective and reliable Bragg-peak-finding method, called robust peak finder (RPF), has been developed. RPF is based on the principle of robust statistics and can be used for SX data analysis., A peak-finding algorithm for serial crystallography (SX) data analysis based on the principle of ‘robust statistics’ has been developed. Methods which are statistically robust are generally more insensitive to any departures from model assumptions and are particularly effective when analysing mixtures of probability distributions. For example, these methods enable the discretization of data into a group comprising inliers (i.e. the background noise) and another group comprising outliers (i.e. Bragg peaks). Our robust statistics algorithm has two key advantages, which are demonstrated through testing using multiple SX data sets. First, it is relatively insensitive to the exact value of the input parameters and hence requires minimal optimization. This is critical for the algorithm to be able to run unsupervised, allowing for automated selection or ‘vetoing’ of SX diffraction data. Secondly, the processing of individual diffraction patterns can be easily parallelized. This means that it can analyse data from multiple detector modules simultaneously, making it ideally suited to real-time data processing. These characteristics mean that the robust peak finder (RPF) algorithm will be particularly beneficial for the new class of MHz X-ray free-electron laser sources, which generate large amounts of data in a short period of time.

This journal is © The Royal Society of Chemistry. Serial femtosecond crystallography (SFX) methods used at X-ray free electron lasers (XFELs) offer a range of new opportunities for structural biology. A crucial component of SFX experiments is sample delivery. Microfluidic devices can be employed in SFX experiments to precisely deliver microcrystals to the X-ray beam and to trigger molecular dynamics via rapid mix-and-inject measurements. Here, for the first time, we have developed a process based on high-resolution photolithography using SU8 on glass to fabricate microfluidic mix-and-inject devices. In order to characterise these devices a broad range of flow rates are used and the mixing and jetting response of the devices monitored. We observe that a stable jet is formed using these devices when injecting DI-water. Three different jetting regimes, liquid column, ribbon, and cylindrical jet, were observed. Furthermore, fluorescence experiments confirm that rapid and uniform mixing of the two injected solutions is possible using these devices indicating that they could be used to probe molecular dynamics on sub-microsecond timescales.

Continuous flow injection is a key technology for serial crystallography measurements of protein crystals suspended in the lipidic cubic phase (LCP). To date, there has been little discussion in the literature regarding the impact of the injection process itself on the structure of the lipidic phase. This is despite the fact that the phase of the injection matrix is critical for the flow properties of the stream and potentially for sample stability. Here we report small-angle X-ray scattering measurements of a monoolein:water mixture during continuous delivery using a high viscosity injector. We observe both an alignment and modification of the LCP as a direct result of the injection process. The orientation of the cubic lattice with respect to the beam was estimated based on the anisotropy of the diffraction pattern and does not correspond to a single low order zone axis. The solvent fraction was also observed to impact the stability of the cubic phase during injection. In addition, depending on the distance traveled by the lipid after exiting the needle, the phase is observed to transition from a pure diamond phase (Pn3m) to a mixture containing both gyriod (Ia3d) and lamellar (L

MyD88 and MAL are Toll-like receptor (TLR) adaptors that signal to induce pro-inflammatory cytokine production. We previously observed that the TIR domain of MAL (MALTIR) forms filaments in vitro and induces formation of crystalline higher-order assemblies of the MyD88 TIR domain (MyD88TIR). These crystals are too small for conventional X-ray crystallography, but are ideally suited to structure determination by microcrystal electron diffraction (MicroED) and serial femtosecond crystallography (SFX). Here, we present MicroED and SFX structures of the MyD88TIR assembly, which reveal a two-stranded higher-order assembly arrangement of TIR domains analogous to that seen previously for MALTIR. We demonstrate via mutagenesis that the MyD88TIR assembly interfaces are critical for TLR4 signaling in vivo, and we show that MAL promotes unidirectional assembly of MyD88TIR. Collectively, our studies provide structural and mechanistic insight into TLR signal transduction and allow a direct comparison of the MicroED and SFX techniques., MAL and MyD88 are downstream adaptors of Toll-like receptors (TLR) and the MAL TIR domain forms filaments in vitro, which in turn nucleate the assembly of crystalline arrays of the MyD88 TIR domain. Here, the authors present the structure of these MyD88 TIR crystalline arrays solved by both microcrystal electron diffraction and serial femtosecond crystallography, and they show with mutagenesis experiments that MyD88 interface residues are important for TLR4 signaling in vivo.

