Selenium Decipher: Trapping of Native Selenomethionine-Containing Peptides in Selenium-Enriched Milk and Unveiling the Deterioration after Ultrahigh-Temperature Treatment

Selenopeptide identification relies on databases to interpret the selenopeptide spectra. A common database search strategy is to set selenium as a variable modification instead of sulfur on peptides. However, this approach generally detects only a fraction of selenopeptides. An alternative approach, termed Selenium Decipher, is proposed in the present study. It involves identifying collision-induced dissociation-cleavable selenomethionine-containing peptides by iteratively matching the masses of seleno-amino acids in selenopeptide spectra. This approach uses variable-data-independent acquisition (vDIA) for peptide detection, providing a flexible and customizable window for secondary mass spectral fragmentation. The attention mechanism was used to capture global information on peptides and determine selenomethionine-containing peptide backbones. The core structure of selenium on selenomethionine-containing peptides generates a series of fragment ions, namely, C3H7Se+, C4H10NSe+, C5H7OSe+, C5H8NOSe+, and C7H11N2O2Se+, with known mass gaps during higher-energy collisional dissociation (HCD) fragmentation. De-selenium spectra are generated by removing selenium originating from selenium replacement and then reassigning the precursors to peptides. Selenium-enriched milk is obtained by feeding selenium-rich forage fed to cattle, which leads to the formation of native selenium through biotransformation. A novel antihypertensive selenopeptide Thr-Asp-Asp-Ile-SeMet-Cys-Val-Lys TDDI(Se)MCVK was identified from selenium-enriched milk. The selenopeptide (IC50 = 60.71 μM) is bound to four active residues of the angiotensin-converting enzyme (ACE) active pocket (Ala354, Tyr523, His353, and His513) and two active residues of zinc ligand (His387 and Glu411) and exerted a competitive inhibitory effect on the spatial blocking of active sites. The integration of vDIA and the iteratively matched seleno-amino acids was applied for Selenium Decipher, which provides high validity for selenomethionine-containing peptide identification.

82Se Metabolically-Labeled Yeast as a Matrix-Matched Isotope Dilution Standard for Quantification of Selenomethionine

Selenized yeast is commonly used as a highly bioavailable source of selenium in dietary supplements and feed additives and is used in research settings in various disciplines due to the large number of selenium-containing metabolites formed during growth. With the selenomethionine being the major form of selenium present in selenized yeasts, its accurate quantitation is essential, however, values are frequently underestimated due to the costly and time-consuming hydrolysis-based sample preparation required to release the selenoamino acid from proteins for analysis. The National Research Council Canada has developed an 82-Se-enriched selenized yeast Certified Reference Material, SEEY-1 (DOI: 10.4224/crm.2023.seey-1) intended to be used as a matrix-matched spike material for isotope dilution analysis of selenized yeasts. The total selenium and selenomethionine contents of SEEY-1 were determined to be 322.1 ± 4.8 mg/kg (k = 2) and 635.6 ± 16.8 mg/kg (k = 2), respectively. Here we present results on the preparation of the 82-Se-enriched yeast, the certification process, and provide an example of the use of SEEY-1 as a matrix-matched spike for the analysis of selenomethionine in a sample of selenized yeast. We demonstrate here that SEEY-1 is able to compensate for the partial digestion of yeast proteins and provide reliable analytical data on Se amino acid content in under an hour instead of the 16 hours required for conventional complete acid hydrolysis.

Chalcogen Bonds Involving Selenium in Protein Structures

Chalcogen bonds are the specific interactions involving group 16 elements as electrophilic sites. The role of chalcogen atoms as sticky sites in biomolecules is underappreciated, and the few available studies have mostly focused on S. Here, we carried out a statistical analysis over 3562 protein structures in the Protein Data Bank (PDB) containing 18 266 selenomethionines and found that Se···O chalcogen bonds are commonplace. These findings may help the future design of functional peptides and contribute to understanding the role of Se in nature.

Expression, purification and crystallization of the N-terminal Solanaceae domain of the Sw-5b NLR immune receptor

Plant nucleotide-binding domain and leucine-rich repeat receptors (NLRs) play crucial roles in recognizing pathogen effectors and activating plant immunity. The tomato NLR Sw-5b is a coiled-coil NLR (CC-NLR) immune receptor that confers resistance against tospoviruses, which cause serious economic losses in agronomic crops worldwide. Compared with other CC-NLRs, Sw-5b possesses an extended N-terminal Solanaceae domain (SD). The SD of Sw-5b is critical for recognition of the tospovirus viral movement protein NSm. An SD is also frequently detected in many NLRs from Solanaceae plants. However, no sequences homologous to the SD have been detected in animals or in plants other than Solanaceae. The properties of the SD protein are largely unknown, and thus 3D structural information is vital in order to better understand its role in pathogen perception and the activation of immune receptors. Here, the expression, purification and crystallization of Sw-5b SD (amino acids 1-245) are reported. Native and selenomethionine-substituted crystals of the SD protein belonged to space group P3112, with unit-cell parameters a = 81.53, b = 81.53, c = 98.44 Å and a = 81.63, b = 81.63, c = 98.80 Å, respectively. This is the first report of a structural study of the noncanonical SD domain of the NLR proteins from Solanaceae plants.

Methionine and Selenomethionine as Energy Transfer Acceptors for Biomolecular Structure Elucidation in the Gas Phase

Mass spectrometry affords rapid and sensitive analysis of peptides and proteins. Coupling spectroscopy with mass spectrometry allows for the development of new methods to enhance biomolecular structure determination. Herein, we demonstrate two new energy acceptors that can be utilized for action-excitation energy transfer experiments. In the first system, C-S bonds in methionine act as energy acceptors from native chromophores, including tyrosine, tryptophan, and phenylalanine. Comparison among chromophores reveals that tyrosine transfers energy most efficiently at 266 nm, but phenylalanine and tryptophan also transfer energy with comparable efficiencies. Overall, the C-S bond dissociation yields following energy transfer are low for methionine, which led to an investigation of selenomethionine, a common analog that is found in many naturally occurring proteins. Sulfur and selenium are chemically similar, but C-Se bonds are weaker than C-S bonds and have lower lying σ* anti-bonding orbitals. Excitation of peptides containing tyrosine and tryptophan results in efficient energy transfer to selenomethionine and abundant C-Se bond dissociation. A series of helical peptides were examined where the positions of the donor or acceptor were systematically scanned to explore the influence of distance and helix orientation on energy transfer. The distance was found to be the primary factor affecting energy transfer efficiency, suggesting that selenomethionine may be a useful acceptor for probing protein structure in the gas phase.

