Large-scale column-free purification of bovine F-ATP synthase.

Mammalian F-ATP synthase is central to mitochondrial bioenergetics and is present in the inner mitochondrial membrane in a dynamic oligomeric state of higher oligomers, tetramers, dimers, and monomers. In vitro investigations of mammalian F-ATP synthase are often limited by the ability to purify the oligomeric forms present in vivo at a quantity, stability, and purity that meets the demand of the planned experiment. We developed a purification approach for the isolation of bovine F-ATP synthase from heart muscle mitochondria that uses a combination of buffer conditions favoring inhibitor factor 1 binding and sucrose density gradient ultracentrifugation to yield stable complexes at high purity in the milligram range. By tuning the glyco-diosgenin to lauryl maltose neopentyl glycol ratio in a final gradient, fractions that are either enriched in tetrameric or monomeric F-ATP synthase can be obtained. It is expected that this large-scale column-free purification strategy broadens the spectrum of in vitro investigation on mammalian F-ATP synthase.

Dynamic interactions in the l-lactate oxidase active site facilitate substrate binding at pH4.5.

The crystal structure of l-lactate oxidase in complex with l-lactate was solved at a 1.33 Å resolution. The electron density of the bound l-lactate was clearly shown and comparisons of the free form and substrate bound complexes demonstrated that l-lactate was bound to the FMN and an additional active site within the enzyme complex. l-lactate interacted with the related side chains, which play an important role in enzymatic catalysis and especially the coupled movement of H265 and D174, which may be essential to activity. These observations not only reveal the enzymatic mechanism for l-lactate binding but also demonstrate the dynamic motion of these enzyme structures in response to substrate binding and enzymatic reaction progression.

Crystal structure of octocoral lectin SLL-2 complexed with Forssman antigen tetrasaccharide.

A symbiosis-related lectin, SLL-2, from the octocoral Sinularia lochmodes, distributes densely on the cell surface of microalgae, Symbiodinium sp., an endosymbiotic dinoflagellate of the coral, and is also shown to be a chemical cue that transforms dinoflagellates into a nonmotile (coccoid) symbiotic state. SLL-2 binds to the sugar chain of the molecule similar to Forssman antigen pentasaccharide (GalNAcα1-3GalNAcß1-3 Galα1-4 Galß1-4Glc) on the surface of microalgae with high affinity. Here we report the crystal structure of the complex between SLL-2 and Forssman antigen tetrasaccharide (GalNAcα1-3GalNAcß1-3 Galα1-4 Galß) at 3.4 Å resolution. In an asymmetric unit of the crystal, there are two hexameric molecules with totally 12 sugar recognition sites. At 9 in 12 sites, the first and second saccharides of the Forssman antigen tetrasaccharide bind directly to galactopyranoside binding site of SLL-2, whereas the third and fourth saccharides have no interaction with the SLL-2 hexameric molecule that binds the first saccharide. The sugar chain bends at α-1,4-glycosidic linkage between the third and fourth saccharides toward the position that we defined as a pyranoside binding site in the crystal structure of the complex between SLL-2 and GalNAc. The structure allowed us to suggest a possible binding mode of the Forssman antigen pentasaccharide to SLL-2. These observations support our hypothesis that the binding of SLL-2 to the cell surface sugars of zooxanthella in a unique manner might trigger some physiological changes of the cell to adapt symbiosis with the host coral.

The catalytic mechanism of decarboxylative hydroxylation of salicylate hydroxylase revealed by crystal structure analysis at 2.5 Å resolution.

The X-ray crystal structure of a salicylate hydroxylase from Pseudomonas putida S-1 complexed with coenzyme FAD has been determined to a resolution of 2.5 Å. Structural conservation with p- or m-hydroxybenzoate hydroxylase is very good throughout the topology, despite a low amino sequence identity of 20-40% between these three hydroxylases. Salicylate hydroxylase is composed of three distinct domains and includes FAD between domains I and II, which is accessible to solvent. In this study, which analyzes the tertiary structure of the enzyme, the unique reaction of salicylate, i.e. decarboxylative hydroxylation, and the structural roles of amino acids surrounding the substrate, are considered.

Crystal structure of a symbiosis-related lectin from octocoral.

