High Resolution X-ray Structure Analysis Research Articles

Delayed Onset and Directionality of X-Ray-Induced Atomic Displacements Observed on Subatomic Length Scales.

Transient structural changes of Al_{2}O_{3} on subatomic length scales following irradiation with an intense x-ray laser pulse (photon energy: 8.70keV; pulse duration: 6fs; fluence: 8×10^{2} J/cm^{2}) have been investigated by using an x-ray pump x-ray probe technique. The measurement reveals that aluminum and oxygen atoms remain in their original positions by ∼20 fs after the intensity maximum of the pump pulse, followed by directional atomic displacements at the fixed unit cell parameters. By comparing the experimental results and theoretical simulations, we interpret that electron excitation and relaxation triggered by the pump pulse modify the potential energy surface and drives the directional atomic displacements. Our results indicate that high-resolution x-ray structural analysis with the accuracy of 0.01Å is feasible even with intense x-ray pulses by making the pulse duration shorter than the timescale needed to complete electron excitation and relaxation processes, which usually take up to a few tens of femtoseconds.

Recent structural insights into the mechanism of lysozyme hydrolysis.

Lysozyme hydrolyzes the glycosidic bonds between N-acetylmuramic acid and N-acetylglucosamine in peptidoglycans located in the bacterial cell wall. The mechanism of the hydrolysis reaction of lysozyme was first studied more than 50 years ago; however, it has not yet been fully elucidated and various mechanisms are still being investigated. One reaction system that has commonly been proposed is that the lysozyme intermediate undergoes covalent ligand binding during hydrolysis. However, these findings resulted from experiments performed under laboratory conditions using fluorine-based ligands, which facilitate the formation of covalent bonds between the ligands and the catalytic side chain of lysozyme. More recently, high-resolution X-ray structural analysis was used to study the complex of lysozyme with an N-acetylglucosamine tetramer. As a result, the carboxyl group of Asp52 was found to form a relatively strong hydrogen-bond network and had difficulty binding covalently to C1 of the carbohydrate ring. To confirm this hydrogen-bond network, neutron test measurements were successfully performed to a resolution of better than 1.9 Å.

Structural analysis of new compound heterozygous variants in PEPD gene identified in a patient with Prolidase Deficiency diagnosed by exome sequencing

Prolidase Deficiency (PD) is an autosomal recessive rare disorder caused by loss or reduction of prolidase enzymatic activity due to variants in the PEPD gene. PD clinical features vary among affected individuals: skin ulcerations, recurrent infections, and developmental delay are common. In this study, we describe a 16-year-old boy with a mild PD phenotype comprising chronic eczema, recurrent infections and elevated IgE. Whole exome sequencing analysis revealed three PEPD variants: c.575T>C p.(Leu192Pro) inherited from the mother, and c.692_694del p.(Tyr231del) and c.1409G>A p.(Arg470His), both inherited from the father. The variant p.(Tyr231del) has been previously characterized by high-resolution X-ray structure analysis as altering protein dynamics/flexibility. In order to study the effects of the other two prolidase variants, we performed site directed mutagenesis purification and crystallization studies. A high-resolution X-ray structure could only be obtained for the p.(Arg470His) variant, which showed no significant structural differences in comparison to WT prolidase. On the other hand, the p.(Leu192Pro) variant led to significant protein destabilization. Hence, we conclude that the maternal p.(Leu192Pro) variant was likely causally associated with the proband´s disease, together with the known pathogenic paternal variant p.(Tyr231del). Our results demonstrated the utility of exome sequencing to perform diagnosis in PD cases with mild phenotype.

Combined high resolution X-ray and DFT Bader analysis to reveal a proposed Ru–H⋯Si interaction in Cp(IPr)Ru(H)2SiH(Ph)Cl

The compound Cp(IPr)Ru(H)2SiH(Ph)Cl (IPr = 1,3-bis(2,6-diisopropylphenyl)-imidazol-2-ylidene) (1) was subject to low temperature (30 K), high resolution X-ray structural analysis to obtain a high quality electron density map. This map was subject to a Bader analysis to ascertain the possibility of a Ru–H⋯Si interaction. For comparison, DFT calculations employing the well known B3LYP functional in conjunction with a triple zeta basis set was employed. Thus, we not only report the results of a possible Ru–H⋯Si interaction but also benchmark the use of the employed level of theory against experimental results.

