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Recent observations suggest late accretion, which is generally nonaxisymmetric, onto protoplanetary disks. We investigated nonaxisymmetric late accretion considering the effects of magnetic fields. Our model assumes a cloudlet encounter event at a few hundred au scale, where a magnetized gas clump (cloudlet) encounters a protoplanetary disk. We studied how the cloudlet size and the magnetic field strength affect the rotational velocity profile in the disk after the cloudlet encounter. The results show that a magnetic field can either decelerate or accelerate the rotational motion of the cloudlet material, primarily depending on the relative size of the cloudlet to the disk thickness. When the cloudlet size is comparable to or smaller than the disk thickness, magnetic fields only decelerate the rotation of the colliding cloudlet material. However, if the cloudlet size is larger than the disk thickness, the colliding cloudlet material can be super-Keplerian as a result of magnetic acceleration. We found that the vertical velocity shear of the cloudlet produces a magnetic tension force that increases the rotational velocity. The acceleration mechanism operates when the initial plasma $\beta$ is $ \beta \lesssim 2\times 10^1 $. Our study shows that magnetic fields modify the properties of spirals formed by tidal effects. These findings may be important for interpreting observations of late accretion., Comment: 18 pages, 15 figures, 1 table, published in The Astrophysical Journal

Artificial metal enzymes that combine proteins with synthesized unnatural metal complexes as cofactors are attracting attention. The preparation of artificial metal enzymes not only clarifies the behavior of metal ions in biology, but also leads to the development of synthetic chemistry fields such as the discovery of new catalytic reactivity and substrate selectivity that are not observed in nature. In addition, a certain Schiff base zinc (II) complex is known to exhibit antioxidant and anticancer activity, too. Therefore, in this study, we investigated a rapid synthesis method of two known amino acid Schiff base zinc (II) complexes using microwave method and the complexation of zinc (II) complex with chicken egg white lysozyme, which is a relatively low molecular weight protein. Furthermore, investigation of weakly non-covalent intermolecular interaction features between the zinc (II) complexes and lysozyme was also carried out using some spectroscopic measurements.

TRPV1, a member of the transient receptor potential (TRP) channels family, has been found to be involved in redox sensing. The crystal structure of the human TRPV1 ankyrin-repeat domain (TRPV1-ARD) was determined at 4.5 Å resolution under nonreducing conditions. This is the first report of the crystal structure of a ligand-free form of TRPV1-ARD and in particular of the human homologue. The structure showed a unique conformation in finger loop 3 near Cys258, which is most likely to be involved in inter-subunit disulfide-bond formation. Also, in human TRPV1-ARD it was possible for solvent to access Cys258. This structural feature might be related to the high sensitivity of human TRPV1 to oxidants. ESI-MS revealed that Cys258 did not form an S–OH functionality even under nonreducing conditions.

S100A3 protein, a member of the EF-hand-type Ca2+-binding S100 protein family, undergoes a Ca2+-/Zn2+-induced structural change to a tetrameric state upon specific citrullination of R51 in human hair cuticular cells. To elucidate the underlying mechanism, we prepared recombinant mutant S100A3 proteins, including R51A, R51C, R51E, R51K, and R51Q, as potential models of post-translationally modified S100A3 and evaluated their biophysical and biochemical properties relative to wild-type (WT) S100A3 and WT citrullinated in vitro. Size exclusion chromatography (SEC) showed that R51Q formed a tetramer in the presence of Ca2+, while Ca2+ titration monitored by Trp fluorescence indicated that R51Q had Ca2+-binding properties similar to those of citrullinated S1003A. We therefore concluded that R51Q is the optimal mutant model of post-translationally modified S100A3. We compared the solution structure of WT S100A3 and the R51Q mutant in the absence and presence of Ca2+ and Zn2+ by SEC-small-angle X-ray scattering. The radius of gyration of R51Q in the metal-free state was almost the same as that of WT; however, it increased by ∼1.5-fold in the presence of Ca2+/Zn2+, indicating a large expansion in molecular size. By contrast, addition of Ca2+/Zn2+ to WT led to nonspecific aggregation in SEC analysis and dynamic light scattering, suggesting that citrullination of S100A3 is essential for stabilization of the Ca2+-/Zn2+-bound state. These findings will lead to the further development of structural analyses for the Ca2+-/Zn2+-bound S100A3.