D-Galactose-binding lectin from the octocoral, Sinularia lochmodes (SLL-2), distributes densely on the cell surface of microalgae, Symbiodinium sp., an endosymbiotic dinoflagellate of the coral, and is also shown to be a chemical cue that transforms dinoflagellate into a non-motile (coccoid) symbiotic state. SLL-2 binds with high affinity to the Forssman antigen (N-acetylgalactosamine(GalNAc)α1-3GalNAcß1-3Galα1-4Galß1-4Glc-ceramide), and the presence of Forssman antigen-like sugar on the surface of Symbiodinium CS-156 cells was previously confirmed. Here we report the crystal structures of SLL-2 and its GalNAc complex as the first crystal structures of a lectin involved in the symbiosis between coral and dinoflagellate. N-Linked sugar chains and a galactose derivative binding site common to H-type lectins were observed in each monomer of the hexameric SLL-2 crystal structure. In addition, unique sugar-binding site-like regions were identified at the top and bottom of the hexameric SLL-2 structure. These structural features suggest a possible binding mode between SLL-2 and Forssman antigen-like pentasaccharide.

Increasing the electron-transfer ability of Cyanidioschyzon merolae ferredoxin by a one-point mutation--a high resolution and Fe-SAD phasing crystal structure analysis of the Asp58Asn mutant.

Cyanidioschyzon merolae (Cm) is a single cell red algae that grows in rather thermophilic (40-50°C) and acidic (pH 1-3) conditions. Ferredoxin (Fd) was purified from this algae and characterized as a plant-type [2Fe-2S] Fd by physicochemical techniques. A high resolution (0.97Å) three-dimensional structure of the CmFd D58N mutant molecule has been determined using the Fe-SAD phasing method to clarify the precise position of the Asn58 amide, as this substitution increases the electron-transfer ability relative to wild-type CmFd by a factor of 1.5. The crystal structure reveals an electro-positive surface surrounding Asn58 that may interact with ferredoxin NADP(+) reductase or cytochrome c.

X-ray structure determination and deuteration of nattokinase.

Nattokinase (NK) is a strong fibrinolytic enzyme, which is produced in abundance by Bacillus subtilis natto. Although NK is a member of the subtilisin family, it displays different substrate specificity when compared with other subtilisins. The results of molecular simulations predict that hydrogen arrangements around Ser221 at the active site probably account for the substrate specificity of NK. Therefore, neutron crystallographic analysis should provide valuable information that reveals the enzymatic mechanism of NK. In this report, the X-ray structure of the non-hydrogen form of undeuterated NK was determined, and the preparation of deuterated NK was successfully achieved. The non-hydrogen NK structure was determined at 1.74 Å resolution. The three-dimensional structures of NK and subtilisin E from Bacillus subtilis DB104 are near identical. Deuteration of NK was carried out by cultivating Bacillus subtilis natto in deuterated medium. The D2O resistant strain of Bacillus subtilis natto was obtained by successive cultivation rounds, in which the concentration of D2O in the medium was gradually increased. NK was purified from the culture medium and its activity was confirmed by the fibrin plate method. The results lay the framework for neutron protein crystallography analysis.

Hydrogen/Deuterium Exchange Behavior During Denaturing/Refolding Processes Determined in Tetragonal Hen Egg-White Lysozyme Crystals.

The hydrogen/deuterium (H/D) exchange of main-chain amide hydrogens in the protein that denatured and refolded in deuterated solvent is considered to contain the traces of hydrogen bond cleavages or the exposure to solvent of the buried part of the protein during the denaturing and refolding (denaturing/refolding) processes. Here, we report the H/D exchange behaviors in hen egg-white lysozymes denatured under acidic conditions, basic conditions, and thermal conditions and then refolded in deuterated solvents, using crystallographic methods. The results indicate that the space containing the Trp28 side chain was hardly exposed to the solvent in acidic conditions, but exposed under basic or heated conditions. Moreover, the ß-bridges between Tyr53 and Ile58 in strands ß2 and ß3, which are in a highly conserved region, show some tolerance to changes in pD. The results indicate that crystallographic method is one of the powerful tools to analyze the denaturing/refolding processes of proteins.

Protonation states of histidine and other key residues in deoxy normal human adult hemoglobin by neutron protein crystallography.

