Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography.

Riboswitches are structural RNA elements that are generally located in the 5' untranslated region of messenger RNA. During regulation of gene expression, ligand binding to the aptamer domain of a riboswitch triggers a signal to the downstream expression platform. A complete understanding of the structural basis of this mechanism requires the ability to study structural changes over time. Here we use femtosecond X-ray free electron laser (XFEL) pulses to obtain structural measurements from crystals so small that diffusion of a ligand can be timed to initiate a reaction before diffraction. We demonstrate this approach by determining four structures of the adenine riboswitch aptamer domain during the course of a reaction, involving two unbound apo structures, one ligand-bound intermediate, and the final ligand-bound conformation. These structures support a reaction mechanism model with at least four states and illustrate the structural basis of signal transmission. The three-way junction and the P1 switch helix of the two apo conformers are notably different from those in the ligand-bound conformation. Our time-resolved crystallographic measurements with a 10-second delay captured the structure of an intermediate with changes in the binding pocket that accommodate the ligand. With at least a 10-minute delay, the RNA molecules were fully converted to the ligand-bound state, in which the substantial conformational changes resulted in conversion of the space group. Such notable changes in crystallo highlight the important opportunities that micro- and nanocrystals may offer in these and similar time-resolved diffraction studies. Together, these results demonstrate the potential of 'mix-and-inject' time-resolved serial crystallography to study biochemically important interactions between biomacromolecules and ligands, including those that involve large conformational changes.

Guided wave skew velocity correction in anisotropic laminates.

Guided ultrasonic wave propagation in anisotropic structures results in directional dependency of velocity and wave skewing effects that can impact the accuracy of damage detection. Phase and group velocities of the A0 guided wave mode, propagating in a unidirectional carbon fiber reinforced laminate, were investigated experimentally and through finite element analysis. A correction for the significant offset in phase and group velocities due to wave skewing effects is illustrated for both point and short line sources, achieving good agreement with theoretical calculations assuming planar wave fronts. The influence of the line excitation length on velocity measurements is discussed.

Post-acquisition mask misalignment correction for edge illumination x-ray phase contrast imaging.

Edge illumination x-ray phase contrast imaging uses a set of apertured masks to translate phase effects into variation of detected intensity. While the system is relatively robust against misalignment, mask movement during acquisition can lead to gradient artifacts. A method has been developed to correct the images by quantifying the misalignment post-acquisition and implementing correction maps to remove the gradient artifact. Images of a woven carbon fiber composite plate containing porosity were used as examples to demonstrate the image correction process. The gradient formed during image acquisition was removed without affecting the image quality, and results were subsequently used for quantification of porosity, indicating that the gradient correction did not affect the quantitative content of the images.

X-ray diffraction from membrane protein nanocrystals.

Membrane proteins constitute > 30% of the proteins in an average cell, and yet the number of currently known structures of unique membrane proteins is < 300. To develop new concepts for membrane protein structure determination, we have explored the serial nanocrystallography method, in which fully hydrated protein nanocrystals are delivered to an x-ray beam within a liquid jet at room temperature. As a model system, we have collected x-ray powder diffraction data from the integral membrane protein Photosystem I, which consists of 36 subunits and 381 cofactors. Data were collected from crystals ranging in size from 100 nm to 2 µm. The results demonstrate that there are membrane protein crystals that contain < 100 unit cells (200 total molecules) and that 3D crystals of membrane proteins, which contain < 200 molecules, may be suitable for structural investigation. Serial nanocrystallography overcomes the problem of x-ray damage, which is currently one of the major limitations for x-ray structure determination of small crystals. By combining serial nanocrystallography with x-ray free-electron laser sources in the future, it may be possible to produce molecular-resolution electron-density maps using membrane protein crystals that contain only a few hundred or thousand unit cells.

In cellulo crystallization of Trypanosoma brucei IMP dehydrogenase enables the identification of genuine co-factors.

Sleeping sickness is a fatal disease caused by the protozoan parasite Trypanosoma brucei (Tb). Inosine-5'-monophosphate dehydrogenase (IMPDH) has been proposed as a potential drug target, since it maintains the balance between guanylate deoxynucleotide and ribonucleotide levels that is pivotal for the parasite. Here we report the structure of TbIMPDH at room temperature utilizing free-electron laser radiation on crystals grown in living insect cells. The 2.80 Å resolution structure reveals the presence of ATP and GMP at the canonical sites of the Bateman domains, the latter in a so far unknown coordination mode. Consistent with previously reported IMPDH complexes harboring guanosine nucleotides at the second canonical site, TbIMPDH forms a compact oligomer structure, supporting a nucleotide-controlled conformational switch that allosterically modulates the catalytic activity. The oligomeric TbIMPDH structure we present here reveals the potential of in cellulo crystallization to identify genuine allosteric co-factors from a natural reservoir of specific compounds.

