X-ray diffraction recording from a small amount of fibrous protein materials oriented by a micro shear-flow cell.

This paper describes a method for recording X-ray diffraction patterns from a small amount of fibrous protein materials while being oriented by using a micro shear-flow cell. This cell consists of two concentrically arranged glass tubes. The inner tube is stationary, while the outer one rotates at a high speed. The gap between the two tubes is about 100 µm, into which the suspension of fibrous protein materials is injected. By using synchrotron-radiation X-ray microbeams (diameter, 10 µm), clear diffraction images from oriented protein materials can be recorded. The required volume of the sample is only about 10 µl. This method can also be combined with the laser-flash photolysis of caged compounds. Examples of application of this method to the flagella of a green alga Chlamydomonas, and sperm of a tunicate Ciona are presented.

Remodeling of skeletal muscle myosin metabolic states in hibernating mammals.

Hibernation is a period of metabolic suppression utilized by many small and large mammal species to survive during winter periods. As the underlying cellular and molecular mechanisms remain incompletely understood, our study aimed to determine whether skeletal muscle myosin and its metabolic efficiency undergo alterations during hibernation to optimize energy utilization. We isolated muscle fibers from small hibernators, Ictidomys tridecemlineatus and Eliomys quercinus and larger hibernators, Ursus arctos and Ursus americanus. We then conducted loaded Mant-ATP chase experiments alongside X-ray diffraction to measure resting myosin dynamics and its ATP demand. In parallel, we performed multiple proteomics analyses. Our results showed a preservation of myosin structure in U. arctos and U. americanus during hibernation, whilst in I. tridecemlineatus and E. quercinus, changes in myosin metabolic states during torpor unexpectedly led to higher levels in energy expenditure of type II, fast-twitch muscle fibers at ambient lab temperatures (20 °C). Upon repeating loaded Mant-ATP chase experiments at 8 °C (near the body temperature of torpid animals), we found that myosin ATP consumption in type II muscle fibers was reduced by 77-107% during torpor compared to active periods. Additionally, we observed Myh2 hyper-phosphorylation during torpor in I. tridecemilineatus, which was predicted to stabilize the myosin molecule. This may act as a potential molecular mechanism mitigating myosin-associated increases in skeletal muscle energy expenditure during periods of torpor in response to cold exposure. Altogether, we demonstrate that resting myosin is altered in hibernating mammals, contributing to significant changes to the ATP consumption of skeletal muscle. Additionally, we observe that it is further altered in response to cold exposure and highlight myosin as a potentially contributor to skeletal muscle non-shivering thermogenesis.

Many animals use hibernation as a tactic to survive harsh winters. During this dormant, inactive state, animals reduce or limit body processes, such as heart rate and body temperature, to minimise their energy use. To conserve energy during hibernation, animals can use different approaches. For example, garden dormice undergo periodic states of extremely low core temperatures (down to 4­8^oC); whereas Eurasian brown bears see milder temperature drops (down to 23­25^oC). An important organ that changes during hibernation is skeletal muscle. Skeletal muscle typically uses large amounts of energy, making up around 50% of body mass. To survive, hibernating animals must change how their skeletal muscle uses energy. Traditionally, active myosin ­ a protein found in muscles that helps muscles to contract ­ was thought to be responsible for most of the energy use by skeletal muscle. But, more recently, resting myosin has also been found to use energy when muscles are relaxed. Lewis et al. studied myosin and skeletal muscle energy use changes during hibernation and whether they could impact the metabolism of hibernating animals. Lewis et al. assessed myosin changes in muscle samples from squirrels, dormice and bears during hibernation and during activity. Experiments showed changes in resting myosin in squirrels and dormice (whose temperature drops to 4­8^oC during hibernation) but not in bears. Further analysis revealed that cooling samples from non-hibernating muscle to 4­8^oC increased energy use in resting myosin, thereby generating heat. However, no increase in energy use was found after cooling hibernating muscle samples to 4­8^oC. This suggest that resting myosin generates heat at cool temperatures ­ a mechanism that is switched off in hibernating animals to allow them to cool their body temperature. These findings reveal key insights into how animals conserve energy during hibernation. In addition, the results show that myosin regulates energy use in skeletal muscles, which indicates myosin may be a potential drug target in metabolic diseases, such as obesity.