The protonation states of the histidine residues key to the function of deoxy (T-state) human hemoglobin have been investigated using neutron protein crystallography. These residues can reversibly bind protons, thereby regulating the oxygen affinity of hemoglobin. By examining the OMIT F(o)-F(c) and 2F(o)-F(c) neutron scattering maps, the protonation states of 35 of the 38 His residues were directly determined. The remaining three residues were found to be disordered. Surprisingly, seven pairs of His residues from equivalent α or ß chains, αHis20, αHis50, αHis58, αHis89, ßHis63, ßHis143 and ßHis146, have different protonation states. The protonation of distal His residues in the α(1)ß(1) heterodimer and the protonation of αHis103 in both subunits demonstrates that these residues may participate in buffering hydrogen ions and may influence the oxygen binding. The observed protonation states of His residues are compared with their ΔpK(a) between the deoxy and oxy states. Examination of inter-subunit interfaces provided evidence for interactions that are essential for the stability of the deoxy tertiary structure.

Purification, crystallization and preliminary X-ray diffraction experiment of nattokinase from Bacillus subtilis natto.

Nattokinase is a single polypeptide chain composed of 275 amino acids (molecular weight 27,724) which displays strong fibrinolytic activity. Moreover, it can activate other fibrinolytic enzymes such as pro-urokinase and tissue plasminogen activator. In the present study, native nattokinase from Bacillus subtilis natto was purified using gel-filtration chromatography and crystallized to give needle-like crystals which could be used for X-ray diffraction experiments. The crystals belonged to space group C2, with unit-cell parameters a=74.3, b=49.9, c=56.3 Å, ß=95.2°. Diffraction images were processed to a resolution of 1.74 Šwith an Rmerge of 5.2% (15.3% in the highest resolution shell) and a completeness of 69.8% (30.0% in the highest resolution shell). This study reports the first X-ray diffraction analysis of nattokinase.

SAXS and SANS observations of abnormal aggregation of human alpha-crystallin.

Aggregation states of human alpha-crystallins are observed complementarily using small-angle X-ray and small-angle neutron scatterings (SAXS and SANS). Infant alpha-crystallin is almost a monodispersed system of the aggregates with gyration radius of ca. 60 A, which is a normal aggregate. On the other hand, the aged and cataract alpha-crystallins have not only the normal but also the larger aggregates. In the aged alpha-crystallin, the normal aggregate is a major component, but in the cataract alpha-crystallin the larger ones are dominant. Both alpha A- and alpha B-crystallins, which are subunits of alpha-crystallin, also form an aggregate with the size close to the normal aggregate. Under UV irradiation, only aggregates of alpha B-crystallin undergo further aggregation. Therefore, considering increase of ratio of alpha B-crystallin in the aggregate of alpha-crystallin as aging, the abnormal aggregation (formation of the huge aggregates) mainly results in the further aggregation of alpha B-crystallin caused by external stresses.

Hydrogen/deuterium exchange behavior in tetragonal hen egg-white lysozyme crystals affected by solution state.

Neutron diffraction studies of hydrogen/deuterium-exchanged hen egg-white lysozyme were performed by a joint X-ray and neutron refinement to elucidate the hydrogen/deuterium exchange behavior. Large crystals for neutron work, consisting of molecules that were exchanged before crystallization, were obtained by repeatedly adding protein solution to the crystal batch using deuterated precipitant reagent. There are differences in hydrogen/deuterium exchange behavior compared with previous crystallographic or NMR studies, which could be due to intermolecular interactions in the crystal or to different lengths of exchange period.

Crystal structure of the de-ubiquitinating enzyme UCH37 (human UCH-L5) catalytic domain.

Ubiquitin C-terminal hydrolases (UCHs) are one of five sub-families of de-ubiquitinating enzymes (DUBs) that hydrolyze the C-terminal peptide bond of ubiquitin. UCH37 (also called UCH-L5) is the only UCH family protease that interacts with the 19S proteasome regulatory complex and disassembles Lys48-linked poly-ubiquitin from the distal end of the chain. The structures of three UCHs, UCH-L1, UCH-L3, and YUH1, have been determined by X-ray crystallography. However, little is known about their physiological substrates. These enzymes do not hydrolyze large adducts of ubiquitin such as proteins. To identify and characterize the hydrolytic specificities of their substrates, the crystal structure of the UCH37 catalytic domain (UCH-domain) was determined and compared with that of the other UCHs. The overall folding patterns are similar in these UCHs. However, helix-3 is collapsed in UCH37 and the pattern of electrostatic potential on the surface of the putative substrate-binding site (P'-site) is different. Helix-3 comprises an edge of the P'-site. As a result, the P'-site is wider than that in other UCHs. These differences indicate that UCH37 can interact with larger adducts such as ubiquitin.