Seleno-l-methionine and l-ascorbic acid differentiate the biological activity of doxorubicin and its metal complexes as a new anticancer drugs candidate

The most important problems of anti-cancer therapy include the toxicity of the drugs applied to healthy cells and the multi-drug cells resistance to chemotherapeutics. One of the most commonly used anticancer drugs is doxorubicin (DOX) used to treat certain leukemias and non-Hodgkin's lymphomas, as well as bladder, breast, stomach, lung, ovarian, thyroid, multiple myeloma and other cancers. Preliminary studies showed that metal complex with DOX improve its cytostatic activity with changes in their molecular structure and distribution of electrons, resulting in a substantial change of its biological activity (including antitumor activity). Thus, there is a chance to receiving derivatives of DOX with low toxicity for the healthy body cells, thus increasing its therapeutic selectivity. In the present study we examined the influence of Mn, Mg, Fe, Co and Ni, seleno-l-methionine and vitamin C on biological activity of DOX in prokaryotic model - Escherichia coli RFM443, with plasmid transcriptional fusion of recA promoter and luxCDABE as a reporter gene. Cytotoxic potency of tested chemicals was calculated on the basis of the bacteria culture growth inhibition (GI%) values. Genotoxic properties were calculated on the basis of the fold increase (FI) of relative luminescence units (RLU) values compared to control. Obtained results showed that doxorubicin metal complexes particularly with Ni, Co and Fe increased the cyto- and genotoxic activities of DOX. Bacteria culture supplemented with SeMet and vitamin C differentiate the DOX and its metal complexes toxicity. It seems, that DOX-Ni, DOX-Fe and DOX-Co complexes could be potent cytostatic drug candidates. Moreover, we noticed different sensitivity of recA::luxCDABE for 3 h and 24 h cultures of bacteria strain. It suggests, that the potency of genetic construct reactivity- recA::luxCDABE in E. coli depends on the growth-phase of bacterial culture.

Crystallization and X-ray diffraction analysis of native and selenomethionine-substituted PhyH-DI from Bacillus sp. HJB17

Phytases are phosphatases that hydrolyze phytates to less phosphorylated myo-inositol derivatives and inorganic phosphate. β-Propeller phytases, which are very diverse phytases with improved thermostability that are active at neutral and alkaline pH and have absolute substrate specificity, are ideal substitutes for other commercial phytases. PhyH-DI, a β-propeller phytase from Bacillus sp. HJB17, was found to act synergistically with other single-domain phytases and can increase their efficiency in the hydrolysis of phytate. Crystals of native and selenomethionine-substituted PhyH-DI were obtained using the vapour-diffusion method in a condition consisting of 0.2 M sodium chloride, 0.1 M Tris pH 8.5, 25%(w/v) PEG 3350 at 289 K. X-ray diffraction data were collected to 3.00 and 2.70 Å resolution, respectively, at 100 K. Native PhyH-DI crystals belonged to space group C121, with unit-cell parameters a = 156.84, b = 45.54, c = 97.64 Å, α = 90.00, β = 125.86, γ = 90.00°. The asymmetric unit contained two molecules of PhyH-DI, with a corresponding Matthews coefficient of 2.17 Å3 Da-1 and a solvent content of 43.26%. Crystals of selenomethionine-substituted PhyH-DI belonged to space group C2221, with unit-cell parameters a = 94.71, b = 97.03, c = 69.16 Å, α = β = γ = 90.00°. The asymmetric unit contained one molecule of the protein, with a corresponding Matthews coefficient of 2.44 Å3 Da-1 and a solvent content of 49.64%. Initial phases for PhyH-DI were obtained from SeMet SAD data sets. These data will be useful for further studies of the structure-function relationship of PhyH-DI.

Spectroscopic Evidences for Strong Hydrogen Bonds with Selenomethionine in Proteins

Careful protein structure analysis unravels many unknown and unappreciated noncovalent interactions that control protein structure; one such unrecognized interaction in protein is selenium centered hydrogen bonds (SeCHBs). We report, for the first time, SeCHBs involving the amide proton and selenium of selenomethionine (Mse), i.e., amide-N-H···Se H-bonds discerned in proteins. Using mass selective and conformer specific high resolution vibrational spectroscopy, gold standard quantum chemical calculations at CCSD(T), and in-depth protein structure analysis, we establish that amide-N-H···Se and amide-N-H···Te H-bonds are as strong as conventional amide-NH···O and amide-NH···O═C H-bonds despite smaller electronegativity of selenium and tellurium than oxygen. It is in fact, electronegativity, atomic charge, and polarizability of the H-bond acceptor atoms are at play in deciding the strength of H-bonds. The amide-N-H···Se and amide-N-H···Te H-bonds presented here are not only new additions to the ever expanding world of noncovalent interactions, but also are of central importance to design new force-fields for better biomolecular structure simulations.

Structure of the cyanobactin oxidase ThcOx from Cyanothece sp. PCC 7425, the first structure to be solved at Diamond Light Source beamline I23 by means of S-SAD

Determination of protein crystal structures requires that the phases are derived independently of the observed measurement of diffraction intensities. Many techniques have been developed to obtain phases, including heavy-atom substitution, molecular replacement and substitution during protein expression of the amino acid methionine with selenomethionine. Although the use of selenium-containing methionine has transformed the experimental determination of phases it is not always possible, either because the variant protein cannot be produced or does not crystallize. Phasing of structures by measuring the anomalous diffraction from S atoms could in theory be almost universal since almost all proteins contain methionine or cysteine. Indeed, many structures have been solved by the so-called native sulfur single-wavelength anomalous diffraction (S-SAD) phasing method. However, the anomalous effect is weak at the wavelengths where data are normally recorded (between 1 and 2 Å) and this limits the potential of this method to well diffracting crystals. Longer wavelengths increase the strength of the anomalous signal but at the cost of increasing air absorption and scatter, which degrade the precision of the anomalous measurement, consequently hindering phase determination. A new instrument, the long-wavelength beamline I23 at Diamond Light Source, was designed to work at significantly longer wavelengths compared with standard synchrotron beamlines in order to open up the native S-SAD method to projects of increasing complexity. Here, the first novel structure, that of the oxidase domain involved in the production of the natural product patellamide, solved on this beamline is reported using data collected to a resolution of 3.15 Å at a wavelength of 3.1 Å. The oxidase is an example of a protein that does not crystallize as the selenium variant and for which no suitable homology model for molecular replacement was available. Initial attempts collecting anomalous diffraction data for native sulfur phasing on a standard macromolecular crystallography beamline using a wavelength of 1.77 Å did not yield a structure. The new beamline thus has the potential to facilitate structure determination by native S-SAD phasing for what would previously have been regarded as very challenging cases with modestly diffracting crystals and low sulfur content.