A facility for performing serial crystallography measurements has been developed at the Australian synchrotron. This facility incorporates a purpose built high viscous injector, Lipidico, as part of the macromolecular crystallography (MX2) beamline to measure large numbers of small crystals at room temperature. The goal of this technique is to enable crystals to be grown/transferred to glass syringes to be used directly in the injector for serial crystallography data collection. The advantages of this injector include the ability to respond rapidly to changes in the flow rate without interruption of the stream. Several limitations for this high viscosity injector (HVI) exist which include a restriction on the allowed sample viscosities to >10 Pa.s. Stream stability can also potentially be an issue depending on the specific properties of the sample. A detailed protocol for how to set up samples and operate the injector for serial crystallography measurements at the Australian synchrotron is presented here. The method demonstrates preparation of the sample, including the transfer of lysozyme crystals into a high viscous media (silicone grease), and the operation of the injector for data collection at MX2.

Solvents that support protein functionality are important for biochemical applications, and new solvents are required. Here we employ FTIR and fluorescence spectroscopies, small angle X-ray scattering (SAXS) and X-ray crystallography to understand conformational changes of lysozyme with ionic liquids (ILs) added. Spectroscopic techniques identified that the secondary structure of lysozyme was maintained at the lower IL concentrations of 1 and 5 mol%, though the Tryptophan environment was significantly altered with nitrate-based ILs present. SAXS experiments indicated that the radius of gyration of lysozyme increased with 1 mol% IL present, and then decreased with increasing IL concentrations. The tertiary structure, particularly the loop regions, changed as a function of IL concentration, and this depended on the IL type. The crystallographic structure of lysozyme with the IL of ethylammonium nitrate present confirmed the loop region was extended, and identified three specific binding sites with nitrate ions, and that the positively charged areas were IL sensitive regions. This work provides a detailed understanding of lysozyme conformational changes in the presence of ILs. This approach can be extended to other functionally-important proteins.

Emergent nanoscale order in materials such as self-assembled lipid phases, colloidal materials and metal-organic frameworks is often characterized by small-angle X-ray scattering (SAXS). Frequently, residual disorder in these materials prevents high-resolution 3D structural characterization. Here we demonstrate that angular intensity variations in SAXS patterns can provide previously inaccessible information about local 3D structure via a rich, real-space distribution of three- and four-body statistics. We present the many-body characterisation of a monoolein-based hexagonal phase doped with a phospholipid, revealing non-uniform curvature in the lipid channels, likely due to phase separation of the lipids in the membrane. Our many-body technique has general applicability to nanomaterials with order in the range 10 nm−1 μm currently targeted by synchrotron SAXS and has the potential to impact diverse research areas within chemistry, biology and materials science. Emergent nanoscale order in organic materials is typically characterized by small-angle X-ray scattering. Here, angular fluctuations in the diffraction patterns are used to probe the 3D structure of self-assembled lipid membranes, revealing previously inaccessible details on the phase geometry.

Characterising and understanding the mechanisms involved in cell death are especially important to combating threats to human health, particularly for the study of antimicrobial peptides and their effectiveness against pathogenic fungi. However, imaging these processes often relies on the use of synthetic molecules which bind to specific cellular targets to produce contrast. Here we study yeast cell death, induced by the anti-fungal peptide, NaD1. By treating yeast as a model organism we aim to understand anti-fungal cell death processes without relying on sample modification. Using a quantitative phase imaging technique, ptychography, we were able to produce label free images of yeast cells during death and use them to investigate the mode of action of NaD1. Using this technique we were able to identify a significant phase shift which provided a clear signature of yeast cell death. Additionally, ptychography identifies cell death much earlier than a comparative fluorescence study, providing new insights into the cellular changes that occur during cell death. The results indicate ptychography has great potential as a means of providing additional information about cellular processes which otherwise may be masked by indirect labelling approaches.