PcyA, a ferredoxin-dependent bilin pigment reductase, catalyzes the site-specific reduction of the two vinyl groups of biliverdin (BV), producing phycocyanobilin. Previous neutron crystallography detected both the neutral BV and its protonated form (BVH

In mammals, the green heme metabolite biliverdin is converted to a yellow anti-oxidant by NAD(P)H-dependent biliverdin reductase (BVR), whereas in O2-dependent photosynthetic organisms it is converted to photosynthetic or light-sensing pigments by ferredoxin-dependent bilin reductases (FDBRs). In NADP+-bound and biliverdin-bound BVR-A, two biliverdins are stacked at the binding cleft; one is positioned to accept hydride from NADPH, and the other appears to donate a proton to the first biliverdin through a neighboring arginine residue. During the FDBR-catalyzed reaction, electrons and protons are supplied to bilins from ferredoxin and from FDBRs and waters bound within FDBRs, respectively. Thus, the protonation sites of bilin and catalytic residues are important for the analysis of site-specific reduction. The neutron structure of FDBR sheds light on this issue.

The second messenger bis(3',5')-cyclic dimeric guanosine monophosphate (c-di-GMP) regulates numerous important physiological functions in bacteria. In this study, we identified and characterized the first dimeric, full-length, non-heme iron-bound phosphodiesterase (PDE) containing bacterial hemerythrin and HD-GYP domains (Bhr-HD-GYP). We found that the amino acid sequence encoded by the

Sortilin is a multifunctional sorting receptor involved in cytokine production in immune cells. To understand the mechanism of Sortilin-mediated cytokine trafficking, we determined the 2.45-Å structure of the dimerized Sortilin ectodomain (sSortilin or the Vps10-domain) crystallized at acidic pH. Substantial conformational changes upon dimerization lead to the intermolecular hydrophobic interaction between the conserved E455 and F137. Analysis of the electrostatic surface and size-exclusion chromatography revealed that sSortilin dimerization occurs due to an increase in hydrophobic interactions at the neutral dimer interface at acidic pH. The N682-attached N-glycan in the vicinity of the dimer interface implies its involvement in the dimerization. The disruption of Sortilin dimerization by mutations impairs efficient interferon-alpha secretion from cells. These results suggest the functional importance of Sortilin dimerization in cytokine trafficking.

Neutron crystallography of proteins requires much larger crystals than those for X-ray crystallography. Obtaining large crystals of an enzyme–substrate complex is especially difficult because strict control of the stoichiometry is needed for crystal growth. Herein is reported a procedure for obtaining crystals large enough for neutron structural analysis of a bilin reductase PcyA I86D mutant complexed with its substrate, biliverdin, an open tetrapyrrol pigment. The enzyme/substrate ratio was estimated by observing changes in absorption spectra and compared to the theoretical value; 1.2 times the amount of biliverdin was required in the experiment. This proper stoichiometric ratio of PcyA I86D mutant/biliverdin reproducibly gave high-quality crystals. The buffer for the reservoir solution in the sitting drop vapor diffusion method was chosen by analysis of Wilson plots of room temperature X-ray data of the crystals obtained using three different buffers. The mixing ratio of the PcyA I86D mutant/biliverdin ...

Peptidylarginine deiminase type III (PAD3) is an isozyme belonging to the PAD enzyme family that converts arginine to citrulline residue(s) within proteins. PAD3 is expressed in most differentiated keratinocytes of the epidermis and hair follicles, while S100A3, trichohyalin, and filaggrin are its principal substrates. In this study, the X-ray crystal structures of PAD3 in six states, including its complex with the PAD inhibitor Cl-amidine, were determined. This structural analysis identified a large space around Gly374 in the PAD3-Ca2+-Cl-amidine complex, which may be used to develop novel PAD3-selective inhibitors. In addition, similarities between PAD3 and PAD4 were found based on the investigation of PAD4 reactivity with S100A3 in vitro. A comparison of the structures of PAD1, PAD2, PAD3, and PAD4 implied that the flexibility of the structures around the active site may lead to different substrate selectivity among these PAD isozymes.