Trifluoroselenomethionine: A New Unnatural Amino Acid

Trifluoroselenomethionine (TFSeM), a new unnatural amino acid, was synthesized in seven steps from N-(tert-butoxycarbonyl)-l-aspartic acid tert-butyl ester. TFSeM shows enhanced methioninase-induced cytotoxicity, relative to selenomethionine (SeM), toward HCT-116 cells derived from human colon cancer. Mechanistic explanations for this enhanced activity are computationally and experimentally examined. Comparison of TFSeM and SeM by selenium EXAFS and DFT calculations showed them to be spectroscopically and structurally very similar. Nonetheless, when two different variants of the protein GB1 were expressed in an Escherichia coli methionine auxotroph cell line in the presence of TFSeM and methionine (Met) in a 9:1 molar ratio, it was found that, surprisingly, 85 % of the proteins contained SeM residues, even though no SeM had been added, thus implying loss of the trifluoromethyl group from TFSeM. The transformation of TFSeM into SeM is enzymatically catalyzed by E. coli extracts, but TFSeM is not a substrate of E. coli methionine adenosyltransferase.

Characterization of the NTPR and BD1 interacting domains of the human PICH-BEND3 complex

Chromosome integrity depends on DNA structure-specific processing complexes that resolve DNA entanglement between sister chromatids. If left unresolved, these entanglements can generate either chromatin bridging or ultrafine DNA bridging in the anaphase of mitosis. These bridge structures are defined by the presence of the PICH protein, which interacts with the BEND3 protein in mitosis. To obtain structural insights into PICH-BEND3 complex formation at the atomic level, their respective NTPR and BD1 domains were cloned, overexpressed and crystallized using 1.56 M ammonium sulfate as a precipitant at pH 7.0. The protein complex readily formed large hexagonal crystals belonging to space group P6122, with unit-cell parameters a = b = 47.28, c = 431.58 Å and with one heterodimer in the asymmetric unit. A complete multiwavelength anomalous dispersion (MAD) data set extending to 2.2 Å resolution was collected from a selenomethionine-labelled crystal at the Swiss Light Source.

An overview of heavy-atom derivatization of protein crystals

Heavy-atom derivatization is one of the oldest techniques for obtaining phase information for protein crystals and, although it is no longer the first choice, it remains a useful technique for obtaining phases for unknown structures and for low-resolution data sets. It is also valuable for confirming the chain trace in low-resolution electron-density maps. This overview provides a summary of the technique and is aimed at first-time users of the method. It includes guidelines on when to use it, which heavy atoms are most likely to work, how to prepare heavy-atom solutions, how to derivatize crystals and how to determine whether a crystal is in fact a derivative.

Synthesis of a Novel Cysteine-Incorporated Anthraquinone Derivative and Its Structural Properties

A novel cysteine-incorporated anthraquinone derivative was synthesized, and its molecular structure was determined by X-ray crystal analysis. Each mercapto group was located separately and did not form a disulfide bond, and hydrogen bondings and π-π interaction were observed from the packing structure.

Cloning, expression, purification, crystallization and X-ray crystallographic analysis of CofB, the minor pilin subunit of CFA/III from human enterotoxigenic Escherichia coli

Colonization factor antigen III (CFA/III) is one of the virulence factors of human enterotoxigenic Escherichia coli (ETEC) that forms the long, thin, proteinaceous fibres of type IV pili through assembly of its major and minor subunits CofA and CofB, respectively. The crystal structure of CofA has recently been reported; however, the lack of structural information for CofB, the largest among the known type IV pilin subunits, hampers a comprehensive understanding of CFA/III pili. In this study, constructs of wild-type CofB with an N-terminal truncation and the corresponding SeMet derivative were cloned, expressed, purified and crystallized. The crystals belonged to the rhombohedral space group R32, with unit-cell parameters a = b = 103.97, c = 364.57 Å for the wild-type construct and a = b = 103.47, c = 362.08 Å for the SeMet-derivatized form. Although the diffraction quality of these crystals was initially very poor, dehydration of the crystals substantially improved the resolution limit from ∼ 4.0 to ∼ 2.0 Å. The initial phase was solved by the single-wavelength anomalous dispersion (SAD) method using a dehydrated SeMet CofB crystal, which resulted in an interpretable electron-density map.

Dietary supplementation of organic selenium could improve performance, antibody response, and yolk oxidative stability in laying hens fed on diets containing oxidized fat

The present study was carried out to investigate the effect of dietary supplementation of organic selenium (Se) on performance, egg quality indices, and yolk oxidative stability in laying hens fed diets with different fat sources. A total of 270 Hy-line W-36 Leghorn hens of 47 weeks of age were randomly distributed into the 5 replicate cages of 9 dietary treatments. Experimental diets consisted of a 3 × 3 factorial arrangement of treatments with three different fat sources (soybean oil, SO; yellow grease, YG; and palm fat powder, PFP) and three different levels of supplemental Se (0, 0.2, and 0.4 mg/kg of diet) as supplied by zinc-L-selenomethionine (ZnSeMet) complex, which fed during a 77-day feeding trial including 7 days for adaptation and 70 days as the main recording period. Results showed that the highest (P < 0.05) egg weights assigned to the hens fed on SO-supplemented diets. Hen-day egg production was affected by both dietary fat source (P < 0.01) and Se level (P < 0.05) throughout the trial period. Regardless of dietary fat source, dietary supplementation of ZnSeMet improved (P < 0.05) egg mass during all trial periods. Moreover, the significant (P < 0.05) fat  source× Se interactions were observed for egg mass, so that dietary supplementation with 0.4 mg/kg Se was more effective in diets supplemented with YG. Although feed intake was not affected by experimental diets during the first 35-day period, dietary inclusion of PFP reduced feed intake during both second 35-day (P < 0.01) and entire trial period (P < 0.05). The best (P < 0.01) feed conversion ratio during the first 35-day period was assigned to the birds fed on SO-diets, followed by those fed YG-diets. Dietary supplementation of ZnSeMet improved (P < 0.05) feed efficiency during the first 35-day period. Supplementation of ZnSeMet into the diets increased yolk index, with more impact in hens fed on YG-diets. The highest concentration of yolk malondialdehyde was observed in YG-fed groups, and ZnSeMet supplementation of diets decreased (P < 0.05) yolk malondialdehyde. The highest (P<0.01) glutathione peroxidase activity was observed for hens fed on diets supplemented by YG, followed by those on SO-diets. Although different fat sources had no effect on antibody titer against Newcastle disease virus, supplemental ZnSeMet improved (P < 0.05) antibody response. The present findings indicate that dietary supplementation of ZnSeMet could improve performance parameters and egg oxidative stability in laying hens, with the highest impact in diets containing oxidized (high peroxide values) fat sources.

p-Cyanophenylalanine and selenomethionine constitute a useful fluorophore-quencher pair for short distance measurements: application to polyproline peptides

The C≡N stretching frequency and fluorescence quantum yield of p-cyanophenylalanine are sensitive to environment. As such, this unnatural amino acid has found broad applications, ranging from studying how proteins fold to determining the local electric field of membranes. Herein, we demonstrate that the fluorescence of p-cyanophenylalanine can be quenched by selenomethionine through an electron transfer process occurring at short distances, thus further expanding its spectroscopic utility. Using this fluorophore-quencher pair, we are able to show that short polyproline peptides (1-4 prolines) are not rigid; instead, they sample a bimodal conformational distribution.