固氮酶催化活性中心及其化学模拟

Nitrogenase catalyzes the reduction of dinitrogen to ammonia in the process of biological nitrogen fixation. In the past few decades, its catalytic mechanism and chemical simulation have been widely studied. The high resolution X-ray structural analysis of the MoFe protein in nitrogenase reveals the iron molybdenum cofactor (FeMo-co) as a cage structure, MoFe7S9C( R -homocit). The molybdenum atom is coordinated by three sulfur atoms, a nitrogen atom from histidine residue and two oxygen atoms from R -homocitrate. Recently, the model has been modified as a protonated structure of MoFe7S9C( R -Hhomocit). Homocitrate and imidazole sidechain may play important roles in delivering proton and stabilizing the MoFe7S9C cluster in the process of N2 reduction. However the mechanism of N2 reduction remains unclear. In this review, the chemistry of molybdenum with homocitrate and imidazole is discussed, including the iron molybdenum sulfur complexes, which will be helpful to understand the coordination environment of molybdenum atom in iron molybdenum cofactor.

ChemInform Abstract: Why Did Nature Select Phosphate for Its Dominant Roles in Biology?

AbstractReview: 49 refs.

Why did nature select phosphate for its dominant roles in biology?

Evolution has placed phosphate mono- and diesters at the heart of biology. The enormous diversity of their roles has called for the evolution of enzyme catalysts for phosphoryl transfer that are among the most proficient known. A combination of high-resolution X-ray structure analysis and 19F NMR definition of metal fluoride complexes of such enzymes, that are mimics of the transition state for the reactions catalysed, has delivered atomic detail of the nature of such catalysis for a range of phosphoryl transfer processes. The catalytic simplicity thus revealed largely explains the paradox of the contrast between the extreme stability of structural phosphate esters and the lability of phosphates in regulation and signaling processes. A brief survey of the properties of oxyacids and their esters for other candidate elements for these vital roles fails to identify a suitable alternative to phosphorus, thereby underpinning Todd’s Hypothesis “Where there’s life there’s phosphorus” as a statement of truly universal validity.

1P104 水素原子レベルでのプロトン輸送機構解明を目的としたチトクロム酸化酵素の高分解能X線結晶構造解析(ヘム蛋白質,第48回日本生物物理学会年会)

1P104 水素原子レベルでのプロトン輸送機構解明を目的としたチトクロム酸化酵素の高分解能X線結晶構造解析(ヘム蛋白質,第48回日本生物物理学会年会)

High-yield Secretion of the Recombinant Sweet-Tasting Protein Thaumatin I

Thaumatin, an intensely sweet-tasting protein used as a sweetener, was secreted by the methylotrophic yeast Pichia pastoris. Approximately 100 mg L-1 of recombinant thaumatin I was obtained using an expression vector which possesses three copies of the thaumatin gene containing the 22-amino acid pre-sequence. Expression yield was about three-fold higher than when the α-factor secretion signal from Saccharomyces cerevisiae was used. The circular dichroism and tryptophan fluorescence spectra for recombinant thaumatin I were almost the same as those for plant thaumatin. Large amounts of homogeneous recombinant thaumatin allowed for preparation of high-quality crystals in the presence of cryoprotective glycerol used in high-resolution x-ray structural analysis to help further understand the perception of the sweet taste of thaumatin.

Why did Nature select phosphate for its dominant roles in biology?