Vapor-phase catalytic dehydration of 1,5-pentanediol (1,5-PDO) was investigated over monoclinic ZrO2 catalysts modified with basic oxides. An unsaturated alcohol, 4-penten-1-ol (4P1OL), was produced together with the formation of tetrahydropyran, δ-valerolactone, 1,4-pentadiene, pentanal, 1-pentanol, and 5-hydroxypentanal, etc. Among the modified ZrO2 catalysts, only ZrO2 modified with MgO enhanced the selectivity to 4P1OL efficiently. The most active modified catalyst was found to have 20 mol% MgO and a calcination at 800 °C (MgO/ZrO2), and the selectivity of 4P1OL exceeded 83% at 400 °C. A pulse adsorption measurement of several chemicals clarified adsorptive interaction between a reactant and a catalyst at 220 °C: the interaction between 1,5-PDO and MgO/ZrO2 was stronger than the other adsorbates and catalysts. Another strong adsorptive interaction between 1,4-butanediol and CaO/ZrO2, which was effective in the dehydration of 1,4-butanediol to produce 3-buten-1-ol, was also observed.

The unusual magnetic/spectroscopic properties of Cytochrome c′ (Cyt c′) have been discussed, especially concerning the possibility of a quantum mechanically mixed-spin configuration of heme Fe(III). Here, four unique-spin species were identified from the magnetic circular dichroism (MCD) spectra of Cyt c′ from Alcaligenes xylosoxidans (AxCyt c′). The electrospray ionization mass spectrometric (ESI-MS) and circular dichroism (CD) spectroscopic data showed the overall conformation of AxCyt c′ was unchanged, in complete contrast to the drastic changes in the heme MCD spectra over the range of pH 3.5 and 11.8. The pH dependency of ESI-MS, electronic absorption, MCD, and CD spectroscopic properties of AxCyt c′ enabled us to reveal the undiscovered correlation between the protein-folding state and the electronic structure of the active site as a function of pH. The mechanism of alkaline spin-state transition through the rearrangement of the hydrogen-bonding linkage between Helix C and D is also proposed on the ...

Hair is one of the defining characteristics of mammals. The hair shaft has a two-layer structure comprising the cortex, which is the inner layer and is composed of cortical cells, and the cuticle, which is the outermost layer. S100 calcium-binding protein A3 (S100A3) is expressed at high levels in the human hair cuticle. Arginine 51 of S100A3 protein is citrullinated specifically by peptidylarginine deiminase 3 (PAD3), and this citrullination is related to maturation of the cuticle. However, the detailed evolutionary processes of S100A3 and PAD3 during mammalian evolution are unknown. Here, we show that nonsynonymous changes in S100A3 accelerated in the common ancestral branch of mammals, probably as a result of positive selection that returned after the acquisition of hair cuticle-specific function in mammals. Later, pseudogenisation or nonfunctionalisation of S100A3 and PAD3 occurred in some species, such as the cetaceans. Our results show that positive selection and relaxation of the functional constraints of genes played important roles in the evolution of mammalian hair.

Advancements in 3D-Flash memory-layer-stacking technology has enabled density scaling that circumvents the lithography limitations which have prevented 2D-NAND Flash memory from scaling [1]. Bit densities as high as 5.95Gb/mm2 on a single die were recently reported [2], where a 512Gb NAND Flash was built on 96 layers of memory. As memory density increases, with memory layers increasing from 96 layers to 128 layers, higher bit density can be achieved by adopting larger capacity die; however, NAND performance per bit density is reducing with the 2-plane architecture. In this work, we propose a 512Gb 3b/cell 128WL-layer NAND Flash, with a bit density of 7.80Gb/mm2: a 31% improvement over the previously reported. Three key performance improving technologies have been implemented. (1) A 4-plane architecture with circuit under array (CUA) technology to improve performance per bit density. (2) A multi-die peak-power management (PPM) system to manage peak-power consumption in the system, via the ZQ pin. (3) A 4KB-page-read mode to reduce power consumption. Figure 13.5.1(a) summarized the key features and Fig. 13.5.1(b) shows the die photograph and the floorplan for this work. Figure 13.5.2 shows a table comparing this work to previous work.