Structure and function of photosystem I.

The past year has been significant advances in the understanding of the structure and function of photosystem I (PS I). The highlights included significant progress in discovering the arrangement and function of subunits of PS I, and improvement of the structure of PS I to 4 degrees resolution, as well as new evidence for the mechanism of the interaction of PS I with its soluble electron carriers plastocyanine, cytochrome c6 and ferredoxin. Substantial progress has been made towards understanding the mechanism of energy transfer from the antenna system to the reaction centre, and the electronic structure of the electron carriers.

Evaluation of the 3D spatial distribution of the Calcium/Phosphorus ratio in bone using computed-tomography dual-energy analysis.

PURPOSE: The Calcium/Phosphorus (Ca/P) ratio was shown to vary between healthy bones and bones with osteoporotic symptoms. The relation of the Ca/P ratio to bone quality remains under investigation. To study this relation and determine if the ratio can be used to predict bone fractures, a non-invasive 3D imaging technique is required. The first aim of this study was to test the effectiveness of a computed-tomography dual-energy analysis (CT-DEA) technique developed to assess the Ca/P ratio in bone apatite (collagen-free bone) in identifying differences between healthy and inflammation-mediated osteoporotic (IMO) bones. The second aim was to extend the above technique for its application to a more complex structure, intact bone, that could potentially lead to clinical use. METHODS: For the first aim, healthy and IMO rabbit cortical bone apatite samples were assessed. For the second aim, some changes were made to the technique, which was applied to healthy and IMO intact bone samples. RESULTS: Statistically significant differences between healthy and IMO bone apatite were found for the bulk Ca/P ratio, low Ca/P ratio proportion and interconnected low Ca/P ratio proportion. For the intact bone samples, the bulk Ca/P ratio was found to be significantly different between healthy and IMO. CONCLUSIONS: Results show that the CT-DEA technique can be used to identify differences in the Ca/P ratio between healthy and osteoporotic, in both bone apatite and intact bone. With quantitative imaging becoming an increasingly important advancement in medical imaging, CT-DEA for bone decomposition could potentially have several applications.

AXSIS: Exploring the frontiers in attosecond X-ray science, imaging and spectroscopy.

X-ray crystallography is one of the main methods to determine atomic-resolution 3D images of the whole spectrum of molecules ranging from small inorganic clusters to large protein complexes consisting of hundred-thousands of atoms that constitute the macromolecular machinery of life. Life is not static, and unravelling the structure and dynamics of the most important reactions in chemistry and biology is essential to uncover their mechanism. Many of these reactions, including photosynthesis which drives our biosphere, are light induced and occur on ultrafast timescales. These have been studied with high time resolution primarily by optical spectroscopy, enabled by ultrafast laser technology, but they reduce the vast complexity of the process to a few reaction coordinates. In the AXSIS project at CFEL in Hamburg, funded by the European Research Council, we develop the new method of attosecond serial X-ray crystallography and spectroscopy, to give a full description of ultrafast processes atomically resolved in real space and on the electronic energy landscape, from co-measurement of X-ray and optical spectra, and X-ray diffraction. This technique will revolutionize our understanding of structure and function at the atomic and molecular level and thereby unravel fundamental processes in chemistry and biology like energy conversion processes. For that purpose, we develop a compact, fully coherent, THz-driven atto-second X-ray source based on coherent inverse Compton scattering off a free-electron crystal, to outrun radiation damage effects due to the necessary high X-ray irradiance required to acquire diffraction signals. This highly synergistic project starts from a completely clean slate rather than conforming to the specifications of a large free-electron laser (FEL) user facility, to optimize the entire instrumentation towards fundamental measurements of the mechanism of light absorption and excitation energy transfer. A multidisciplinary team formed by laser-, accelerator,- X-ray scientists as well as spectroscopists and biochemists optimizes X-ray pulse parameters, in tandem with sample delivery, crystal size, and advanced X-ray detectors. Ultimately, the new capability, attosecond serial X-ray crystallography and spectroscopy, will be applied to one of the most important problems in structural biology, which is to elucidate the dynamics of light reactions, electron transfer and protein structure in photosynthesis.