The development of ultrafast X-ray free-electron laser (XFEL) sources and third-generation synchrotrons has opened many new horizons for the study of complex molecular structures and their reaction kinetics. An essential element of these types of experiment is the method used for sample delivery. Microfluidics technology provides the ideal platform for performing these types of measurements since it enables control, manipulation and delivery of small volumes of fluid inside microchannels. Several key functions including mixing, particle separation, and injection, can be integrated on a single chip making the technology very attractive for use in Xray characterisation of molecular dynamics. Key challenges however, in using microfluidics to both mix and deliver samples, include chemical inertness and mechanical stability of the devices, particularly at micron length scales. Here we report a repeatable method for fabricating microfluidic mixer-jet devices based on photolithography and SU8 with a glass substrate. In experiments we have shown that these devices can withstand the high gas pressures required to produce stable, long-range, liquid jets. Coupled with their chemical inertness and reproducibility this makes them promising candidates for time-resolved X-ray diffraction measurements of molecular dynamics. Incorporating an integrated serpentine micromixer capable of homogeneous mixing prior to the liquid jet the devices presented here can be applied to the study of the dynamics of chemically driven biomolecular reactions. The focus of the current work is on the experimental characterization of the mixer through analysis of the concentration profiles along the length of the serpentineshaped microchannel.

Serial Synchrotron Crystallography (SSX) is rapidly emerging as a promising technique for collecting data for time-resolved structural studies or for performing room temperature micro-crystallography measurements using micro-focused beamlines. SSX is often performed using high frame rate detectors in combination with continuous sample scanning or high-viscosity or liquid jet injectors. When performed using ultra-bright X-ray Free Electron Laser (XFEL) sources serial crystallography typically involves a process known as &rsquo, diffract-and-destroy&rsquo, where each crystal is measured just once before it is destroyed by the intense XFEL pulse. In SSX, however, particularly when using high-viscosity injectors (HVIs) such as Lipidico, the crystal can be intercepted multiple times by the X-ray beam prior to exiting the interaction region. This has a number of important consequences for SSX including whether these multiple-hits can be incorporated into the data analysis or whether they need to be excluded due to the potential impact of radiation damage. Here, we investigate the occurrence and characteristics of multiple hits on single crystals using SSX with lipidico. SSX data are collected from crystals as they tumble within a high viscous stream of silicone grease flowing through a micro-focused X-ray beam. We confirmed that, using the Eiger 16M, we are able to collect up to 42 frames of data from the same single crystal prior to it leaving the X-ray interaction region. The frequency and occurrence of multiple hits may be controlled by varying the sample flow rate and X-ray beam size. Calculations of the absorbed dose confirm that these crystals are likely to undergo radiation damage but that nonetheless incorporating multiple hits into damage-free data should lead to a significant reduction in the number of crystals required for structural analysis when compared to just looking at a single diffraction pattern from each crystal.

The success of the lipidic cubic phase for crystallization, particularly of integral membrane proteins, is increasing. In the past two years, more than 25% of membrane protein structures have been solved within the biomimetic environment of the lipidic cubic phase. However, the relationship between the lipid matrix and crystal growth still remains a mystery. Herein we show that the bilayer structure of the lipidic cubic phase is crucial to retention of the functionality of the dopamine D2 long receptor. Destruction of the cubic architecture at higher protein concentrations is associated with a significant drop in the amount of functional receptor. This has profound implications for in meso crystallization and suggests that preliminary experiments to determine the maximum protein loading within the lipidic cubic phase must be carried out prior to in meso crystallization experiments.

The precise details of the interaction of intense X-ray pulses with matter are a topic of intense interest to researchers attempting to interpret the results of femtosecond X-ray free electron laser (XFEL) experiments. An increasing number of experimental observations have shown that although nuclear motion can be negligible, given a short enough incident pulse duration, electronic motion cannot be ignored. The current and widely accepted models assume that although electrons undergo dynamics driven by interaction with the pulse, their motion could largely be considered 'random'. This would then allow the supposedly incoherent contribution from the electronic motion to be treated as a continuous background signal and thus ignored. The original aim of our experiment was to precisely measure the change in intensity of individual Bragg peaks, due to X-ray induced electronic damage in a model system, crystalline C-60. Contrary to this expectation, we observed that at the highest X-ray intensities, the electron dynamics in C-60 were in fact highly correlated, and over sufficiently long distances that the positions of the Bragg reflections are significantly altered. This paper describes in detail the methods and protocols used for these experiments, which were conducted both at the Linac Coherent Light Source (LCLS) and the Australian Synchrotron (AS) as well as the crystallographic approaches used to analyse the data.