Crystallization of the carboxy-terminal region of the bacteriophage T4 proximal long tail fibre protein gp34

The phage-proximal part of the long tail fibres of bacteriophage T4 consists of a trimer of the 1289 amino-acid gene product 34 (gp34). Different carboxy-terminal parts of gp34 have been produced and crystallized. Crystals of gp34(726-1289) diffracting X-rays to 2.9 Å resolution, crystals of gp34(781-1289) diffracting to 1.9 Å resolution and crystals of gp34(894-1289) diffracting to 3.0 and 2.0 Å resolution and belonging to different crystal forms were obtained. Native data were collected for gp34(726-1289) and gp34(894-1289), while single-wavelength anomalous diffraction data were collected for selenomethionine-containing gp34(781-1289) and gp34(894-1289). For the latter, high-quality anomalous signal was obtained.

Structural modeling of djenkolic acid with sulfur replaced by selenium and tellurium

The comparative structural modeling of djenkolic acid and its derivatives containing selenium and tellurium in chalcogen sites (Ch = Se, Te) has provided detailed information about the bond lengths and bond angles, filling the gap in what we know about the structural characteristics of these aminoacids. The investigation using the molecular mechanics technique with good approximation confirmed the available information on X-ray refinements for the related compounds methionine and selenomethionine, as well as for an estimate made earlier for telluromethionine. It was shown that the Ch-C(3) and Ch-C(4) bond lengths grow in parallel with the increasing anionic radii. Although the distances C-C, C-O, and C-N are very similar, the geometry of conformers is quite different owing to the possibility of rotation about four carbon atoms, hence the remarkable variability observed in dihedral angles. It was shown that the compounds contain a rigid block with two Ch atoms connected through a methylene group. The standard program Gaussian 03 with graphical interface Gaussview 4.1.2 has proved to be satisfactory tool for the structural description of less-common bioactive compositions when direct X-ray results are absent.

Structural characterization of a novel autonomous cohesin from Ruminococcus flavefaciens

Ruminococcus flavefaciens is a cellulolytic bacterium found in the rumen of herbivores and produces one of the most elaborate and variable cellulosome systems. The structure of an R. flavefaciens protein (RfCohG, ZP_06142108), representing a freestanding (non-cellulosomal) type III cohesin module, has been determined. A selenomethionine derivative with a C-terminal histidine tag was crystallized and diffraction data were measured to 2.44 Å resolution. Its structure was determined by single-wavelength anomalous dispersion, revealing eight molecules in the asymmetric unit. RfCohG exhibits the most complex among all known cohesin structures, possessing four α-helical elements and a topographical protuberance on the putative dockerin-binding surface.

Protective effect of selenomethionine on aflatoxin B1-induced oxidative stress in MDCK cells

AFB1 is a mycotoxin which exerts their cytotoxicity through increasing oxidative damage in target organ. Kidney is one of target organs vulnerable to damage caused by AFB1. In this study, Madin-Darby canine kidney (MDCK) cells were used to evaluate the AFB1-induced cell damage by the MTT assay. The results revealed that the toxic effect of AFB1 on MDCK cells is both dose and time dependent. Half maximal toxic concentration (IC50) was noted at 0.25 μg/ml of AFB1. Further, protective effect of six different concentrations (0.2, 0.8, 1, 2, 4, and 8 μM) of selenomethionine (SeMet) was observed against 0.25 μg/ml of AFB1-induced damage. The results showed that 0.25 μg/ml of AFB1 caused significant increase in oxidative stress, which was demonstrated by significant increase of malondialdehyde (MDA) level, reduction of intracellular GSH level, as well as GPX1 activity and mRNA level in MDCK cells when compared with control. SeMet protected the cells from AFB1-induced oxidative damage in a dose-dependant manner. Good protection could be achieved between 1 and 4 μM of concentration. Amid this range, MDA level significantly decreased while intracellular GSH level and GPX1 activity in addition to mRNA level significantly increased. Moreover, cell viability was significantly improved. It could be concluded that SeMet is a potential antioxidative agent to alleviate AFB1-induced oxidative stress.

Combining secondary-structure and protein solvent-accessibility predictions in methionine substitution for anomalous dispersion

In X-ray crystallographic analysis, the single-wavelength and multi-wavelength anomalous diffraction (SAD and MAD) methods have been widely used in order to solve the phase problem. Selenium-labelled methionine has been shown to be very effective for anomalous dispersion phasing, and at least one selenomethionine is required for every 100 amino acids. Some proteins, such as the Arabidopsis thaliana thylakoid lumen protein AtTLP18.3, can be overexpressed in an Escherichia coli system and high-quality protein crystals can be obtained. However, AtTLP18.3 contains no methionine residues, and site-directed mutagenesis was required in order to introduce methionine residues into the protein. A criterion for the mutated residues is that they should avoid affecting the structure and function. In this study, several leucine and isoleucine residues were selected for methionine substitution by combining secondary-structure and solvent-accessibility predictions. From the secondary-structure prediction, mutated residues were first determined in the coil or loop regions at the junction of two secondary structures. Since leucine and isoleucine residues are hydrophobic and are normally buried within the protein core, these residues should have a higher solvent-accessibility prediction so that they would be partially buried or exposed in the protein. In addition, five residues (Leu107, Leu202, Ile133, Leu128 and Ile159) of AtTLP18.3 were mutated to methionine residues. After overexpression and purification, only two single-mutant lines, L128M and I159M, could be crystallized. Finally, a double-mutation line of truncated AtTLP18.3 with L128M and I159M mutations was constructed. The structure of the double mutant AtTLP18.3 protein was resolved using the single-wavelength anomalous diffraction method at 2.6 Å resolution. The results indicated that a combination of secondary-structure and solvent-accessibility prediction for methionine substitution is a useful method in SAD and MAD phasing.