Activation/inactivation and uni-site catalysis by the reconstituted ATP-synthase from chloroplasts.

The proton-translocating ATP-synthase of chloroplasts, CF0F1, was isolated and reconstituted into asolectin liposomes. CF0F1 can exist in at least four different states, oxidized or reduced, either inactive or active. These states are characterized by different kinetics of ADP binding: There is no binding of ADP to the inactive, oxidized state, the rate constant for ADP binding to the inactive, reduced states is 7.10(2) M-1.s-1. ADP binding to the active, reduced state occurs under deenergized conditions with 10(5) M-1.s-1 and transforms the enzyme into the inactive, reduced state. Parallel to the ADP-dependent inactivation, the enzyme can also inactivate without ADP binding with a first-order rate constant of 7.10(-3) M-1.s-1. With the active, reduced enzyme ATP-hydrolysis was measured under uni-site conditions as has been carried out with MF1 (Grubmeyer, C., Cross, R.C. and Penefsky, H.S. (1982) J. Biol. Chem. 257, 12092-12100). The rate constant for ATP binding is 10(6) M-1.s-1, the 'equilibrium constant' on the enzyme EADPPi/EATP is 0.4. The rate constants for Pi release and ADP release are 0.2 s-1 and o.1 s-1, respectively. This indicates that the enzyme carries out a complete turnover under uni-site conditions with rates much higher than that reported for MF1.

Structure of photosystem I.

In plants and cyanobacteria, the primary step in oxygenic photosynthesis, the light induced charge separation, is driven by two large membrane intrinsic protein complexes, the photosystems I and II. Photosystem I catalyses the light driven electron transfer from plastocyanin/cytochrome c(6) on the lumenal side of the membrane to ferredoxin/flavodoxin at the stromal side by a chain of electron carriers. Photosystem I of Synechococcus elongatus consists of 12 protein subunits, 96 chlorophyll a molecules, 22 carotenoids, three [4Fe4S] clusters and two phylloquinones. Furthermore, it has been discovered that four lipids are intrinsic components of photosystem I. Photosystem I exists as a trimer in the native membrane with a molecular mass of 1068 kDa for the whole complex. The X-ray structure of photosystem I at a resolution of 2.5 A shows the location of the individual subunits and cofactors and provides new information on the protein-cofactor interactions. [P. Jordan, P. Fromme, H.T. Witt, O. Klukas, W. Saenger, N. Krauss, Nature 411 (2001) 909-917]. In this review, biochemical data and results of biophysical investigations are discussed with respect to the X-ray crystallographic structure in order to give an overview of the structure and function of this large membrane protein.

First photosystem II crystals capable of water oxidation.

Oxygen evolution and proton release of crystallised photosystem II core complexes isolated from Synechococcus elongatus were measured. The yields show that the crystals themselves are capable of highly active water oxidation. This opens the possibility for the structural analysis of the outstanding water-oxidising apparatus.

The structural organization of the PsaC protein in Photosystem I from single crystal EPR and X-ray crystallographic studies.

In Photosystem I (PS I) the terminal electron acceptors, FA and FB, are iron-sulfur (4Fe-4S) centers, which are bound to the stromal subunit PsaC. The orientation of PsaC is determined relative to the whole PS I complex (see Schubert, W.-D. et al. (1995) in From Light to Biosphere (Mathis, P. ed.), Vol. II, pp. 3-10, Kluwer) from which a molecular model for the structure of PsaC within PS I is derived. Two strategies are followed: (i) PS I single crystal EPR data on the orientation of the g tensors of both FA- and FB- relative to each other and relative to the crystal axes (see preceding paper) are used in conjunction with the central structural part of the bacterial 2 [Fe4S4] ferredoxins, the cysteine binding motifs of which are known to be homologous to those of PsaC; (ii) the same core structure is fitted into the intermediate resolution electron density map of PS I. The PsaC orientation obtained both ways agree well. The local twofold symmetry axis inherent to the ferredoxin model leaves a twofold ambiguity in the structural conclusion. Deviations from this C2-symmetry in the amino acid sequence of PsaC are analyzed with respect to observable properties which would resolve the remaining structural ambiguity. Arguments both for and against FA being the distal iron-sulfur center (to FX) are discussed.