Evolution has placed phosphate mono- and diesters at the heart of biology. The enormous diversity of their roles has called for the evolution of enzyme catalysts for phosphoryl transfer that are among the most proficient known. A combination of high-resolution X-ray structure analysis and 19F NMR definition of metal fluoride complexes of such enzymes, that are mimics of the transition state for the reactions catalysed, has delivered atomic detail of the nature of such catalysis for a range of phosphoryl transfer processes. The catalytic simplicity thus revealed largely explains the paradox of the contrast between the extreme stability of structural phosphate esters and the lability of phosphates in regulation and signalling processes. A brief survey of the properties of oxyacids and their esters for other candidate elements for these vital roles fails to identify a suitable alternative to phosphorus, thereby underpinning Todd’s Hypothesis “Where there’s life there’s phosphorus” as a statement of truly universal validity.

The 1.2 Å crystal structure of an E. coli tRNA Ser acceptor stem microhelix reveals two magnesium binding sites

tRNA identity elements assure the correct aminoacylation of tRNAs by the cognate aminoacyl-tRNA synthetases. tRNA Ser belongs to the so-called class II system, in which the identity elements are rather simple and are mostly located in the acceptor stem region, in contrast to ‘class I’, where tRNA determinants are more complex and are located within different regions of the tRNA. The structure of an Escherichia coli tRNA Ser acceptor stem microhelix was solved by high resolution X-ray structure analysis. The RNA crystallizes in the space group C2, with one molecule per asymmetric unit and with the cell constants a = 35.79, b = 39.13, c = 31.37 Å, and β = 111.1°. A defined hydration pattern of 97 water molecules surrounds the tRNA Ser acceptor stem microhelix. Additionally, two magnesium binding sites were detected in the tRNA Ser aminoacyl stem.

Elucidation of the mechanism and end products of glutaraldehyde crosslinking reaction by X‐ray structure analysis

Glutaraldehyde has been used for several decades as an effective crosslinking agent for many applications including sample fixation for microscopy, enzyme and cell immobilization, and stabilization of protein crystals. Despite of its common use as a crosslinking agent, the mechanism and chemistry involved in glutaraldehyde crosslinking reaction is not yet fully understood. Here we describe feasibility study and results obtained from a new approach to investigate the process of protein crystals stabilization by glutaraldehyde crosslinking. It involves exposure of a model protein crystal (Lysozyme) to glutaraldehyde in alkaline or acidic pH for different incubation periods and reaction arrest by medium exchange with crystallization medium to remove unbound glutaraldehyde. The crystals were subsequently incubated in diluted buffer affecting dissolution of un-crosslinked crystals. Samples from the resulting solution were subjected to protein composition analysis by gel electrophoresis and mass spectroscopy while crosslinked, dissolution resistant crystals were subjected to high resolution X-ray structural analysis. Data from gel electrophoresis indicated that the crosslinking process starts at specific preferable crosslinking site by lysozyme dimer formation, for both acidic and alkaline pH values. These dimer formations were followed by trimer and tetramer formations leading eventually to dissolution resistant crystals. The crosslinking initiation site and the end products obtained from glutaraldehyde crosslinking in both pH ranges resulted from reactions between lysine residues of neighboring protein molecules and the polymeric form of glutaraldehyde. Reaction rate was much faster at alkaline pH. Different reaction end products, indicating different reaction mechanisms, were identified for crosslinking taking place under alkaline or acidic conditions.

Extended Substrate Recognition in Caspase-3 Revealed by High Resolution X-ray Structure Analysis

Caspases are cysteine proteases involved in the signalling cascades of programmed cell death in which caspase-3 plays a central role, since it propagates death signals from intrinsic and extrinsic stimuli to downstream targets. The atomic resolution (1.06 Å) crystal structure of the caspase-3 DEVD-cmk complex reveals the structural basis for substrate selectivity in the S4 pocket. A low-barrier hydrogen bond is observed between the side-chains of the P4 inhibitor aspartic acid and Asp179 of the N-terminal tail of the symmetry related p12 subunit. Site-directed mutagenesis of Asp179 confirmed the significance of this residue in substrate recognition. In the 1.06 Å crystal structure, a radiation damage induced rearrangement of the inhibitor methylketone moiety was observed. The carbon atom that in a substrate would represent the scissile peptide bond carbonyl carbon clearly shows a tetrahedral coordination and resembles the postulated tetrahedral intermediate of the acylation reaction.