Crystallization and preliminary X-ray crystallographic analysis of the amylomaltase from Corynebacterium glutamicum

Amylomaltase (AM; EC 2.4.1.25) belongs to the 4-α-glucanotransferase group of the α-amylase family. The enzyme can produce cycloamylose or large-ring cyclodextrin through intramolecular transglycosylation or cyclization reactions of α-1,4-glucan. Amylomaltase from the mesophilic bacterium Corynebacterium glutamicum (CgAM) contains extra residues at the N-terminus for which the three-dimensional structure is not yet known. In this study, CgAM was overexpressed and purified to homogeneity using DEAE FF and Phenyl FF columns. The purified CgAM was crystallized by the vapour-diffusion method. Preliminary X-ray data showed that the CgAM crystal diffracted to 1.7 Å resolution and belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 73.28, b = 82.61, c = 118.64 Å. To obtain the initial phases, crystals of selenomethionyl-substituted amylomaltase were produced, and multiple-wavelength anomalous dispersion phasing and structure refinement are now in progress.

Structure of isochorismate synthase DhbC from Bacillus anthracis

The isochorismate synthase DhbC from Bacillus anthracis is essential for the biosynthesis of the siderophore bacillibactin by this pathogenic bacterium. The structure of the selenomethionine-substituted protein was determined to 2.4 Å resolution using single-wavelength anomalous diffraction. B. anthracis DhbC bears the strongest resemblance to the Escherichia coli isochorismate synthase EntC, which is involved in the biosynthesis of another siderophore, namely enterobactin. Both proteins adopt the characteristic fold of other chorismate-utilizing enzymes, which are involved in the biosynthesis of various products, including siderophores, menaquinone and tryptophan. The conservation of the active-site residues, as well as their spatial arrangement, suggests that these enzymes share a common Mg(2+)-dependent catalytic mechanism.

Structure of an atypical periplasmic adaptor from a multidrug efflux pump of the spirochete Borrelia burgdorferi

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Periplasmic adaptors are essential to tripartite drug efflux pump assembly.

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We present the structure of the periplasmic adaptor BesA from Borrelia burgdorferi.

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BesA lacks the α-hairpin shown to underpin exit duct recruitment and pump assembly.

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Recruitment of the TolC exit duct must be different in this pump.

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The BesA structure has implications for proposed models of pump assembly.

Periplasmic adaptor proteins are essential components of bacterial tripartite multidrug efflux pumps. Here we report the 2.35 Å resolution crystal structure of the BesA adaptor from the spirochete Borrelia burgdorferi solved using selenomethionine derivatized protein. BesA shows the archetypal linear, flexible, multi-domain architecture evident among proteobacteria and retains the lipoyl, β-barrel and membrane-proximal domains that interact with the periplasmic domains of the inner membrane transporter. However, it lacks the α-hairpin domain shown to establish extensive coiled-coil interactions with the periplasmic entrance helices of the outer membrane-anchored TolC exit duct. This has implications for the modelling of assembled tripartite efflux pumps.

The use of a mini-κ goniometer head in macromolecular crystallography diffraction experiments

Most macromolecular crystallography (MX) diffraction experiments at synchrotrons use a single-axis goniometer. This markedly contrasts with small-molecule crystallography, in which the majority of the diffraction data are collected using multi-axis goniometers. A novel miniaturized κ-goniometer head, the MK3, has been developed to allow macromolecular crystals to be aligned. It is available on the majority of the structural biology beamlines at the ESRF, as well as elsewhere. In addition, the Strategy for the Alignment of Crystals (STAC) software package has been developed to facilitate the use of the MK3 and other similar devices. Use of the MK3 and STAC is streamlined by their incorporation into online analysis tools such as EDNA. The current use of STAC and MK3 on the MX beamlines at the ESRF is discussed. It is shown that the alignment of macromolecular crystals can result in improved diffraction data quality compared with data obtained from randomly aligned crystals.

Crystallization and preliminary X-ray analysis of human leukocyte cell-derived chemotaxin 2 (LECT2)

Human leukocyte cell-derived chemotaxin 2 (LECT2) is a chemotactic factor for neutrophils that plays multifunctional roles in liver regeneration, regulation of neuritic development and proliferation of chondrocytes and osteoblasts. In addition, the C-terminal region of LECT2 belongs to the zinc metalloendopeptidase M23 (PF01551) family. Purified LECT2 was crystallized using the sitting-drop vapour-diffusion method at 293 K. Crystals of selenomethionine-substituted LECT2 that diffracted X-rays to 1.94 Å resolution were obtained using a reservoir solution consisting of 0.2 M ammonium sulfate, 0.1 M HEPES pH 7.5, 25%(w/v) PEG 8000. The crystal belonged to space group P2₁2₁2₁, with unit-cell parameters a=59.4, b=63.5, c=64.0 Å. The calculated Matthews coefficient (VM=2.10 Å3 Da(-1), solvent content 40%) indicates that the crystal consists of two molecules per asymmetric unit.

Expression, purification, crystallization and preliminary X-ray crystallographic analysis of the L,D-transpeptidase LdtMt1 from Mycobacterium tuberculosis

Mycobacterium tuberculosis is capable of adapting to prolonged periods of dormancy, a state which is resistant to killing by antimycobacterial agents. The L,D-transpeptidation reaction catalysed by the L,D-transpeptidase LdtMt1 is likely to play an essential role in the adaptation of M. tuberculosis to its dormant state. LdtMt1 has been successfully crystallized using vapour-diffusion methods. The crystals of this protein belonged to space group P6₅22, with unit-cell parameters a=57.25, b=57.25, c=257.96 Å, α=90, β=90, γ=120°. Diffraction data have also been collected from a selenomethionine derivative to 2.9 Å resolution. Model building using the phases derived from the multiwavelength anomalous dispersion experiment is in progress.

Se-adenosyl-L-selenomethionine cofactor analogue as a reporter of protein methylation

Posttranslational methylation by S-adenosyl-L-methionine(SAM)-dependent methyltransferases plays essential roles in modulating protein function in both normal and disease states. As such, there is a growing need to develop chemical reporters to examine the physiological and pathological roles of protein methyltransferases. Several sterically bulky SAM analogues have previously been used to label substrates of specific protein methyltransferases. However, broad application of these compounds has been limited by their general incompatibility with native enzymes. Here we report a SAM surrogate, ProSeAM (propargylic Se-adenosyl-l-selenomethionine), as a reporter of methyltransferases. ProSeAM can be processed by multiple protein methyltransferases for substrate labeling. In contrast, sulfur-based propargylic SAM undergoes rapid decomposition at physiological pH, likely via an allene intermediate. In conjunction with fluorescent/affinity-based azide probes, copper-catalyzed azide-alkyne cycloaddition chemistry, in-gel fluorescence visualization and proteomic analysis, we further demonstrated ProSeAM's utility to profile substrates of endogenous methyltransferases in diverse cellular contexts. These results thus feature ProSeAM as a convenient probe to study the activities of endogenous protein methyltransferases.