Contrast variation method applied to structural evaluation of catalysts by X-ray small-angle scattering.

In the process of developing carbon-supported metal catalysts, determining the catalyst particle-size distribution is an essential step, because this parameter is directly related to the catalytic activities. The particle-size distribution is most effectively determined by small-angle X-ray scattering (SAXS). When metal catalysts are supported by high-performance mesoporous carbon materials, however, their mesopores may lead to erroneous particle-size estimation if the sizes of the catalysts and mesopores are comparable. Here we propose a novel approach to particle-size determination by introducing contrast variation-SAXS (CV-SAXS). In CV-SAXS, a multi-component sample is immersed in an inert solvent with a density equal to that of one of the components, thereby rendering that particular component invisible to X-rays. We used a mixture of tetrabromoethane and dimethyl sulfoxide as a contrast-matching solvent for carbon. As a test sample, we prepared a mixture of a small amount of platinum (Pt) catalyst and a bulk of mesoporous carbon, and subjected it to SAXS measurement in the absence and presence of the solvent. In the absence of the solvent, the estimated Pt particle size was affected by the mesopores, but in the presence of the solvent, the Pt particle size was correctly estimated in spite of the low Pt content. The results demonstrate that the CV-SAXS technique is useful for correctly determining the particle-size distribution for low-Pt-content catalysts, for which demands are increasing to reduce the use of expensive Pt.

Remodelling of Skeletal Muscle Myosin Metabolic States in Hibernating Mammals.

Hibernation is a period of metabolic suppression utilized by many small and large mammal species to survive during winter periods. As the underlying cellular and molecular mechanisms remain incompletely understood, our study aimed to determine whether skeletal muscle myosin and its metabolic efficiency undergo alterations during hibernation to optimize energy utilization. We isolated muscle fibers from small hibernators, Ictidomys tridecemlineatus and Eliomys quercinus and larger hibernators, Ursus arctos and Ursus americanus. We then conducted loaded Mant-ATP chase experiments alongside X-ray diffraction to measure resting myosin dynamics and its ATP demand. In parallel, we performed multiple proteomics analyses. Our results showed a preservation of myosin structure in U. arctos and U. americanus during hibernation, whilst in I. tridecemlineatus and E. quercinus, changes in myosin metabolic states during torpor unexpectedly led to higher levels in energy expenditure of type II, fast-twitch muscle fibers at ambient lab temperatures (20°C). Upon repeating loaded Mant-ATP chase experiments at 8°C (near the body temperature of torpid animals), we found that myosin ATP consumption in type II muscle fibers was reduced by 77-107% during torpor compared to active periods. Additionally, we observed Myh2 hyper-phosphorylation during torpor in I. tridecemilineatus, which was predicted to stabilize the myosin molecule. This may act as a potential molecular mechanism mitigating myosin-associated increases in skeletal muscle energy expenditure during periods of torpor in response to cold exposure. Altogether, we demonstrate that resting myosin is altered in hibernating mammals, contributing to significant changes to the ATP consumption of skeletal muscle. Additionally, we observe that it is further altered in response to cold exposure and highlight myosin as a potentially contributor to skeletal muscle non-shivering thermogenesis.

Human skeletal myopathy myosin mutations disrupt myosin head sequestration.