An abnormal pK(a) value of internal histidine of the insulin molecule revealed by neutron crystallographic analysis.

Insulin is stored in pancreatic beta-cell as hexameric form with Zn2+ ions, while the hormonally active form is monomer. The hexamer requires the coordination of Zn2+ ions to the HisB10. In order to reveal the mechanism of the hexamerization of insulin, we investigated the Zn2+ free insulin at pD6.6 and pD9 by neutron crystallographic analyses. HisB10 is doubly protonated not only at pD6.6 but also at pD9, indicating an abnormal pK(a) of this histidine. It is suggested that HisB10 acts on a strong cation capture and contributes to the high stability of the hexameric form in pancreas.

Structural evolution of human recombinant alpha B-crystallin under UV irradiation.

External stresses cause certain proteins to lose their regular structure and aggregate. In order to clarify this abnormal aggregation process, a structural evolution of human recombinant alphaB-crystallin under UV irradiation was observed with in situ small-angle neutron scattering. The abnormal aggregation process was identified to fall in three time zones: incubation, aggregation, and saturation. During the incubation time, the size of aggregates was almost unchanged but a deformation in the local structure was developing. After the incubation time, abnormal aggregation proceed. When the volume of the aggregates reached around twice the size as that of the initial aggregates, the aggregation rate slowed down, which marked the onset of saturation.

Six tris-(bipyrid-yl)iron(II) complexes with 2-substituted 1,1,3,3-tetra-cyano-propenide, perchlorate and tetra-fluorido-borate anions; order versus disorder, hydrogen bonding and C-N⋯π inter-actions.

Structures are reported for six closely related salts of tris-(bipyrid-yl)iron(II) cations, namely tris-(2,2'-bi-pyridine)-iron(II) bis-(1,1,3,3-tetra-cyano-2-meth-oxy-propenide) 0.776-hydrate, [Fe(C10H8N2)3](C8H3N4O)2.0.776H2O, (I), tris-(2,2'-bi-pyridine)-iron(II) 1,1,3,3-tetra-cyano-2-(propyl-sulfan-yl)propenide perchlor-ate, [Fe(C10H8N2)3](C10H7N4S)(ClO4), (II), tris-(5,5'-dimethyl-2,2'-bi-pyridine)-iron(II) 1,1,3,3-tetra-cyano-2-meth-oxy-propenide tetra-fluorido-borate ethanol 0.926-solvate, [Fe(C12H12N2)3](C8H3N4O)(BF4).0.926C2H2O, (III), tris-(5,5'-dimethyl-2,2'-bi-pyridine)-iron(II) 1,1,3,3-tetra-cyano-2-eth-oxy-propenide tetra-fluorido-borate, [Fe(C12H12N2)3](C9H5N4O)(BF4), (IV), tris-(5,5'-dimethyl-2,2'-bi-pyridine)-iron(II) 1,1,3,3-tetra-cyano-2-(ethyl-sufanyl)propenide tetra-fluorido-borate, [Fe(C12H12N2)3](C9H5N4S)(BF4), (V), and tris-(5,5'-dimethyl-2,2'-bi-pyri-dine)-iron(II) 1,1,3,3-tetra-cyano-2-prop-oxypropenide tetra-fluorido-borate, [Fe(C12H12N2)3](C10H7N4O)(BF4), (VI). In compound (I), one of the anions is disordered over two sets of atomic sites with equal occupancies while, in the second anion, just one of the C(CN)2 units is disordered, again over two sets of atomic sites with equal occupancies: the anionic components are linked by multiple C-H⋯N hydrogen bonds to form a three-dimensional framework. In compound (II), the polynitrile anion is disordered over two sets of atomic sites with occupancies in the approximate ratio 3:1, while the perchlorate anion is disordered over three sets of atomic sites: there are C-N⋯π inter-actions between the cations and the polynitrile anion. The polynitrile anion in compound (III) is fully ordered, but the tetra-fluorido-borate anion is disordered over two sets of atomic sites with occupancies 0.671 (4) and 0.329 (4): the cations and the tetra-fluorido-borate anions are linked by C-H⋯F inter-actions to form an inter-rupted chain. Compounds (IV) and (V) are isostructural and all of the ionic components are fully ordered in both of them: the cations and tetra-fluorido-borate anions are linked into C 2 2(12) chains. The polynitrile anion in compound (VI) is disordered over two sets of atomic sites with approximately equal occupancies, and here the chains formed by the cations and the tetra-fluorido-borate anions are of the C 2 2(13) type.