A common ancestor for oxygenic and anoxygenic photosynthetic systems: a comparison based on the structural model of photosystem I.

The 4 A structural model of photosystem I (PSI) has elucidated essential features of this protein complex. Inter alia, it demonstrates that the core proteins of PSI, PsaA and PsaB each consist of an N-terminal antenna-binding domain, and a C-terminal reaction center (RC)-domain. A comparison of the RC-domain of PSI and the photosynthetic RC of purple bacteria (PbRC), reveals significantly analogous structures. This provides the structural support for the hypothesis that the two RC-types (I and II) share a common evolutionary origin. Apart from a similar set of constituent cofactors of the electron transfer system, the analogous features include a comparable cofactor arrangement and a corresponding secondary structure motif of the RC-cores. Despite these analogies, significant differences are evident, particularly as regards the distances between and the orientation of individual cofactors, and the length and orientation of alpha-helices. Inferred roles of conserved amino acids are discussed for PSI, photosystem II (PSII), photosystem C (PSC, green sulfur bacteria) and photosystem H (PSH, heliobacteria). Significant sequence homology between the N-terminal, antenna-binding domains of the core proteins of type-I RCs, PsaA, PsaB, PscA and PshA (of PSI, PSC and PSH respectively) with the antenna-binding subunits CP43 and CP47 of PSII indicate that PSII has a modular structure comparable to that of PSI.

Photosystem I of Synechococcus elongatus at 4 A resolution: comprehensive structure analysis.

An improved structural model of the photosystem I complex from the thermophilic cyanobacterium Synechococcus elongatus is described at 4 A resolution. This represents the most complete model of a photosystem presently available, uniting both a photosynthetic reaction centre domain and a core antenna system. Most constituent elements of the electron transfer system have been located and their relative centre-to-centre distances determined at an accuracy of approximately 1 A. These include three pseudosymmetric pairs of Chla and three iron-sulphur centres, FX, FA and FB. The first pair, a Chla dimer, has been assigned to the primary electron donor P700. One or both Chla of the second pair, eC2 and eC'2, presumably functionally link P700 to the corresponding Chla of the third pair, eC3 and eC'3, which is assumed to constitute the spectroscopically-identified primary electron acceptor(s), A0, of PSI. A likely location of the subsequent phylloquinone electron acceptor, QK, in relation to the properties of the spectroscopically identified electron acceptor A1 is discussed. The positions of a total of 89 Chla, 83 of which constitute the core antenna system, are presented. The maximal centre-to-centre distance between antenna Chla is < or = 16 A; 81 Chla are grouped into four clusters comprising 21, 23, 17 and 20 Chla, respectively. Two "connecting" Chla are positioned to structurally (and possibly functionally) link the Chla of the core antenna to those of the electron transfer system. Thus the second and third Chla pairs of the electron transfer system may have a dual function both in energy transfer and electron transport. A total of 34 transmembrane and nine surface alpha-helices have been identified and assigned to the 11 subunits of the PSI complex. The connectivity of the nine C-terminal (seven transmembrane, two "surface") alpha-helices of each of the large core subunits PsaA and PsaB is described. The assignment of the amino acid sequence to the transmembrane alpha-helices is proposed and likely residues involved in co-ordinating the Chla of the electron transfer system discussed.

Diffraction and imaging from a beam of laser-aligned proteins: resolution limits.

The effect of the limited alignment of hydrated molecules is considered in a laser-aligned molecular beam, on diffraction patterns taken from the beam. Simulated patterns for a protein beam are inverted using the Fienup-Gerchberg-Saxton phasing algorithm, and the effect of limited alignment on the resolution of the resulting potential maps is studied. For a typical protein molecule (lysozyme) with anisotropic polarizability, it is found that up to 1 kW of continuous-wave near-infrared laser power (depending on dielectric constant), together with cooling to liquid-nitrogen temperatures, may be needed to produce sufficiently accurate alignment for direct observation of the secondary structure of proteins in the reconstructed potential or charge-density map. For a typical virus (TMV), a 50 W continuous-wave laser is adequate for subnanometre resolution at room temperature. The dependence of resolution on laser power, temperature, molecular size, shape and dielectric constant is analyzed.

Uni-site catalysis in thylakoids. The influence of membrane energization on ATP hydrolysis and ATP-Pi exchange.