Myosin heavy chains encoded by MYH7 and MYH2 are abundant in human skeletal muscle and important for muscle contraction. However, it is unclear how mutations in these genes disrupt myosin structure and function leading to skeletal muscle myopathies termed myosinopathies. Here, we used multiple approaches to analyze the effects of common MYH7 and MYH2 mutations in the light meromyosin (LMM) region of myosin. Analyses of expressed and purified MYH7 and MYH2 LMM mutant proteins combined with in silico modeling showed that myosin coiled coil structure and packing of filaments in vitro are commonly disrupted. Using muscle biopsies from patients and fluorescent ATP analog chase protocols to estimate the proportion of myosin heads that were super-relaxed, together with x-ray diffraction measurements to estimate myosin head order, we found that basal myosin ATP consumption was increased and the myosin super-relaxed state was decreased in vivo. In addition, myofiber mechanics experiments to investigate contractile function showed that myofiber contractility was not affected. These findings indicate that the structural remodeling associated with LMM mutations induces a pathogenic state in which formation of shutdown heads is impaired, thus increasing myosin head ATP demand in the filaments, rather than affecting contractility. These key findings will help design future therapies for myosinopathies.

Predominant myosin superrelaxed state in canine myocardium with naturally occurring dilated cardiomyopathy.

Dilated cardiomyopathy (DCM) is a naturally occurring heart failure condition in humans and dogs, notably characterized by a reduced contractility and ejection fraction. As the identification of its underlying cellular and molecular mechanisms remain incomplete, the aim of the present study was to assess whether the molecular motor myosin and its known relaxed conformational states are altered in DCM. For that, we dissected and skinned thin cardiac strips from left ventricle obtained from six DCM Doberman Pinschers and six nonfailing (NF) controls. We then used a combination of Mant-ATP chase experiments and X-ray diffraction to assess both energetic and structural changes of myosin. Using the Mant-ATP chase protocol, we observed that in DCM dogs, the amount of myosin molecules in the ATP-conserving conformational state, also known as superrelaxed (SRX), is significantly increased when compared with NF dogs. This alteration can be rescued by applying EMD-57033, a small molecule activating myosin. Conversely, with X-ray diffraction, we found that in DCM dogs, there is a higher proportion of myosin heads in the vicinity of actin when compared with NF dogs (1,0 to 1,1 intensity ratio). Hence, we observed an uncoupling between energetic (Mant-ATP chase) and structural (X-ray diffraction) data. Taken together, these results may indicate that in the heart of Doberman Pinschers with DCM, myosin molecules are potentially stuck in a nonsequestered but ATP-conserving SRX state, that can be counterbalanced by EMD-57033 demonstrating the potential for a myosin-centered pharmacological treatment of DCM.NEW & NOTEWORTHY The key finding of the present study is that, in left ventricles of dogs with a naturally occurring dilated cardiomyopathy, relaxed myosin molecules favor a nonsequestered superrelaxed state potentially impairing sarcomeric contractility. This alteration is rescuable by applying a small molecule activating myosin known as EMD-57033.

Effects of a Nanophase-Separated Structure on Mechanical Properties and Proton Conductivity of Acid-Infiltrated Block Polymer Electrolyte Membranes under Non-Humidification.

Acid-infiltrated block polymer electrolyte membranes adopting a spherical or lamellar nanophase-separated structure were prepared by infiltrating sulfuric acid (H2SO4) into polystyrene-b-poly(4-vinylpyridine)-b-polystyrene (S-P-S) triblock copolymers to investigate the effects of its nanophase-separated structure on mechanical properties and proton conductivities under non-humidification. Lamellae-forming S-P-S/H2SO4 membranes with a continuous hard phase generally exhibited higher tensile strength than sphere-forming S-P-S/H2SO4 membranes with a discontinuous hard phase even if the same amount of Sa was infiltrated into each neat S-P-S film. Meanwhile, the conductivities of lamellae-forming S-P-S/H2SO4 membranes under non-humidification were comparable or superior to those of sphere-forming S-P-S/H2SO4 membranes, even though they were infiltrated by the same weight fraction of H2SO4. This result is attributed to the conductivities of S-P-S/H2SO4 membranes being greatly influenced by the acid/base stoichiometry associated with acid-base complex formation rather than the nanophase-separated structure adopted in the membranes. Namely, there are more free H2SO4 moieties that can release free protons contributing to the conductivity in lamellae-forming S-P-S/H2SO4 membranes than sphere-forming S-P-S/H2SO4, even when the same amount of H2SO4 was infiltrated into the S-P-S.