Phycocyanobilin:ferredoxin oxidoreductase (PcyA) catalyzes the reduction of biliverdin (BV) to produce phycocyanobilin, a linear tetrapyrrole pigment used for light harvesting and light sensing. Spectroscopic and HPLC analyses inidicate that BV bound to the I86D mutant of PcyA is fully protonated (BVH+ ) and can accept an electron, but I86D is unable to donate protons for the reduction; therefore, compared to the wild-type PcyA, the I86D mutant stabilizes BVH+ . To elucidate the structural basis of the I86D mutation, we determined the atomic-resolution structure of the I86D-BVH+ complex and the protonation states of the essential residues Asp105 and Glu76 in PcyA. Our study revealed that Asp105 adopted a fixed conformation in the I86D mutant, although it had dual conformations in wild-type PcyA which reflected the protonation states of BV. Taken together with biochemical/spectroscopic results, our analysis of the I86D-BVH+ structure supports the hypothesis that flexibility of Asp105 is essential for the catalytic activity of PcyA.

Crystal structure refinement of pseudoazurin from Achromobacter cycloclastes (AcPAz) was carried out at atomic (1.10 A) resolution. The copper ion was localized in two positions at the metal binding site of AcPAz. The occupancies of the copper sites are consistent with the ratio of axial and rhombic signals from EPR spectra and the intensity ratios for blue (axial) and green (rhombic) copper sites from UV-VIS spectroscopy. Computational modelling using an approximately 6 A protein environment around the Cu site for both the oxidized and reduced forms showed that a small scale inner sphere rearrangement can account for the co-existence of two different redox active sites for a mononuclear cupredoxin independently from the employed density functionals.

Herein we report quantum mechanical/molecular mechanical (QM/MM) studies to investigate the most probable protonation states of active site amino acids and bound substrate based on a recently reported neutron diffraction structure of phycocyanobilin:ferredoxin oxidoreductase (PcyA) by Unno et al. This structure was considered to be bound in its initial state of biliverdin IXα (BV), which has the C-pyrrole ring in the deprotonated state. The protonation state of BV suggested by neutron and spectroscopic studies is a stable, two-electron reduced complex with a bound hydronium ion. Several ambiguities in the neutron structure were observed which prompted a further theoretical analysis of the structure. This structural investigation provides new understanding of the PcyA and BV protonation states not previously reported in the literature. Our calculations suggest that the hydronium ion (H3 O+ ) is energetically unfavorable, preferentially protonating the neighboring His88 residue and that the C-ring of BV is not protonated.

Local anesthetics (LAs) inhibit endoplasmic reticulum-associated protein degradation, however the mechanisms remain elusive. Here, we show that the clinically used LAs pilsicainide and lidocaine bind directly to the 20S proteasome and inhibit its activity. Molecular dynamic calculation indicated that these LAs were bound to the β5 subunit of the 20S proteasome, and not to the other active subunits, β1 and β2. Consistently, pilsicainide inhibited only chymotrypsin-like activity, whereas it did not inhibit the caspase-like and trypsin-like activities. In addition, we confirmed that the aromatic ring of these LAs was critical for inhibiting the proteasome. These LAs stabilized p53 and suppressed proliferation of p53-positive but not of p53-negative cancer cells.

The first X-ray crystallographic study for the alkaline structure transition of cytochrome c′ was performed. Precise X-ray crystal structures of acidic (pH 6.0) and alkaline (pH 10.4) iron(III) cyt...

Heme oxygenase catalyzes the degradation of heme to biliverdin, iron, and carbon monoxide. Here, we present crystal structures of the substrate-free, Fe3+-biliverdin-bound, and biliverdin-bound forms of HmuO, a heme oxygenase from Corynebacterium diphtheriae, refined to 1.80, 1.90, and 1.85 Å resolution, respectively. In the substrate-free structure, the proximal and distal helices, which tightly bracket the substrate heme in the substrate-bound heme complex, move apart, and the proximal helix is partially unwound. These features are supported by the molecular dynamic simulations. The structure implies that the heme binding fixes the enzyme active site structure, including the water hydrogen bond network critical for heme degradation. The biliverdin groups assume the helical conformation and are located in the heme pocket in the crystal structures of the Fe3+-biliverdin-bound and the biliverdin-bound HmuO, prepared by in situ heme oxygenase reaction from the heme complex crystals. The proximal His serves as the Fe3+-biliverdin axial ligand in the former complex and forms a hydrogen bond through a bridging water molecule with the biliverdin pyrrole nitrogen atoms in the latter complex. In both structures, salt bridges between one of the biliverdin propionate groups and the Arg and Lys residues further stabilize biliverdin at the HmuO heme pocket. Additionally, the crystal structure of a mixture of two intermediates between the Fe3+-biliverdin and biliverdin complexes has been determined at 1.70 Å resolution, implying a possible route for iron exit.