Protonation states of buried histidine residues in human deoxyhemoglobin revealed by neutron crystallography.

The protonation states of buried histidine residues in human deoxyhemoglobin were unambiguously identified by using a neutron crystallographic technique. Unexpectedly, the neutron structure reveals that both the alpha- and beta-distal histidines (Hisalpha58 and Hisbeta63) adopt a positively charged, fully (doubly) protonated form, suggesting their contribution to the Bohr effect. In addition, the neutron data provide an accurate picture of the alpha1beta1 hydrogen-bonding network and allow us to observe unambiguously the nature of the intradimeric interactions at an atomic level.

Determination of the role of the Carboxyl-terminal leucine-122 in FMN-binding protein by mutational and structural analysis.

Mutants of flavin mononucleotide-binding protein (FMN-bp) were made by site-directed mutagenesis to investigate the role of carboxyl-terminal Leu122 of the pairing subunit in controlling redox potentials, binding the prosthetic group, and forming the tertiary and quaternary structure. We compared the oxidation-reduction potentials, FMN-binding properties, and higher structures of wild-type FMN-bp and four mutant proteins (L122Y, L122E, L122K and L122-deleted). We found that the redox potentials were affected by mutations. Also, the affinities of L122E, L122K and L122 deletion mutant apoproteins for FMN were lower than for the wild-type apoprotein, whereas the affinity of L122Y for FMN was increased. Analytical ultracentrifugation showed that the dissociation constants for dimerization of L122E and L122K were larger than for wild-type FMN-bp, whereas the dissociation constants for L122Y and the deletion mutant were lower than for the wild type. Finally, we determined the higher structures of L122Y, L122E and L122K mutants by X-ray crystallography. Our results show that the mutation of Leu122 in FMN-bp changes midpoint potentials, dissociation constants for FMN, and dimer formation, indicating that this residue is important in the pairing subunit.

Inhibitory effects of local anesthetics on the proteasome and their biological actions.

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 ß5 subunit of the 20S proteasome, and not to the other active subunits, ß1 and ß2. 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.

Structure of a cyanobacterial BLUF protein, Tll0078, containing a novel FAD-binding blue light sensor domain.

The sensor proteins for blue light using the FAD (BLUF) domain belong to the third family of the photoreceptor proteins using a flavin chromophore, where the other two families are phototropins and cryptochromes. As the first structure of this BLUF domain, we have determined the crystal structure of the Tll0078 protein from Thermosynechococcus elongatus BP-1, which contains a BLUF domain bound to FAD, at 2A resolution. Five Tll0078 monomers are located around the non-crystallographic 5-fold axis to form a pentamer, and two pentamers related by 2-fold non-crystallographic symmetry form a decameric assembly. The monomer consists of two domains, the BLUF domain at the N-terminal region and the C-terminal domain. The overall structure of the BLUF domain consists of a five-stranded mixed beta-sheet with two alpha-helices running parallel with it. The isoalloxazine ring of FAD is accommodated in a pocket formed by several highly conserved amino acid residues in the BLUF domain. Of these, the three apparent key residues (Asn31, Asn32 and Gln50) were substituted with Ala. Mutant proteins of N31A and N32A showed a nearly normal 10nm spectral shift of the flavin upon illumination, while the Q50A mutant did not exhibit such a shift at all. On the basis of the crystal structure, we discussed a possible role of Gln50, which is structurally and functionally linked with the critical Tyr8 (FAD-Gln50-Tyr8 network), with regard to the light-induced spectral shift of the BLUF proteins.