Structure of the Flight Muscle Thick Filament from the Bumble Bee, Bombus ignitus, at 6 Å Resolution.

Four insect orders have flight muscles that are both asynchronous and indirect; they are asynchronous in that the wingbeat frequency is decoupled from the frequency of nervous stimulation and indirect in that the muscles attach to the thoracic exoskeleton instead of directly to the wing. Flight muscle thick filaments from two orders, Hemiptera and Diptera, have been imaged at a subnanometer resolution, both of which revealed a myosin tail arrangement referred to as "curved molecular crystalline layers". Here, we report a thick filament structure from the indirect flight muscles of a third insect order, Hymenoptera, the Asian bumble bee Bombus ignitus. The myosin tails are in general agreement with previous determinations from Lethocerus indicus and Drosophila melanogaster. The Skip 2 region has the same unusual structure as found in Lethocerus indicus thick filaments, an α-helix discontinuity is also seen at Skip 4, but the orientation of the Skip 1 region on the surface of the backbone is less angled with respect to the filament axis than in the other two species. The heads are disordered as in Drosophila, but we observe no non-myosin proteins on the backbone surface that might prohibit the ordering of myosin heads onto the thick filament backbone. There are strong structural similarities among the three species in their non-myosin proteins within the backbone that suggest how one previously unassigned density in Lethocerus might be assigned. Overall, the structure conforms to the previously observed pattern of high similarity in the myosin tail arrangement, but differences in the non-myosin proteins.

The 3D structure of fibrous material is fully restorable from its X-ray diffraction pattern.

X-ray fiber diffraction is potentially a powerful technique to study the structure of fibrous materials, such as DNA and synthetic polymers. However, only rotationally averaged diffraction patterns can be recorded and it is difficult to correctly interpret them without the knowledge of esoteric diffraction theories. Here we demonstrate that, in principle, the non-rotationally averaged 3D structure of a fibrous material can be restored from its fiber diffraction pattern. The method is a simple puzzle-solving process and in ideal cases it does not require any prior knowledge about the structure, such as helical symmetry. We believe that the proposed method has a potential to transform the fiber diffraction to a 3D imaging technique, and will be useful for a wide field of life and materials sciences.

Rapid recovery of phytic acid from rice brans using chitosan nanofiber-based porous hydrogels.

Phytic acid (PA) is a new type of naturally occurring pharmaceutical for afflictions such as cancer, diabetes, and renal calculi. The efficient, low-cost extraction of PA from biowaste is much sought after. Herein, highly pure PA was obtained from rice bran by adsorption at low pH onto porous chitosan nanofiber hydrogels. Due to the large surface area of the chitosan nanofiber-based porous hydrogels, the adsorption equilibrated within 60 min. Adsorption of PA was influenced by the buffer pH, temperature, and the ratio of chitosan in the hydrogel. PA was recovered by soaking the hydrogel in alkaline solution. After concentrating the solution and washing the residue with ethanol, highly pure sodium phytate was obtained with 32.2%-38.7% yield, as confirmed by Fourier transform infrared and high-performance liquid chromatography. To our knowledge, this is the first report on the recovery of pure PA in high yield without using toxic solvents.

Structural model for differential cap maturation at growing microtubule ends.