Molecular structures of peptidylarginine deiminase (PAD) isozymes are strongly associated with their functions. This chapter summarizes the X-ray structures of PAD1, PAD2, and PAD4 as well as that of the PAD from the periodontal pathogen Porphyromonas gingivalis. It is interesting to understand structural differences among these isozymes in detail and to discuss their association with the function of each isozyme. These structures also provide critical insights that will aid in the development of isozyme-selective PAD inhibitors.

This paper describes the implementation and estimation of a hybrid implicit-explicit (HIE)-finite-difference time-domain (FDTD) method on graphics processing unit (GPU) for massively parallel electromagnetic field simulation. The HIE-FDTD method was proposed for the analysis of the shielding effectiveness of an enclosure and is very useful for the simulation of computational domain with thin unit cell such as printed circuit board. Since the computational domain can be divided arbitrarily along the x- and y-directions in the HIE-FDTD method, this method can be suitable for the parallel computing. Thus, the HIE-FDTD method is implemented on GPU and applied to the large-scale problems. Finally, it is shown that the performance of the HIE-FDTD method on GPU is drastically superior to the HIE-FDTD method on single CPU.

Dysiherbaine (DH) and neodysiherbaine A (NDH) selectively bind and activate two kainate-type ionotropic glutamate receptors, GluK1 and GluK2. The ligand-binding domains of human GluK1 and GluK2 were crystallized as bound forms with a series of DH analogues including DH, NDH, 8-deoxy-NDH, 9-deoxy-NDH and 8,9-dideoxy-NDH (MSVIII-19), isolated from natural sources or prepared by total synthesis. Since the DH analogues exhibit a wide range of binding affinities and agonist efficacies, it follows that the detailed analysis of crystal structure would provide us with a significant opportunity to elucidate structural factors responsible for selective binding and some aspects of gating efficacy. We found that differences in three amino acids (Thr503, Ser706 and Ser726 in GluK1 and Ala487, Asn690 and Thr710 in GluK2) in the ligand-binding pocket generate differences in the binding modes of NDH to GluK1 and GluK2. Furthermore, deletion of the C9 hydroxy group in NDH alters the ligand conformation such that it is no longer suited for binding to the GluK1 ligand-binding pocket. In GluK2, NDH pushes and rotates the side chain of Asn690 (substituted for Ser706 in GluK1) and disrupts an interdomain hydrogen bond with Glu409. The present data support the idea that receptor selectivities of DH analogues resulted from the differences in the binding modes of the ligands in GluK1/GluK2 and the steric repulsion of Asn690 in GluK2. All ligands, regardless of agonist efficacy, induced full domain closure. Consequently, ligand efficacy and domain closure did not directly coincide with DH analogues and the kainate receptors.

S100A3, a member of the EF-hand-type Ca(2+)-binding S100 protein family, is unique in its exceptionally high cysteine content and Zn(2+) affinity. We produced human S100A3 protein and its mutants in insect cells using a baculovirus expression system. The purified wild-type S100A3 and the pseudo-citrullinated form (R51A) were crystallized with ammonium sulfate in N,N-bis(2-hydroxyethyl)glycine buffer and, specifically for postrefolding treatment, with Ca(2+)/Zn(2+) supplementation. We identified two previously undocumented disulfide bridges in the crystal structure of properly folded S100A3: one disulfide bridge is between Cys30 in the N-terminal pseudo-EF-hand and Cys68 in the C-terminal EF-hand (SS1), and another disulfide bridge attaches Cys99 in the C-terminal coil structure to Cys81 in helix IV (SS2). Mutational disruption of SS1 (C30A+C68A) abolished the Ca(2+) binding property of S100A3 and retarded the citrullination of Arg51 by peptidylarginine deiminase type III (PAD3), while SS2 disruption inversely increased both Ca(2+) affinity and PAD3 reactivity in vitro. Similar backbone structures of wild type, R51A, and C30A+C68A indicated that neither Arg51 conversion by PAD3 nor SS1 alters the overall dimer conformation. Comparative inspection of atomic coordinates refined to 2.15-1.40 Å resolution shows that SS1 renders the C-terminal classical Ca(2+)-binding loop flexible, which are essential for its Ca(2+) binding properties, whereas SS2 structurally shelters Arg51 in the metal-free form. We propose a model of the tetrahedral coordination of a Zn(2+) by (Cys)(3)His residues that is compatible with SS2 formation in S100A3.