Selenate-enriched urea granules are a highly effective fertilizer for selenium biofortification of paddy rice grain

This study examined the effects of applied selenium (Se) species, time of application, method of application, and soil water management regimen on the accumulation of Se in rice plants. Plants were grown to maturity in a temperature- and humidity-controlled growth chamber using three water management methods: field capacity (FC), submerged until harvest, and submerged and drained 2 weeks before harvest. Two Se species, selenate (SeO4(2-)) and selenite (SeO3(2-)), were applied at a rate equivalent to 30 g ha(-1). Four application methods were employed as follows: (i) Se applied at soil preparation, (ii) Se-enriched urea granules applied to floodwater at heading; (iii) foliar Se applied at heading; and (iv) fluid fertilizer Se applied to soil or floodwater at heading. Total Se concentrations in rice grains, husks, leaves, culms, and roots were measured, as well as Se speciation in grains from the Se-enriched urea granule treatment. Highest Se concentrations in the grain occurred with SeO4(2-) and with fertilizer applied at heading stage; SeO4(2-)-enriched urea granules applied at heading increased grain Se concentrations 5-6-fold (by 450-600 μg kg(-1)) compared to the control (no fertilizer Se applied) in all water treatments. Under paddy conditions other Se fertilization strategies were much less effective. Drainage before harvesting caused Se to accumulate in/on rice roots, possibly through adsorption onto iron plaque on roots. Rice grains contained Se mainly in the organic form as selenomethionine (SeM), which comprised >90% of the total grain Se in treatments fertilized with SeO4(2-)-enriched urea granules. The results of this study clearly show that of the fertilizer strategies tested biofortification of Se in rice grains can best be achieved in lowland rice by broadcast application of SeO4(2-)-enriched urea granules to floodwater at heading stage.

Interactions between methylmercury and selenomethionine injected into mallard eggs

Methylmercury chloride and seleno-L-methionine were injected separately or in combinations into mallard eggs (Anas platyrhynchos), and embryo mortality and teratogenic effects (deformities) were modeled using a logistic regression model. Methylmercury was injected at doses that resulted in concentrations of 0, 0.2, 0.4, 0.8, and 1.6 µg/g Hg in the egg on a wet weight basis and selenomethionine at doses that resulted in concentrations of 0, 0.1, 0.2, 0.4, and 0.6 µg/g Se in the egg, also on a wet weight basis. When selenomethionine and methylmercury were injected separately, hatching probability decreased in both cases. However, when methylmercury was injected at 1.6 µg/g in combination with selenomethionine at 0.2 µg/g, the presence of the methylmercury resulted in less embryo mortality than had been seen with 0.2 µg/g Se by itself, but it increased the number of deformed embryos and hatchlings. Selenomethionine appeared to be more embryotoxic than equivalent doses of methylmercury when injected into eggs, and both injected methylmercury and selenomethionine were more toxic to mallard embryos than when deposited naturally in the egg by the mother. The underlying mechanisms behind the interactions between methylmercury and selenomethionine and why methylmercury appeared to improve hatching probability of Se-dosed eggs yet increased deformities when the two compounds were combined are unclear. These findings warrant further studies to understand these mechanisms in both laboratory and field settings.

Catalytic activity of selenomethionine in removing amino acid, peptide, and protein hydroperoxides

Selenium is a critical trace element, with deficiency associated with numerous diseases including cardiovascular disease, diabetes, and cancer. Selenomethionine (SeMet; a selenium analogue of the amino acid methionine, Met) is a major form of organic selenium and an important dietary source of selenium for selenoprotein synthesis in vivo. As selenium compounds can be readily oxidized and reduced, and selenocysteine residues play a critical role in the catalytic activity of the key protective enzymes glutathione peroxidase and thioredoxin reductase, we investigated the ability of SeMet (and its sulfur analogue, Met) to scavenge hydroperoxides present on amino acids, peptides, and proteins, which are key intermediates in protein oxidation. We show that SeMet, but not Met, can remove these species both stoichiometrically and catalytically in the presence of glutathione (GSH) or a thioredoxin reductase (TrxR)/thioredoxin (Trx)/NADPH system. Reaction of the hydroperoxide with SeMet results in selenoxide formation as detected by HPLC. Recycling of the selenoxide back to SeMet occurs rapidly with GSH, TrxR/NADPH, or a complete TrxR/Trx/NADPH reducing system, with this resulting in an enhanced rate of peroxide removal. In the complete TrxR/Trx/NADPH system loss of peroxide is essentially stoichiometric with NADPH consumption, indicative of a highly efficient system. Similar reactions do not occur with Met under these conditions. Studies using murine macrophage-like J774A.1 cells demonstrate a greater peroxide-removing capacity in cells supplemented with SeMet, compared to nonsupplemented controls. Overall, these findings demonstrate that SeMet may play an important role in the catalytic removal of damaging peptide and protein oxidation products.

Interactions of Cu(I) with selenium-containing amino acids determined by NMR, XAS, and DFT studies

Cu(I) coordination by organoselenium compounds was recently reported as a mechanism for their prevention of copper-mediated DNA damage. To establish whether direct Se-Cu coordination may be involved in selenium antioxidant activity, Cu(I) coordination of the selenoamino acids methyl-Se-cysteine (MeSeCys) and selenomethionine (SeMet) was investigated. NMR results in D(2)O indicate that Cu(I) binds to the Se atom of both MeSeCys and SeMet as well as the carboxylic acid oxygen atom(s) or amine nitrogen atoms. X-ray absorption spectroscopy (XAS) and density functional theory (DFT) results confirm Se-Cu coordination, with the identification of a 2.4 Å Se-Cu vector in both the Se- and Cu-EXAFS data. XAS studies also show Cu(I) in an unusual three-coordinate environment with the additional two ligands arising from O/N (2.0 Å). DFT models of 1:1 Cu-selenoamino acid complexes suggest that both selenoamino acids coordinate Cu(I) through the selenium and amino groups, with the third ligand assumed to be water. These compounds represent the first structurally characterized copper(I) complexes with sulfur- or selenium-containing amino acids.