ATP-hydrolysis was measured with thylakoid membranes during continuous illumination. The concentrations of free and enzyme-bound ATP, ADP and Pi were measured using either cold ATP, [gamma-32P]ATP or [14C]ATP. The concentration of free ATP was constant, free ADP and enzyme-bound ATP were below the detection limit. Nevertheless, [gamma-32P]ATP was bound, hydrolyzed and 32Pi was released. The ADP was not released from the enzyme but cold Pi was bound from the medium, cold ATP was resynthesized and released. A quantitative analysis gave the following rate constants: ATP-binding kATP = 2 . 10(5) M-1 s-1, ADP-release: kADP less than 10(-2)s-1, Pi-release: kPi = 0.1 s-1. These rate constants are considerably smaller than under deenergized conditions. The rate constant for the release of ATP can be estimated to be at least 0.2 s-1 under energized conditions. Obviously, energization of the membrane, i.e. protonation of the enzyme leads mainly to a decrease of the rate of ATP-binding, to an increase of the rate of ATP release and to a decrease of the rate of ADP-release.

Uni-site ATP synthesis in thylakoids.

Uni-site ATP synthesis was measured with thylakoids. The membrane-bound ATP-synthase, CF0F1, was brought into the active, reduced state by illumination in the presence of thioredoxin, dithiothreitol and phosphate. This enzyme contains two tightly bound ATP per CF0F1. ATP was released from the enzyme when ADP was added in substoichiometric amounts during illumination. Experiments with [14C]ADP indicated that after binding the same nucleotide was phosphorylated and released as [14C]ATP, i.e. only one site is involved in ATP-synthesis ('uni-site ATP-synthesis'). The two tightly bound ATP are not involved in the catalytic turnover. The rate constant for ADP binding was (4 +/- 2) x 10(6) M-1s-1. Compared to deenergized conditions the rate constant for ADP binding and that for ATP-release were drastically increased, i.e. membrane energization increased the rate constants for the ATP-synthesis direction.

Spectroscopic characterization of PS I core complexes from thermophilic Synechococcus sp. Identical reoxidation kinetics of A1- before and after removal of the iron-sulfur-clusters FA and FB.

Monomeric and trimeric PS I complexes missing the three stromal subunits E,C and D (termed PS I core complexes) were prepared from the thermophilic cyanobacterium Synechococcus sp. by incubation with urea. The subunits E,C and D are sequentially removed. In the monomeric PS I the subunit C is removed with a half life of approx. 5 min. This is about eight times faster than in the trimeric PS I complex. In parallel with the removal of the FA/B containing subunit C the reduction kinetics of P700+ changed from a half life of about 25 ms to about 750 microseconds. The partner of P700+ in the 750 microseconds charge recombination was identified to be FX by the difference spectrum of this phase. There are some minor differences in the spectra of trimeric and monomeric PS I core complexes. At 77K the forward electron transfer from A1- to FX is blocked in the major fraction of the PS I core complexes and P700+ A1- recombines with a half life of about 220 microseconds. In the remaining fraction P700+FX- is formed and decays with a half life of approx. 10 ms at 77 K. The kinetics of the forward electron transfer from A1- to the iron-sulfur-clusters was measured in the native PS I and the corresponding core complexes. The reoxidation kinetics of A1- are identical in both cases (t1/2 = 180 ns). We conclude that FX is an obligatory intermediate in the normal forward electron transfer.

Effect of amputation level on the stress transferred to the femur by an artificial limb directly attached to the bone.

Attachment of an artificial limb directly to the skeleton has a number of potential benefits and the technique has been implemented for several amputation sites. In this paper the transfer of stress from an external, transfemoral prosthesis to the femur during normal walking activity is investigated. The stress distribution in the femur and at the implant-bone interface is calculated using finite element analysis for the 3D geometry and inhomogeneous, anisotropic material properties obtained from a CT scan of a healthy femur. Attachment of the prosthetic leg at three different levels of amputation is considered. Stress concentrations are found at the distal end of the bone and adjacent to the implant tip and stress shielding is observed adjacent to the implant. It is found that the stress distribution in the femur distal to the epiphysis, where the femur geometry is close to cylindrical, can be predicted from a cylindrical finite element model, using the correct choice of bone diameter as measured from a radiograph. Proximal to the lesser trochanter the stress decreases as the femur geometry diverges significantly from a cylinder. The stress concentration at the distal, resected end of the bone is removed when a collared implant is employed. These findings form the basis for appropriate settings of an external fail-safe device to protect the bone from excessive stress in the event of an undue load.