Crystallization and preliminary X-ray analysis of alpha-isopropylmalate synthase from Mycobacterium tuberculosis.

alpha-Isopropylmalate synthase catalyses the aldol condensation of alpha-ketoisovalerate and acetyl coenzyme A to produce alpha-isopropylmalate. This reaction is the first committed step of leucine biosynthesis, which is interrelated with the pathways for production of the other branched-chain amino acids, valine and isoleucine. The absence of these pathways in mammals suggests that these enzymes could be useful targets for drug design against microbial pathogens. The gene for alpha-IPMS in Mycobacterium tuberculosis (Rv3710) has been cloned, expressed in Escherichia coli, both in native and selenomethionine-substituted forms, and crystallized. The SeMet crystals are suitable for high-resolution X-ray structural analysis. These crystals are monoclinic, with unit-cell parameters a = 54.25, b = 154.73, c = 68.82 angstoms, space group P2(1) and two molecules in the asymmetric unit. X-ray diffraction data to 2.0 angstroms resolution have been collected.

Crystallization and preliminary X-ray analysis of N-acetyl-1-D-myo-inosityl-2-deoxy-alpha-D-glucopyranoside deacetylase (MshB) from Mycobacterium tuberculosis.

Mycobacteria synthesize mycothiol (MSH) as a low-molecular-weight thiol that protects against oxidative stress in a similar role to that of glutathione in many other species. The absence of MSH in mammals suggests that enzymes from its biosynthetic pathway in Mycobacterium tuberculosis could be useful targets for drug design. The gene for MshB (Rv1170), the enzyme that catalyses the second step in MSH biosynthesis in M. tuberculosis, has been cloned and the protein has been expressed in Escherichia coli both in native and SeMet-substituted forms and crystallized in two crystal forms. One of these, prepared in the presence of beta-octylglucoside as a key additive, is suitable for high-resolution X-ray structural analysis. The crystals are orthorhombic, with unit-cell parameters a = 71.69, b = 83.74, c = 95.65 A, space group P2(1)2(1)2(1) and two molecules in the asymmetric unit. X-ray diffraction data to 1.9 A resolution have been collected.

Determination of the Electron Density Distribution in the Bonds of a Fullerene Derivative by High-Resolution X-Ray Structure Analysis.

Bent bonds in the strained fullerene system, restricted to the [5,6] bonds, were detected by high-resolution X-ray structure analysis of the 1,2-dihydro[60]fullerene derivative 1. In addition the maxima of electron densities are higher in the [6,6] bonds than in the [5,6] bonds-an important finding with respect to the question of the extent of electron delocalization in fullerenes.

Tetrabenzo[ab, f, jk,o][18]annulene: synthesis, crystal structure analysis, ab initio quantum-chemical studies of intermolecular interactions in the gas phase and in crystalline states, photodimerization and photopolymerization

The synthesized title compound 8 crystallizes in three different modifications, which were investigated by electron crystallography, high resolution electron microscopy and X-ray structural analysis. The formation of molecular pairs was studied by an ab initio quantum-chemical approach. The calculated “dimers” were compared to the mutual orientations of nearest neighboring molecules in the crystal structures and to covalently bonded dimers obtained by a topochemical photodimerization.

Unusual ligand structure in Ni-Fe active center and an additional Mg site in hydrogenase revealed by high resolution X-ray structure analysis.