In meso crystallization uses bicontinuous cubic lipidic mesophases as matrices for the crystallization of membrane proteins. In this work, we look at the impact of a screen specifically marketed as compatible with the cubic mesophase, the Cubic crystallization screen (Emerald BioSystems), on the cubic mesophases formed by three different lipids: monoolein, monopalmitolein, and phytantriol. The Cubic screen was found to be compatible with cubic mesophase retention under most crystallization conditions for all three lipids studied. The effect of the individual components comprising the multicomponent screen was deconvoluted in two ways. Initially, the effect of specific poly(ethylene glycol) (PEG) and salt components on the cubic mesophase was determined using small-angle X-ray scattering (SAXS). The effect of high-molecular-weight (Mw) PEG was shown to dominate the phase behavior within the screen. The effect of additional salts present within the screen becomes important for low Mw PEG molecules. Finally,...

A serial millisecond crystallography (SMX) facility has recently been implemented at the macromolecular crystallography beamline, MX2 at the Australian Synchrotron. The setup utilizes a combination of an EIGER X 16M detector system and an in-house developed high-viscosity injector, "Lipidico." Lipidico uses a syringe needle to extrude the microcrystal-containing viscous media and it is compatible with commercially available syringes. The combination of sample delivery via protein crystals suspended in a viscous mixture and a millisecond frame rate detector enables high-throughput serial crystallography at the Australian Synchrotron. A hit-finding algorithm, based on the principles of "robust-statistics," is employed to rapidly process the data. Here we present the first SMX experimental results with a detector frame rate of 100 Hz (10 ms exposures) and the Lipidico injector using a mixture of lysozyme microcrystals embedded in high vacuum silicon grease. Details of the experimental setup, sample injector, and data analysis pipeline are designed and developed as part of the Australian Synchrotron SMX instrument and are reviewed here.

Coherent electron dynamics in a periodic array of C60 molecular targets driven by intense x-ray pulses of femtosecond duration., X-ray free-electron lasers (XFELs) deliver x-ray pulses with a coherent flux that is approximately eight orders of magnitude greater than that available from a modern third-generation synchrotron source. The power density of an XFEL pulse may be so high that it can modify the electronic properties of a sample on a femtosecond time scale. Exploration of the interaction of intense coherent x-ray pulses and matter is both of intrinsic scientific interest and of critical importance to the interpretation of experiments that probe the structures of materials using high-brightness femtosecond XFEL pulses. We report observations of the diffraction of extremely intense 32-fs nanofocused x-ray pulses by a powder sample of crystalline C60. We find that the diffraction pattern at the highest available incident power significantly differs from the one obtained using either third-generation synchrotron sources or XFEL sources operating at low output power and does not correspond to the diffraction pattern expected from any known phase of crystalline C60. We interpret these data as evidence of a long-range, coherent dynamic electronic distortion that is driven by the interaction of the periodic array of C60 molecular targets with intense x-ray pulses of femtosecond duration.

Journal of synchrotron radiation 24(1), 83 - 94(2017). doi:10.1107/S1600577516017525, The proliferation of extremely intense synchrotron sources has enabled ever higher-resolution structures to be obtained using data collected from smaller and often more imperfect biological crystals (Helliwell, 1984). Synchrotron beamlines now exist that are capable of measuring data from single crystals that are just a few micrometres in size. This provides renewed motivation to study and understand the radiation damage behaviour of small protein crystals. Reciprocal-space mapping and Bragg coherent diffractive imaging experiments have been performed on cryo-cooled microcrystals of hen egg-white lysozyme as they undergo radiation damage. Several well established metrics, such as intensity-loss and lattice expansion, are applied to the diffraction data and the results are compared with several new metrics that can be extracted from the coherent imaging experiments. Individually some of these metrics are inconclusive. However, combining metrics, the results suggest that radiation damage behaviour in protein micro-crystals differs from that of larger protein crystals and may allow them to continue to diffract for longer. A possible mechanism to account for these observations is proposed., Published by IUCr, Chester

The recent development of X-ray free electron lasers (XFELs) has spurred the development of serial femtosecond nanocrystallography (SFX) which, for the first time, is enabling structure retrieval from sub-micron protein crystals. Although there are already a growing number of structures published using SFX, the technology is still very new and presents a number of unique challenges as well as opportunities for structural biologists. One of the biggest barriers to the success of SFX experiments is the preparation and selection of suitable protein crystal samples. Here we outline a protocol for preparing and screening for suitable XFEL targets.

A protocol is presented for the high-throughput (HT) production of lyotropic liquid crystalline phases from libraries of lipids and lipid mixtures using standard liquid dispensing robotics, implementing methods that circumvent the problems traditionally associated with handling the highly viscous cubic phase. In addition, the ability to structurally characterize lipidic phases and assess functionality for membrane proteins contained within cubic phases, in a HT manner, is demonstrated. The techniques are combined and exemplified using the application of membrane protein crystallization within lipidic cubic phases.