X-ray crystallographic analysis of a metalloprotein requires knowing the electronic state of the metal center, if one wants to elucidate the exact function and/or reaction mechanism. As an example, we show our recent structural analysis of the heme oxygenase reaction intermediate which is involved in the third step of the heme degradation reaction. The reaction intermediate was crystallized under anaerobic condition, and the obtained crystals were frozen into liquid nitrogen. The absorption spectra of the single crystal before and after X-ray irradiation were compared with that of the frozen solution in 100 K cold nitrogen stream. The determined structure offers the first solid evidence for the presence of a water cluster in the distal pocket of this catalytically critical intermediate. This structure combined with the QM/MM calculation supports our proposal that the biliverdin is produced via Fe-OOH verdoheme intermediate.

The least understood mechanism during heme degradation by the enzyme heme oxygenase (HO) is the third step of ring opening of verdoheme to biliverdin, a process which maintains iron homeostasis. In response to this mechanistic uncertainty, we launched a combined study of X-ray crystallography and theoretical QM/MM calculations, designed to elucidate the mechanism. The air-sensitive ferrous verdoheme complex of HmuO, a heme oxygenase from Corynebacterium diphtheriae, was crystallized under anaerobic conditions. Spectral analysis of the azide-bound verdoheme-HmuO complex crystals assures that the verdoheme group remains intact during the crystallization and X-ray diffraction measurement. The structure offers the first solid evidence for the presence of a water cluster in the distal pocket of this catalytically critical intermediate. The subsequent QM/MM calculations based on this crystal structure explore the reaction mechanisms starting from the FeOOH-verdoheme and FeHOOH-verdoheme complexes, which mimic, respectively, the O(2)- and H(2)O(2)-supported degradations. In both mechanisms, the rate-determining step is the initial O-O bond breaking step, which is either homolytic (for FeHOOH-verdoheme) or coupled to electron and proton transfers (in FeOOH-verdoheme). Additionally, the calculations indicate that the FeHOOH-verdoheme complex is more reactive than the FeOOH-verdoheme complex in accord with experimental findings. QM energies with embedded MM charges are close to and yield the same conclusions as full QM/MM energies. Finally, the calculations highlight the dominant influence of the distal water cluster which acts as a biocatalyst for the conversion of verdoheme to biliverdin in the two processes, by fixing the departing OH and directing it to the requisite site of attack, and by acting as a proton shuttle and a haven for the highly reactive OH(-) nucleophile.

Phycocyanobilin, a light-harvesting and photoreceptor pigment in higher plants, algae, and cyanobacteria, is synthesized from biliverdin IXα (BV) by phycocyanobilin:ferredoxin oxidoreductase (PcyA) via two steps of two-proton-coupled two-electron reduction. We determined the neutron structure of PcyA from cyanobacteria complexed with BV, revealing the exact location of the hydrogen atoms involved in catalysis. Notably, approximately half of the BV bound to PcyA was BVH(+), a state in which all four pyrrole nitrogen atoms were protonated. The protonation states of BV complemented the protonation of adjacent Asp105. The "axial" water molecule that interacts with the neutral pyrrole nitrogen of the A-ring was identified. His88 Nδ was protonated to form a hydrogen bond with the lactam O atom of the BV A-ring. His88 and His74 were linked by hydrogen bonds via H3O(+). These results imply that Asp105, His88, and the axial water molecule contribute to proton transfer during PcyA catalysis.