Microtubules (MTs) are hollow cylinders made of tubulin, a GTPase responsible for essential functions during cell growth and division, and thus, key target for anti-tumor drugs. In MTs, GTP hydrolysis triggers structural changes in the lattice, which are responsible for interaction with regulatory factors. The stabilizing GTP-cap is a hallmark of MTs and the mechanism of the chemical-structural link between the GTP hydrolysis site and the MT lattice is a matter of debate. We have analyzed the structure of tubulin and MTs assembled in the presence of fluoride salts that mimic the GTP-bound and GDP•Pi transition states. Our results challenge current models because tubulin does not change axial length upon GTP hydrolysis. Moreover, analysis of the structure of MTs assembled in the presence of several nucleotide analogues and of taxol allows us to propose that previously described lattice expansion could be a post-hydrolysis stage involved in Pi release.

Relationship between the induced-fit loop and the activity of Klebsiella pneumoniae pullulanase.

Klebsiella pneumoniae pullulanase (KPP) belongs to glycoside hydrolase family 13 subfamily 13 (GH13_13) and is the only enzyme that is reported to perform an induced-fit motion of the active-site loop (residues 706-710). Comparison of pullulanase structures indicated that only KPP has Leu680 present behind the loop, in contrast to the glycine found in other GH13_13 members. Analysis of the structure and activity of recombinant pullulanase from K. pneumoniae ATCC 9621 (rKPP) and its mutant (rKPP-G680L) indicated that the side chain of residue 680 is important for the induced-fit motion of the loop 706-710 and alters the binding affinity of the substrate.

Synchrotron radiation X-ray diffraction studies on muscle: past, present, and future.

X-ray diffraction is a technique to study the structure of materials at spatial resolutions up to an atomic scale. In the field of life science, the X-ray diffraction technique is especially suited to study materials having periodical structures, such as protein crystals, nucleic acids, and muscle. Among others, muscle is a dynamic structure and the molecular events occurring during muscle contraction have been the main interest among muscle researchers. In early days, the laboratory X-ray generators were unable to deliver X-ray flux strong enough to resolve the dynamic molecular events in muscle. This situation has dramatically been changed by the advent of intense synchrotron radiation X-rays and advanced detectors, and today X-ray diffraction patterns can be recorded from muscle at sub-millisecond time resolutions. In this review, we shed light mainly on the technical aspects of the history and the current status of the X-ray diffraction studies on muscle and discuss what will be made possible for muscle studies by the advance of new techniques.

Molecular Consequences of the Myopathy-Related D286G Mutation on Actin Function.

Myopathies are notably associated with mutations in genes encoding proteins known to be essential for the force production of skeletal muscle fibers, such as skeletal alpha-actin. The exact molecular mechanisms by which these specific defects induce myopathic phenotypes remain unclear. Hence, in the present study, to better understand actin dysfunction, we conducted a molecular dynamic simulation together with ex vivo experiments of the specific muscle disease-causing actin mutation, D286G located in the actin-actin interface. Our computational study showed that D286G impairs the flexural rigidity of actin filaments. However, upon activation, D286G did not have any direct consequences on actin filament extension. Hence, D286G may alter the structure of actin filaments but, when expressed together with normal actin molecules, it may only have minor effects on the ex vivo mechanics of actin filaments upon skeletal muscle fiber contraction.

Elucidation of the mechanism of interaction between Klebsiella pneumoniae pullulanase and cyclodextrin.

Crystal structures of Klebsiella pneumoniae pullulanase (KPP) in complex with α-cyclodextrin (α-CD), ß-cyclodextrin (ß-CD) and γ-cyclodextrin (γ-CD) were refined at around 1.98-2.59 Šresolution from data collected at SPring-8. In the structures of the complexes obtained with 1 mM α-CD or γ-CD, one molecule of CD was found at carbohydrate-binding module 41 only (CBM41). In the structures of the complexes obtained with 1 mM ß-CD or with 10 mM α-CD or γ-CD, two molecules of CD were found at CBM41 and in the active-site cleft, where the hydrophobic residue of Phe746 occupies the inside cavity of the CD rings. In contrast to α-CD and γ-CD, one ß-CD molecule was found at the active site only in the presence of 0.1 mM ß-CD. These results were coincident with the solution experiments, which showed that ß-CD inhibits this enzyme more than a thousand times more potently than α-CD and γ-CD. The strong inhibition of ß-CD is caused by the optimized interaction between ß-CD and the side chain of Phe746. The increased Ki values of the F746A mutant for ß-CD supported the importance of Phe746 in the strong interaction of pullulanase with ß-CD.