The application of powder diffraction methods to problems in structural biology is generally regarded as intractable because of the large number of unresolved, overlapping X-ray reflections. Here, we use information about unit cell lattice parameters, space group transformations, and chemical composition as a priori information in a bootstrap process that resolves the ambiguities associated with overlapping reflections. The measured ratios of reflections that can be resolved experimentally are used to refine the position, the shape, and the orientation of low-resolution molecular structures within the unit cell, in leading to the resolution of the overlapping reflections. The molecular model is then made progressively more sophisticated as additional diffraction information is included in the analysis. We apply our method to the recovery of the structure of the bacteriorhodopsin molecule (bR) to a resolution of 7 A using experimental data obtained from two-dimensional purple membrane crystals. The approach can be used to determine the structure factors directly or to provide reliable low-resolution phase information that can be refined further by the conventional methods of protein crystallography.

Intrinsic difficulties in characterizing the structure of combined membrane protein–lyotropic liquid crystalline lipidic cubic systems have hampered the development of techniques such as membrane protein (MP) crystallization, which remain largely empirical with consequently low success rates. Here we have incorporated an integral membrane protein and important neurological drug target, the dopamine D2L receptor, within nanostructured nanoparticles of lipidic cubic phase, known as Cubosomes. We show that MPs are incorporated within Cubosomes and that they exert a structural effect which is qualitatively similar to that seen in bulk cubic phase for some systems, exemplifying the potential of Cubosomes to characterize MP incorporation. In addition we have shown, for Cubosomes doped with Ni(II) chelated EDTA amphiphiles, that the strong affinity interaction between the bio-engineered histidine(His)-tag on the protein and the Ni(II) chelated EDTA headgroup of the doped amphiphile leads to enhanced interaction between the membrane protein and the nanostructured cubic nanoparticle. This indicates that protein loading within a cubic phase can be increased as required either to facilitate crystal growth within cubic mesophases or for drug loading. In addition it exemplifies the potential of Cubosome nanostructured nanoparticles to be targeted to specific sites in the body.

The malaria parasite pigment, hemozoin, is a crystal of ferriprotoporphyrin IX (FP-Fe(III)), a product of hemoglobin digestion. Hemozoin formation is essential for FP-Fe(III) detoxification in the parasite; it is the main target of quinoline antimalarials and can modulate immune and inflammation responses. To gain further insight into the likely mechanisms of crystal formation and hemozoin reactivity, we have reanalyzed the crystal structure data for beta-hematin and solved the crystal structure of Plasmodium falciparum hemozoin. The analysis reveals that the structures are very similar and highlights two previously unexplored modes of FP-Fe(III) self-association involving pi-pi interactions that may initiate crystal formation and help to stabilize the extended structure. Hemozoin can be considered to be a crystal composed of pi-pi dimers stabilized by iron-carboxylate linkages. As a result, it is predicted that two surfaces of the crystal would consist of pi-pi dimers with Fe(III) partly exposed to solvent and capable of undergoing redox reactions. Accordingly, we demonstrate that the crystal possesses both general peroxidase activity and the ability to cause lipid oxidation.

A novel acoustic microfluidic nebulization platform is demonstrated, which, due to its unique ability to access intermediate evaporation rate regimes-significantly faster than that in slow solvent evaporation but considerably below that achieved in spray drying, is capable of producing novel crystal morphologies that have yet to be reported in both model inorganic and organic systems. In addition, the potential for simultaneously encapsulating single crystals within a biodegradable polymeric coating in a single simultaneous step together with the crystallization process as the solvent evaporates during nebulization is briefly shown. The platform not only has the potential to be highly scalable by employing a large number of these low-cost miniature devices in parallel to achieve industrially relevant particle production rates, but could also be advantageous over conventional spray drying in terms of energy utilization, given the tremendous efficiency associated with the high-frequency ultrasonic microdevice as well as its ambient temperature operation.

For laboratory and synchrotron based X-ray sources, radiation damage has posed a significant barrier to obtaining high-resolution structural data from biological macromolecules. The problem is particularly acute for micron-sized crystals where the weaker signal often necessitates the use of higher intensity beams to obtain the relevant data. Here, we employ a combination of techniques, including Bragg coherent diffractive imaging to characterise the radiation induced damage in a micron-sized protein crystal over time. The approach we adopt here could help screen for potential protein crystal candidates for measurement at X-ray free election laser sources.