Method development and optimization for the determination of selenium in bean and soil samples using hydride generation electrothermal atomic absorption spectrometry

The present investigation is the first part of an initiative to prepare a regional map of the natural abundance of selenium in various areas of Brazil, based on the analysis of bean and soil samples. Continuous-flow hydride generation electrothermal atomic absorption spectrometry (HG-ET AAS) with in situ trapping on an iridium-coated graphite tube has been chosen because of the high sensitivity and relative simplicity. The microwave-assisted acid digestion for bean and soil samples was tested for complete recovery of inorganic and organic selenium compounds (selenomethionine). The reduction of Se(VI) to Se(IV) was optimized in order to guarantee that there is no back-oxidation, which is of importance when digested samples are not analyzed immediately after the reduction step. The limits of detection and quantification of the method were 30 ng L(-1) Se and 101 ng L(-1) Se, respectively, corresponding to about 3 ng g(-1) and 10 ng g(-1), respectively, in the solid samples, considering a typical dilution factor of 100 for the digestion process. The results obtained for two certified food reference materials (CRM), soybean and rice, and for a soil and sediment CRM confirmed the validity of the investigated method. The selenium content found in a number of selected bean samples varied between 5.5±0.4 ng g(-1) and 1726±55 ng g(-1), and that in soil samples varied between 113±6.5 ng g(-1) and 1692±21 ng g(-1).

Additional phase information from UV damage of selenomethionine labelled proteins

Currently, selenium is the most widely used phasing vehicle for experimental phasing, either by single anomalous scattering or multiple-wavelength anomalous dispersion (MAD) procedures. The use of the single isomorphous replacement anomalous scattering (SIRAS) phasing procedure with selenomethionine containing proteins is not so commonly used, as it requires isomorphous native data. Here it is demonstrated that isomorphous differences can be measured from intensity changes measured from a selenium labelled protein crystal before and after UV exposure. These can be coupled with the anomalous signal from the dataset collected at the selenium absorption edge to obtain SIRAS phases in a UV-RIPAS phasing experiment. The phasing procedure for two selenomethionine proteins, the feruloyl esterase module of xylanase 10B from Clostridium thermocellum and the Mycobacterium tuberculosis chorismate synthase, have been investigated using datasets collected near the absorption edge of selenium before and after UV radiation. The utility of UV radiation in measuring radiation damage data for isomorphous differences is highlighted and it is shown that, after such measurements, the UV-RIPAS procedure yields comparable phase sets with those obtained from the conventional MAD procedure. The results presented are encouraging for the development of alternative phasing approaches for selenomethionine proteins in difficult cases.

Anti-hemolytic and peroxyl radical scavenging activity of organoselenium compounds: an in vitro study

Selenium-containing amino acids, selenocystine (CysSeSeCys), methylselenocysteine (MeSeCys), and selenomethionine (SeMet) have been examined for anti-hemolytic and peroxyl radical scavenging ability. Effect of these compounds on membrane lipid peroxidation, release of hemoglobin, and loss of intracellular K(+) ion as a consequence of peroxyl radicals-induced oxidation of human red blood cells were used to evaluate their anti-hemolytic ability. The peroxyl radicals were generated from thermal degradation of 2,2'-azobis(2-methylpropionamidine) dihydrochloride. Significant delay (t(eff)) was observed in oxidative damage in the presence of the selenium compounds. From the IC(50) values for the inhibition of hemolysis, lipid peroxidation, and K(+) ion leakage, the relative anti-hemolytic ability of the compounds were found to be in the order of CysSeSeCys > MeSeCys > SeMet. The anti-hemolytic abilities of the compounds, when compared with sodium selenite (Na(2)SeO(3)) under identical experimental conditions, were found to be better than Na(2)SeO(3). Relative rate constants estimated for the reaction of MeSeCys and SeMet with peroxyl radicals by competition kinetics using ABTS(2-) as a reference confirmed that all the compounds are efficient peroxyl radical scavengers. Comparison of the GPx-like activity of these compounds, by NADPH-GSH reductase coupled assay, indicated that CysSeSeCys exhibits the highest activity. Based on these results, it is concluded that among the compounds examined, CysSeSeCys, possessing the ability to reduce peroxyl radicals and hydroperoxides showed efficient anti-hemolytic activity.

Crystallization and preliminary diffraction analysis of Wzi, a member of the capsule export and assembly pathway in Escherichia coli

External polysaccharide capsules provide a physical barrier that is employed by many species of bacteria for the purposes of host evasion and persistence. Wzi is a 53 kDa outer membrane β-barrel protein that is thought to play a role in the attachment of group 1 capsular polysaccharides to the cell surface. The purification and crystallization of an Escherichia coli homologue of Wzi is reported and diffraction data from native and selenomethionine-incorporated protein crystals are presented. Crystals of C-terminally His6-tagged Wzi diffracted to 2.8 Å resolution. Data processing showed that the crystals belonged to the orthorhombic space group C222, with unit-cell parameters a=128.8, b=152.8, c=94.4 Å, α=β=γ=90°. A His-tagged selenomethionine-containing variant of Wzi has also been crystallized in the same space group and diffraction data have been recorded to 3.8 Å resolution. Data processing shows that the variant crystal has similar unit-cell parameters to the native crystal.

Expression, crystallization and preliminary X-ray analysis of an anomeric inverting agarase from Pseudoalteromonas sp. CY24

AgaB from Pseudoalteromonas sp. CY24 is a novel agarase that hydrolyzes agarose to generate products with inverted anomeric configuration and that has been proposed to have a larger catalytic cleft than other β-agarases. Here, the expression, purification, crystallization and data collection of AgaB in both wild-type and selenomethionine-substituted forms is described. The crystals of wild-type AgaB diffracted to 1.97 Å resolution and belonged to space group C222(1). The selenomethionine derivative crystallized in space group I222. The phasing problem was solved by the multiwavelength anomalous dispersion (MAD) method. These results will facilitate detailed structural and enzymatic analysis of AgaB.

Sites and extent of selenomethionine incorporation into recombinant Cas6 protein by top-down and bottom-up proteomics with 14.5 T Fourier transform ion cyclotron resonance mass spectrometry

Selenomethionine-modified proteins can improve X-ray crystallographic structural resolution by multi-wavelength anomalous diffraction (MAD) phasing. However, the specificity and extent of selenomethionine incorporation must first be assessed. Bottom-up and top-down proteomics with a modified 14.5 T LTQ Fourier transform ion cyclotron resonance mass spectrometer offer a quick, accurate, and robust method to locate and quantify selenomethionine incorporation after auxotrophic expression. Selenomethionine (methionine with sulfur replaced by selenium) has a different natural-abundance isotopic distribution and a mass increase of 47.94 Da relative to wild-type methionine. Here, both wild-type and selenomethionine-substituted forms of the Cas6 protein containing 'clustered regularly interspaced short palindromic repeats' (CRISPRs) were expressed and purified. Comparative bottom-up and top-down proteomics confirmed that all six methionines were fully replaced by selenomethionines in Se-Cas6.