Kinesin-binding-triggered conformation switching of microtubules contributes to polarized transport.

Kinesin-1, the founding member of the kinesin superfamily of proteins, is known to use only a subset of microtubules for transport in living cells. This biased use of microtubules is proposed as the guidance cue for polarized transport in neurons, but the underlying mechanisms are still poorly understood. Here, we report that kinesin-1 binding changes the microtubule lattice and promotes further kinesin-1 binding. This high-affinity state requires the binding of kinesin-1 in the nucleotide-free state. Microtubules return to the initial low-affinity state by washing out the binding kinesin-1 or by the binding of non-hydrolyzable ATP analogue AMPPNP to kinesin-1. X-ray fiber diffraction, fluorescence speckle microscopy, and second-harmonic generation microscopy, as well as cryo-EM, collectively demonstrated that the binding of nucleotide-free kinesin-1 to GDP microtubules changes the conformation of the GDP microtubule to a conformation resembling the GTP microtubule.

Effects of myosin inhibitors on the X-ray diffraction patterns of relaxed and calcium-activated rabbit skeletal muscle fibers.

We studied the effect of myosin inhibitors, N-benzyl-p-toluenesulfonamide (BTS), blebbistatin, and butanedione monoxime (BDM) on X-ray diffraction patterns from rabbit psoas fibers under relaxing and contracting conditions. The first two inhibitors suppressed the contractile force almost completely at a 100 µM concentration, and a similar effect was obtained at 50 mM for BDM. However, still substantial changes were observed in the diffraction patterns upon calcium-activation of inhibited muscle fibers. (1) The 2nd actin layer-line reflection was enhanced normally, indicating that calcium binding to troponin and the subsequent movement of tropomyosin are not inhibited, (2) the myosin layer-line reflections became much weaker, and (3) the 1,1/1,0 intensity ratio of the equatorial reflections was increased. The observations (2) and (3) indicate that, even in the presence of the inhibitors at a saturating concentration, myosin heads leave the helix on the thick filaments and approach the thin filaments. Interestingly, the d1,0 spacing of the filament lattice remained unchanged upon activation of inhibited fibers, in contrast to the case of normal activation in which the spacing is decreased. This suggests that the normal activated myosin heads exert a pull in both axial and radial directions, but in the presence of the inhibitors, the pull is suppressed, and as a result, the heads simply bind to actin without exerting any force. The results support the idea that the inhibitors do not block the myosin binding to actin, but block the step of force-producing transition of the bound actomyosin complex.

Synchrotron Radiation X-ray Diffraction Techniques Applied to Insect Flight Muscle.

X-ray fiber diffraction is a powerful tool used for investigating the molecular structure of muscle and its dynamics during contraction. This technique has been successfully applied not only to skeletal and cardiac muscles of vertebrates but also to insect flight muscle. Generally, insect flight muscle has a highly ordered structure and is often capable of high-frequency oscillations. The X-ray diffraction studies on muscle have been accelerated by the advent of 3rd-generation synchrotron radiation facilities, which can generate brilliant and highly oriented X-ray beams. This review focuses on some of the novel experiments done on insect flight muscle by using synchrotron radiation X-rays. These include diffraction recordings from single myofibrils within a flight muscle fiber by using X-ray microbeams and high-speed diffraction recordings from the flight muscle during the wing-beat of live insects. These experiments have provided information about the molecular structure and dynamic function of flight muscle in unprecedented detail. Future directions of X-ray diffraction studies on muscle are also discussed.