Autoantibodies to the diabetes autoantigen, the 65 kDa isoform of glutamic acid decarboxylase (GAD65), react with conformational epitopes defined according to linear sequences but not according to structural information, or contact sites with the antibody paratope. To ascertain such information for an exemplary human monoclonal antibody (mAb) to GAD65, b78, we combined antibody screening of phage-displayed peptide libraries, alanine mutagenesis of selected motifs, homology modelling of the PLP and C-terminal regions of GAD65, and molecular dynamics to examine for structural effects of mutagenesis. By phage display, mAb b78 selected phagotopes containing acidic residues (D, E), hydrophobic residues (Y, F or W) and LRS that localised to a possible surface-exposed conformational epitope on the combined homology model. Alanine mutants of GAD65 based on deduced contact residues were examined for binding with b78 and control sera. Mutation of 524 SRL 526 , 572 DF 573 and 498 KPQ 500 reduced reactivity of b78 with mutant GAD65 > 50%. Molecular dynamics indicated that mutation of 498 KPQ 500 caused structural changes that could account for effects of this mutation. Thus phage display in combination with molecular modelling identified contact residues within a highly conformational epitope for mAb b78 in the C-terminus of GAD65. These techniques should have broad applicability to definition of epitope structure.

Sorbitol dehydrogenase (SDH) is the second enzyme in the polyol pathway of glucose metabolism and is a possible target for the treatment of the complications of diabetes. In this study the molecular modelling program DOCK was used to analyse 249,071 compounds from the National Cancer Institute Database and predict those with high affinity for SDH. From a total of 21 tested the 7 compounds including flavin adenine dinucleotide disodium hydrate, (+)-Amethopterin, 3-hydroxy-2-napthoic(2-hydroxybenzylidene) hydrazide, folic acid, N-2,4-dinitrophenyl-L-cysteic acid, Vanillin azine and 1H-indole-2,3-dione,5-bromo-6-nitro-1-(2,3,4-tri-O-acetyl-alpha-L-arabinopyranosyl)-(9Cl), were shown to inhibit SDH and displayed IC50 values of 0.192 microM, 1.1 microM, 1.2 microM, 4.5 microM, 5.3 microM, 7 microM and 28 microM, respectively. These compounds may aid the design of pharmaceutical agents for the treatment of diabetes complications.

Structure determinations of human aldose reductase holoenzyme in complex with the 2S4R-,2R4S- and 2R4R-isomers of the potent inhibitor Fidarestat ((2S,4S)-6-fluoro-2',5'-dioxospiro[chroman-4,4'-imidazoline]-2-carboxamide) were carried out in order to elucidate the binding modes responsible for the differences in their inhibitory potencies. In the complex structure with the 2R4S-isomer the cyclic imide moiety formed hydrogen bonds with the side-chains of Trp111, Tyr48 and His110. In the attempt to determine the complex structure with the least potent 2R4R-isomer this ligand was not observed, and instead, the active site was simultaneously occupied by two citrate molecules (occupancies of 60% and 40%). In the case of 2S4R, the active site was occupied by a citrate molecule which anchors the 2S4R-isomer from its carbamoyl group. The structures of the complexes suggest that the differences in the interactions between the cyclic imide rings and carbamoyl groups of the compounds with residues His110, Trp111, Trp219 and Cys298 account for differences in their inhibitory potencies.

Aldose reductase, the first and rate-limiting enzyme of the polyol pathway, is a target for drug design for the treatment of diabetes complications. The structures of aldose reductase in complex with the cyclic imide inhibitors Fidarestat and Minalrestat were recently determined at ultra-high resolution (Proteins 2004, 55, 805). We have used the detailed structural information revealed at atomic resolution, including the assignment of protonation states for the inhibitors and active site residues, together with molecular modelling and noncovalent mass spectrometry to characterise the type and strength of the interactions between the enzyme and the inhibitors, and to attempt the design of novel potential inhibitors with enhanced binding energies of the complexes. The VC50 values measured by mass spectrometry (accelerated voltage of ions needed to dissociate 50% of a noncovalent complex in the gas phase) for the aldose reductase inhibitors correlate with the IC50 values (concentration of inhibitor giving 50% inhibition in solution) and with the electrostatic binding energies calculated between the active site residues Tyr48, His110 and Trp111 and the inhibitors, suggesting that electrostatic interactions play a major role in inhibitor binding. Our molecular modelling and design studies suggest that the replacement of the fluorine atom in Minalrestat's bromo-fluorobenzyl group with nitro, amide and carboxylate functional groups enhanced the predicted net binding energies of the complexes by 16%, 31% and 68%, respectively. When the carbamoyl group of Fidarestat was replaced with a nitro, 4-hydroxyl phenyl and carboxylate functional groups, the predicted net binding energies of the complexes were enhanced by 13%, 34% and 46%, respectively.