Heme oxygenases found in mammals, plants, and bacteria catalyze degradation of heme using the same mechanism. Roles of distal Asp (Asp-136) residue in HmuO, a heme oxygenase of Corynebacterium diphtheriae, have been investigated by site-directed mutagenesis, enzyme kinetics, resonance Raman spectroscopy, and x-ray crystallography. Replacements of the Asp-136 by Ala and Phe resulted in reduced heme degradation activity due to the formation of ferryl heme, showing that the distal Asp is critical in HmuO heme oxygenase activity. D136N HmuO catalyzed heme degradation at a similar efficiency to wild type and D136E HmuO, implying that the carboxylate moiety is not required for the heme catabolism by HmuO. Resonance Raman results suggest that the inactive ferryl heme formation in the HmuO mutants is induced by disruption of the interaction between a reactive Fe-OOH species and an adjacent distal pocket water molecule. Crystal structural analysis of the HmuO mutants confirms partial disappearance of this nearby water in D136A HmuO. Our results provide the first experimental evidence for the catalytic importance of the nearby water molecule that can be universally critical in heme oxygenase catalysis and propose that the distal Asp helps in positioning the key water molecule at a position suitable for efficient activation of the Fe-OOH species.

Peptidylarginine deiminase (PAD) catalyzes the post-translational conversion of peptidylarginine to peptidylcitrulline in the presence of calcium ions. Among the five known human PAD isozymes (PAD1-4 and PAD6), PAD1 exhibits the broadest substrate specificity. Crystals of PAD1 obtained using polyethylene glycol 3350 as a precipitant diffracted to 3.70 Å resolution using synchrotron radiation. Two PAD1 molecules were contained in the asymmetric unit and the crystals belonged to space group P6(1), with unit-cell parameters a = b = 90.3, c = 372.3 Å. The solvent content was 58.2%.

HmuO, a heme oxygenase of Corynebacterium diphtheriae, catalyzes degradation of heme using the same mechanism as the mammalian enzyme. The oxy form of HmuO, the precursor of the catalytically active ferric hydroperoxo species, has been characterized by ligand binding kinetics, resonance Raman spectroscopy, and x-ray crystallography. The oxygen association and dissociation rate constants are 5 μm-1 s-1 and 0.22 s-1, respectively, yielding an O2 affinity of 21 μm-1, which is ∼20 times greater than that of mammalian myoglobins. However, the affinity of HmuO for CO is only 3–4-fold greater than that for mammalian myoglobins, implying the presence of strong hydrogen bonding interactions in the distal pocket of HmuO that preferentially favor O2 binding. Resonance Raman spectra show that the Fe–O2 vibrations are tightly coupled to porphyrin vibrations, indicating the highly bent Fe–O–O geometry that is characteristic of the oxy forms of heme oxygenases. In the crystal structure of the oxy form the Fe–O–O angle is 110°, the O–O bond is pointed toward the heme α-meso-carbon by direct steric interactions with Gly-135 and Gly-139, and hydrogen bonds occur between the bound O2 and the amide nitrogen of Gly-139 and a distal pocket water molecule, which is a part of an extended hydrogen bonding network that provides the solvent protons required for oxygen activation. In addition, the O–O bond is orthogonal to the plane of the proximal imidazole side chain, which facilitates hydroxylation of the porphyrin α-meso-carbon by preventing premature O–O bond cleavage.

The 20S proteasome is the catalytic portion of the 26S proteasome. Constitutively expressed mammalian 20S proteasomes have three active subunits, beta 1, beta 2, and beta 5, which are replaced in the immunoproteasome by interferon-gamma-inducible subunits beta 1i, beta 2i, and beta 5i, respectively. Here we determined the crystal structure of the bovine 20S proteasome at 2.75 A resolution. The structures of alpha 2, beta 1, beta 5, beta 6, and beta 7 subunits of the bovine enzyme were different from the yeast enzyme but enabled the bovine proteasome to accommodate either the constitutive or the inducible subunits. A novel N-terminal nucleophile hydrolase activity was proposed for the beta 7 subunit. We also determined the site of the nuclear localization signals in the molecule. A model of the immunoproteasome was predicted from this constitutive structure.

