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.

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.

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.

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.

Six tris-(bipyrid-yl)iron(II) complexes with 2-substituted 1,1,3,3-tetra-cyano-propenide, perchlorate and tetra-fluorido-borate anions; order 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(CHN)](CHNO).0.

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 β5 subunit of the 20S proteasome, and not to the other active subunits, β1 and β2.

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 (GalNAcα1-3GalNAcβ1-3 Galα1-4 Galβ1-4Glc) on the surface of microalgae with high affinity.

Structural Insight Into Protein Binding of Boron Tracedrug UTX-97 Revealed by the Co-Crystal Structure With Lysozyme at 1.26 Å Resolution.

Boron neutron capture therapy (BNCT) is one of the numbers of radiotherapies for treatment of certain cancers. The ability of low-dose irradiation with neutrons or radioactive beams to provide an acceptable quality of life is an objective which has not yet been achieved; therefore it will be necessary to increase the efficiency of the neutron capture reaction by lower dose irradiation and by achieving higher drug concentrations in living cells. Drug selectivity in targeting the affected cellular compartment is most important.

An Effective Deuterium Exchange Method for Neutron Crystal Structure Analysis with Unfolding-Refolding Processes.

A method of hydrogen/deuterium (H/D) exchange with an unfolding-refolding process has been applied to hen egg-white lysozyme (HWL), and accurate evaluation of its deuteration was carried out by time-of-flight mass spectroscopy. Neutron crystallography requires a suitable crystal with enough deuterium exchanged in the protein to decrease incoherent scattering from hydrogens. It is very expensive to prepare a fully deuterated protein, and therefore a simple H/D exchange technique is desirable for this purpose.

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.

Crystal structure of (2-{[3,5-bis-(1,1-di-methyl-eth-yl)-4-hy-droxy-phen-yl](5-methyl-2H-pyrrol-2-yl-idene)meth-yl}-5-methyl-1H-pyrrolido-κ(2) N,N')di-fluoridoboron.

The title compound, C25H31BF2N2O, is a potential boron tracedrug in boron neutron capture therapy (BNCT), in which the B atom adopts a distorted BN2F2 tetra-hedral geometry: it is soluble in dimethyl sulfoxide, di-methyl-formamide and methanol. The pyrrolyl-idene-methyl-pyrrole triple fused ring system is almost planar (r.m.

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)α1-3GalNAcβ1-3Galα1-4Galβ1-4Glc-ceramide), and the presence of Forssman antigen-like sugar on the surface of Symbiodinium CS-156 cells was previously confirmed.

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.

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.

Cyanidioschyzon merolae ferredoxin: a high resolution crystal structure analysis and its thermal stability.

Cyanidioschyzon merolae (Cm) is a single-cell red alga that grows under moderately thermophilic (40-50°C), acidic (pH 1-3) conditions. We purified a Cm ferredoxin (Fd) that was characterized as a plant-type [2Fe-2S] Fd by physicochemical techniques. X-ray crystallography revealed that the overall three-dimensional structure of CmFd was highly similar to, but slightly different from, the [2Fe-2S] Fd from Spinacia oleracea, whose growth temperature is 15-20°C.

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.

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.

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.

Large conformational changes in the Escherichia coli tryptophan synthase beta(2) subunit upon pyridoxal 5'-phosphate binding.

To understand the basis for the lower activity of the tryptophan synthase beta(2) subunit in comparison to the alpha(2)beta(2) complex, we determined the crystal structures of apo-beta(2) and holo-beta(2) from Escherichia coli at 3.0 and 2.9 A resolutions, respectively.

Direct determination of protonation states of histidine residues in a 2 A neutron structure of deoxy-human normal adult hemoglobin and implications for the Bohr effect.

We have investigated the protonation states of histidine residues (potential Bohr groups) in the deoxy form (T state) of human hemoglobin by direct determination of hydrogen (deuterium) positions with the neutron protein crystallography technique. The reversible binding of protons is key to the allosteric regulation of human hemoglobin. The protonation states of 35 of the 38 His residues were directly determined from neutron scattering omit maps, with 3 of the remaining residues being disordered.

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.

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.

Hydrogen bonds of DsrD protein revealed by neutron crystallography.

The features of hydrogen bonds in DsrD protein from sulfate-reducing bacteria have been investigated by neutron protein crystallography. The function of DsrD has not yet been elucidated clearly, but its X-ray crystal structure revealed that it comprises a winged-helix motif and shows the highest structural homology to the DNA-binding proteins. Since any neutron structure of a DNA recognition protein has not yet been obtained, here detailed information on the hydrogen bonds in the winged-helix-motif protein is given and the following features found.

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.

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.