L-Xylulose reductase (XR), an enzyme in the uronate cycle of glucose metabolism, belongs to the short-chain dehydrogenase/reductase (SDR) superfamily. Among the SDR enzymes, XR shows the highest sequence identity (67%) with mouse lung carbonyl reductase (MLCR), but the two enzymes show different substrate specificities. The crystal structure of human XR in complex with reduced nicotinamide adenine dinucleotide phosphate (NADPH) was determined at 1.96 A resolution by using the molecular replacement method and the structure of MLCR as the search model. Features unique to human XR include electrostatic interactions between the N-terminal residues of subunits related by the P-axis, termed according to SDR convention, and an interaction between the hydroxy group of Ser185 and the pyrophosphate of NADPH. Furthermore, identification of the residues lining the active site of XR (Cys138, Val143, His146, Trp191, and Met200) together with a model structure of XR in complex with L-xylulose, revealed structural differences with other members of the SDR family, which may account for the distinct substrate specificity of XR. The residues comprising a recently proposed catalytic tetrad in the SDR enzymes are conserved in human XR (Asn107, Ser136, Tyr149, and Lys153). To examine the role of Asn107 in the catalytic mechanism of human XR, mutant forms (N107D and N107L) were prepared. The two mutations increased Km for the substrate (>26-fold) and Kd for NADPH (95-fold), but only the N107L mutation significantly decreased kcat value. These results suggest that Asn107 plays a critical role in coenzyme binding rather than in the catalytic mechanism. Proteins 2004. © 2004 Wiley-Liss, Inc.

Sorbitol dehydrogenase (SDH), a member of the medium-chain dehydrogenase / reductase protein family and the second enzyme of the polyol pathway of glucose metabolism, converts sorbitol to fructose strictly using NAD+ as coenzyme. SDH is expressed almost ubiquitously in all mammalian tissues. The enzyme has attracted considerable interest due to its implication in the development of diabetic complications and thus its tertiary structure may facilitate the development of drugs for the treatment of diabetes sufferers. Modelling studies suggest that SDH is structurally homologous to mammalian alcohol dehydrogenase with respect to conserved zinc binding motif and a hydrophobic substrate-binding pocket. Recently, the three-dimensional (3- D) structure of a mammalian SDH was solved, and it was found that while the overall 3-D structures of SDH and alcohol dehydrogenase are similar, the zinc coordination in the active sites of the two enzymes is different. The available structural and biochemical information of SDH are currently being utilized in a structure-based approach to develop drugs for the treatment or prevention of the complications of diabetes. This review provides an overview of the recent advances in the structure, function and drug development fields of sorbitol dehydrogenase.

The unique properties of nanodiamonds make them suitable for use in a wide range of applications, including as biomarkers for cellular tracking in vivo at the molecular level. The sustained fluorescence of nanodiamonds containing nitrogen-vacancy (N-V) centres is related to their internal structure and strain state. Theoretical studies predict that the location of the N-V centre and the nanodiamonds' residual elastic strain state have a major influence on their photoluminescence properties. However, to date there have been no direct measurements made of their spatially resolved deformation fields owing to the challenges that such measurements present. Here we apply the recently developed technique of Bragg coherent diffractive imaging (BCDI) to map the three-dimensional deformation field within a single nanodiamond of approximately 0.5 µm diameter. The results indicate that there are high levels of residual elastic strain present in the nanodiamond which could have a critical influence on its optical and electronic properties.