The hydrogenase of Desulfovibrio sp. catalyzes the reversible oxidoreduction of molecular hydrogen, in conjunction with a specific electron acceptor, cytochrome c3. The Ni-Fe active center of Desulfovibrio hydrogenase has an unusual ligand structure with non-protein ligands. An atomic model at high resolution is required to make concrete assignment of the ligands which coordinate the Ni-Fe center. These in turn will provide insight into the mechanism of electron transfer, during the reaction catalysed by hydrogenase. The X-ray structure of the hydrogenase from Desulfovibrio vulgaris Miyazaki has been solved at 1.8 A resolution and refined to a crystallographic R factor of 0.229. The overall folding pattern and the spatial arrangement of the metal centers are very similar to those found in Desulfovibrio gigas hydrogenase. This high resolution crystal structure enabled us to assign the non-protein ligands to the Fe atom in the Ni-Fe site and revealed the presence of a Mg center, located approximately 13 A from the Ni-Fe active center. From the nature of the electron-density map, stereochemical geometry and atomic parameters of the refined structure, the most probable candidates for the four ligands, coordinating the Ni-Fe center, have been proposed to be diatomic S=O, C triple bond O and C triple bond N molecules and one sulfur atom. The assignment was supported by pyrolysis mass spectrometry measurements. These ligands may have a role as an electron sink during the electron transfer reaction between the hydrogenase and its biological counterparts, and they could stabilize the redox state of Fe(II), which may not change during the catalytic cycle and is independent of the redox transition of the Ni. The hydrogen-bonding system between the Ni-Fe and the Mg centers suggests the possible.

Crystallization and preliminary X-ray crystallographic analysis of chitosanase from Bacillus circulans MH-K1.

Chitosanase, an enzyme which hydrolyzes chitosan, isolated from Bacillus circulans MH-K1, was crystallized by a vapor-diffusion procedure at 293 K using ammonium sulfate as a precipitant. Rod-shaped colorless crystals, which grew to 0.05 x 0.15 x 1.2 mm within a week, belong to the orthorhombic system and the space group P222(1) or P2(1)2(1)2 with unit-cell dimensions of a = 43.3, b = 57.7, and c = 128.0 A. The asymmetric unit is thought to contain one chitosanase molecule (29 024 Da). The crystals diffract X-rays to at least 2.3 A resolution and are suitable for high-resolution X-ray structure analysis.

Mechanism of the Reaction Catalyzed by Mandelate Racemase: Importance of Electrophilic Catalysis by Glutamic Acid 317

In the high-resolution X-ray structure of mandelate racemase (MR) with the competitive inhibitor (S)-atrolactate bound in the active site [Landro, J. A., Gerlt, J. A., Kozarich, J. W., Koo, C. W., Shah, V. J., Kenyon, G. L., Neidhart, D. J., Fujita, J., & Petsko, G. A. (1994) Biochemistry 33, 635-643], the carboxylic acid group of Glu 317 is hydrogen-bonded to the carboxylate group of the bound inhibitor. This geometry suggests that the carboxylic acid functional group of Glu 317 participates as a general acid catalyst in the concerted general acid-general base catalyzed formation of a stabilized enolic tautomer of mandelic acid as a reaction intermediate. To test this hypothesis, the E317Q mutant of MR was constructed and subjected to high-resolution X-ray structural analysis in the presence of (S)-atrolactate. No conformational alterations were observed to accompany the E317Q substitution at 2.1 A resolution. The values for kcat were reduced 4.5 x 10(3)-fold for (R)-mandelate and 2.9 x 10(4)-fold for (S)-mandelate; the values for kcat/Km were reduced 3 x 10(4)-fold. The substrate and solvent deuterium isotope effects measured for both wild-type MR and the E317Q mutant are not multiplicative when deuteriated substrate is studied in D2O, which suggests that the reactions catalyzed by both enzymes are stepwise and involve the formation of stabilized enolic intermediates. In contrast to wild-type MR, E317Q does not catalyze detectable elimination of bromide ion from either enantiomer of p-(bromomethyl)mandelate. However, E317Q is irreversibly inactivated by racemic alpha-phenylglycidate at a rate comparable to that measured for wild-type MR. Taken together, these mechanistic properties confirm the importance of Glu 317 as a general acid catalyst in the reaction catalyzed by wild-type MR. The kcat for wild-type MR and the reduction in kcat observed for E317O are discussed in terms of the analysis recently described by Gerlt and Gassman for understanding the rates and mechanisms of enzyme-catalyzed proton abstraction reactions from carbon acids [Gerlt, J. A., & Gassman, P. G. (1993) J. Am. Chem. Soc. 115, 11552-11568; Gerlt, J. A., & Gassman, P. G. (1993) Biochemistry 32, 11943-11952].