In this letter, we extend the 3-D HIE-FDTD method to the simulation of hybrid electromagnetic system including the linear/nonlinear lumped elements and the conductive media. First, numerical formulation of the HIE-FDTD method for the conductive media and the lumped elements are presented. Furthermore, we simulated the crosstalk effect among the coupled multi-conductor lines, and then the accuracy and effectiveness are validated by the comparison of our method with the conventional FDTD method and the ADI-FDTD method.

The crystal structure of the Pyrus pyrifolia pistil ribonuclease (S(3)-RNase) responsible for gametophytic self-incompatibility was determined at 1.5-A resolution. It consists of eight helices and seven beta-strands, and its folding topology is typical of RNase T(2) family enzymes. Based on a structural comparison of S(3)-RNase with RNase Rh, a fungal RNase T(2) family enzyme, the active site residues of S(3)-RNase assigned were His(33) and His(88) as catalysts and Glu(84) and Lys(87) as stabilizers of an intermediate in the transition state. Moreover, amino acid residues that constitute substrate binding sites of the two RNases could be superimposed geometrically. A hypervariable (HV) region that has an S-allele-specific sequence comprises a long loop and short alpha-helix. This region is far from the active site cleft, exposed on the molecule's surface, and positively charged. Four positively selected (PS) regions, in which the number of nonsynonymous substitutions exceeds that of synonymous ones, are located on either side of the active site cleft, and accessible to solvent. These structural features suggest that the HV or PS regions may interact with a pollen S-gene product(s) to recognize self and non-self pollen.

In mammalian hair follicles, Ca2+-dependent peptidylarginine deiminases catalyze the conversion of arginines into citrullines in S100A3, a cysteine-rich member of the S100 protein family, and trichohyalin, a member of the S100 fused-type protein family. These irreversible posttranslational modifications were first described in the inner root sheath and medulla, and later, in hair cuticles. In the inner root sheath and medullary cells, arginine residues in the repetitive peptide domains of trichohyalin are converted to peptidylcitrullines. Consequently, the α-helix rich structures are unfolded due to decreased intramolecular ionic interaction. Citrullinated trichohyalin, which is susceptible to further introduction of isopeptide bonds, is cross-linked to keratin intermediate filaments, the cornified envelope, or to itself in the inner root sheath. Interconnected trichohyalin is predominantly deposited in amorphous vacuoles of the mature medulla. In cuticular cells, hair-dominant-type peptidylarginine deiminase specifically converts a symmetric pair of Arg51 on the S100A3 dimer to a citrulline pair. The citrullinated S100A3 dimer assembles as a homotetramer in the presence of Ca2+ and Zn2+. This trichocytic pathway is likely to be associated with homeostatic Ca2+ and Zn2+ regulation during hair cuticular maturation. This chapter summarizes previous reports of pioneering research updated with our current view of protein deimination in the hair follicle.

The S100A3 homotetramer assembles upon citrullination of a specific symmetric Arg51 pair on its homodimer interface in human hair cuticular cells. Each S100A3 subunit contains two EF-hand-type Ca 2 + -binding motifs and one (Cys) 3 His-type Zn 2 + -binding site in the C-terminus. The C-terminal coiled domain is cross-linked to the presumed docking surface of the dimeric S100A3 via a disulfide bridge. The aim of this study was to determine the structural and functional role of the C-terminal Zn 2 + -binding domain, which is unique to S100A3, in homotetramer assembly. The binding of either Ca 2 + or Zn 2 + reduced the α-helix content of S100A3 and modulated its affinity for the other cation. The binding of a single Zn 2 + accelerated the Ca 2 + -dependent tetramerization of S100A3 while inducing an extensive unfolding of helix IV. The Ca 2 + and Zn 2 + binding affinities of S100A3 were enhanced when the other cation bound in concert with the tetramerization of S100A3. Small angle scattering analyses revealed that the overall structure of the S100A3 tetramer bound both Ca 2 + and Zn 2 + had a similar molecular shape to the Ca 2 + -bound form in solution. The binding states of the Ca 2 + or Zn 2 + to each S100A3 subunit within a homotetramer appear to be propagated by sensing the repositioning of helix III and the rearrangement of the C-terminal tail domain. This article is part of a Special Issue entitled: 12th European Symposium on Calcium.