The butyrate G-protein coupled receptors (GPCRs), GPR41 and GPR43, have been implicated in colorectal cancer and leptin production. To date their function has not been elucidated as low levels of protein expression and difficulties in producing diffraction quality crystals have hindered their structural determination. In meso crystallization, which uses an artificial lipid membrane matrix to facilitate crystal growth, is becoming an increasingly successful crystallization technique, particularly for GPCRs. We report herein the lipid membrane matrix structural characterization for GPR41 and GPR43 within two lipid self-assembly systems (monoolein and phytantriol) commonly used for in meso crystallization and comment on their suitability for crystallizing these GPCRs. Synchrotron small angle X-ray scattering (SAXS) studies were used to determine the initial phase and uptake of these receptors within the lipid matrix and investigate the role of cholesterol in this process. The self-assembled lipid nanostructure was retained in the presence of GPR43 for both lipids but was destabilized for GPR41 in the phytantriol lipid system. The structural changes to the lipid matrix upon protein incorporation were greater for cholesterol-doped systems, potentially indicative of increased receptor uptake.

The program GRID was used to design novel potential inhibitors of human sorbitol dehydrogenase based on a model of the holoenzyme in complex with the inhibitor WAY135 706. Replacement of the methyl hydroxyl group of the inhibitor with methyl phosphate and methyl carboxylate functional groups increased the net binding energy of the complex by 2.0- and 1.7-fold, respectively. This study may be useful in the development of potent and more specific inhibitors of the enzyme.

Three-dimensional imaging of protein crystals during x-ray diffraction experiments opens up a range of possibilities for optimizing crystal quality and gaining new insights into the fundamental processes that drive radiation damage. Obtaining this information at the appropriate length-scales however is extremely challenging. One approach that has been recently demonstrated as a promising avenue for characterizing the size and shape of protein crystals at nanometre length-scales is Bragg coherent diffractive imaging (BCDI). BCDI is a recently developed technique that is able to recover the phase of the continuous diffraction intensity signal around individual Bragg peaks. When data is collected at multiple points on a rocking curve, a reciprocal space map (RSM) can be assembled and then inverted using BCDI to obtain a three-dimensional image of the crystal. The first demonstration of two-dimensional biological BCDI was reported by Boutet et al on holoferritin, recently this work was extended to the study of radiation damage in micron-sized protein crystals. Here we present the first three-dimensional reconstructions of a Lysozyme protein crystal using BDI. The results are validated against RSM and transmission electron microscopy data and have implications for both radiation damage studies and for developing new approaches for structure retrieval from micron-sized protein crystals.

We have tracked the structural evolution of the monoolein bicontinuous cubic phase under in meso crystallogenesis conditions. Significantly, all measurements have been carried out in situ within a crystallisation plate reproducing the exact conditions during a crystallisation trial. The structure of the MO cubic phase, doped with a small concentration of amyloid-beta peptide, was measured 1 day, 5 days, 7 days and 21 days after addition of PACT crystallisation screen, which systematically varies cation, anion, pH and polyethylene glycol (PEG). The components of the screen had a significant impact on the structure of the cubic phase. We have rationalised the structural variation with respect to the effect of the individual screen components. Specifically addition of higher Mw PEG effected a transition from a diamond cubic phase (QIID) to a gyroid cubic phase (QIIG) across the majority of the plate and the QIIG phase became more prevalent with time. The effect of individual salts was correlated with their position in the Hofmeister series. Changes in pH and buffer system had a more minor effect on mesophase structure. We have discussed the implications of the observed structural changes with respect to the putative mechanism of protein crystal growth within a lipidic cubic phase.

Self-assembled lipidic cubic phases are attracting increasing interest as biocompatible carriers of large biomolecules including proteins, peptides, DNA and drugs.1 Their unique structure of interpenetrating but unconnected water channels divided by a lipid bilayer can accommodate hydrophobic, hydrophilic and amphiphilic moieties without significant structural perturbation. This has led to their use in a diverse range of applications including the delivery of drugs and other active agents, as biomimetic crystallization media for membrane proteins, as the basis of biofuel cells, and as biosensors.2Lipidic cubic phases can be emulsified into diluted non-viscous aqueous dispersions consisting of cubic nanoparticles, offering significant advantages for many of the applications listed above.3 Here we have incorporated an integral membrane protein and important neurological drug target within cubic nanoparticles. We have characterised the structural effect on the micro- and meso-scale properties of the nanoparticles. In addition we have shown that protein loading can be significantly enhanced by doping the cubic nanoparticles with a second amphiphile which chemically binds to the integral membrane protein.1Yaghmur A, Glatter O. Advances in Colloid and Interface Science 2009; 147-148; 333-342.2Nazaruk E, Bilewicz R, Lindblom G, Lindholm-Sethson B. Anal Bioanal Chem 2008; 391; 1569-1578.3Spicer PT. Current Opinion in Colloid & Interface Science 2005; 10; 274 - 279.