Omp85 from the thermophilic cyanobacterium Thermosynechococcus elongatus differs from proteobacterial Omp85 in structure and domain composition

Omp85 proteins are essential proteins located in the bacterial outer membrane. They are involved in outer membrane biogenesis and assist outer membrane protein insertion and folding by an unknown mechanism. Homologous proteins exist in eukaryotes, where they mediate outer membrane assembly in organelles of endosymbiotic origin, the mitochondria and chloroplasts. We set out to explore the homologous relationship between cyanobacteria and chloroplasts, studying the Omp85 protein from the thermophilic cyanobacterium Thermosynechococcus elongatus. Using state-of-the art sequence analysis and clustering methods, we show how this protein is more closely related to its chloroplast homologue Toc75 than to proteobacterial Omp85, a finding supported by single channel conductance measurements. We have solved the structure of the periplasmic part of the protein to 1.97 A resolution, and we demonstrate that in contrast to Omp85 from Escherichia coli the protein has only three, not five, polypeptide transport-associated (POTRA) domains, which recognize substrates and generally interact with other proteins in bigger complexes. We model how these POTRA domains are attached to the outer membrane, based on the relationship of Omp85 to two-partner secretion system proteins, which we show and analyze. Finally, we discuss how Omp85 proteins with different numbers of POTRA domains evolved, and evolve to this day, to accomplish an increasing number of interactions with substrates and helper proteins.

Antioxidant capacity of Macaronesian traditional medicinal plants

The use of many traditional medicinal plants is often hampered by the absence of a proper biochemical characterization, essential to identify the bioactive compounds present. The leaves from five species endemic to the Macaronesian islands with recognized ethnobotanical applications were analysed: Apollonias barbujana (Cav.) Bornm., Ocotea foetens (Ainton) Baill, Prunus azorica (Mouill.) Rivas-Mart., Lousã, Fern. Prieto, E. Días, J.C. Costa & C. Aguiar, Rumex maderensis Lowe and Plantago arborescens Poir. subsp. maderensis (Dcne.) A. Hans. et Kunk.. Since oxidative stress is a common feature of most diseases traditionally treated by these plants, it is important to assess their antioxidant capacity and determine the molecules responsible for this capacity. In this study, the antioxidant capacity of these plants against two of the most important reactive species in human body (hydroxyl and peroxyl radicals) was determined. To trace the antioxidant origin total phenol and flavonoid contents as well as the polyphenolic profile and the amount of trace elements were determined. There was a wide variation among the species analysed in what concerns their total leaf phenol and flavonoid contents. From the High Performance Liquid Chromatography (HPLC) electrochemically detected peaks it was possible to attribute to flavonoids the antioxidant capacity detected in A. barbujana, O. foetens, R. maderensis and P. azorica extracts. These potential reactive flavonoids were identified for A. barbujana, R. maderensis and P. azorica. For R. maderensis a high content (7 mg g-1 dry weight) of L-ascorbic acid, an already described antioxidant phytomolecule, was found. A high content in selenomethionine (414.35 microg g-1 dry weight) was obtained for P. arborescens subsp. maderensis extract. This selenocompound is already described as a hydroxyl radical scavenger is reported in this work as also possessing peroxyl radical scavenging capacity. This work is a good illustration of different phytomolecules (flavonoids, organic acids and selenocompounds), presents in leaves of the five traditional medicinal plants endemic to Macaronesia, all exhibiting antioxidant properties.

Crystallization and preliminary X-ray diffraction studies of FAD synthetase from Corynebacterium ammoniagenes

FAD synthetase from Corynebacterium ammoniagenes (CaFADS), a prokaryotic bifunctional enzyme that catalyses the phosphorylation of riboflavin as well as the adenylylation of FMN, has been crystallized using the hanging-drop vapour-diffusion method at 277 K. Diffraction-quality cubic crystals of native and selenomethionine-labelled (SeMet-CaFADS) protein belonged to the cubic space group P2(1)3, with unit-cell parameters a = b = c = 133.47 A and a = b = c = 133.40 A, respectively. Data sets for native and SeMet-containing crystals were collected to 1.95 and 2.42 A resolution, respectively.

Crystal structure of Bfr A from Mycobacterium tuberculosis: incorporation of selenomethionine results in cleavage and demetallation of haem

Emergence of tuberculosis as a global health threat has necessitated an urgent search for new antitubercular drugs entailing determination of 3-dimensional structures of a large number of mycobacterial proteins for structure-based drug design. The essential requirement of ferritins/bacterioferritins (proteins involved in iron storage and homeostasis) for the survival of several prokaryotic pathogens makes these proteins very attractive targets for structure determination and inhibitor design. Bacterioferritins (Bfrs) differ from ferritins in that they have additional noncovalently bound haem groups. The physiological role of haem in Bfrs is not very clear but studies indicate that the haem group is involved in mediating release of iron from Bfr by facilitating reduction of the iron core. To further enhance our understanding, we have determined the crystal structure of the selenomethionyl analog of bacterioferritin A (SeMet-BfrA) from Mycobacterium tuberculosis (Mtb). Unexpectedly, electron density observed in the crystals of SeMet-BfrA analogous to haem location in bacterioferritins, shows a demetallated and degraded product of haem. This unanticipated observation is a consequence of the altered spatial electronic environment around the axial ligands of haem (in lieu of Met52 modification to SeMet52). Furthermore, the structure of Mtb SeMet-BfrA displays a possible lost protein interaction with haem propionates due to formation of a salt bridge between Arg53-Glu57, which appears to be unique to Mtb BfrA, resulting in slight modulation of haem binding pocket in this organism. The crystal structure of Mtb SeMet-BfrA provides novel leads to physiological function of haem in Bfrs. If validated as a drug target, it may also serve as a scaffold for designing specific inhibitors. In addition, this study provides evidence against the general belief that a selenium derivative of a protein represents its true physiological native structure.

In vitro radioprotection studies of organoselenium compounds: differences between mono- and diselenides

Organoselenium compounds belonging to the class of monoselenides, such as selenomethionine (SeM) and methylselenocysteine (MSeCys) and diselenides including selenocystine (SeCys) and selenopropionic acid (SePA), were examined for their comparative radioprotective effects using in vitro models. Effects of these compounds on the inhibition of gamma-radiation induced lipid peroxidation in liposomes, protein carbonylation in bovine serum albumin (BSA) and strand breaks in pBR322 plasmid DNA, assessed, respectively, by the formation of thiobarbituric acid reactive substances, formation of 2,2'-dinitrophenyl hydrazine (DNPH) carbonyl complex and horizontal gel electrophoresis, were used to compare their radioprotective ability. The IC 50 values for SeCys, SePA, SeM and MSeCys for lipid peroxidation were 27 +/- 1, 33 +/- 2, 200 +/- 8 and 163 +/- 4 microM, respectively, and the values for inhibition of protein carbonylation were >200, 300 +/- 6, 464 +/- 8 and 436 +/- 3 microM, respectively. Inhibition of DNA strand break formation was tested at 200 microM for all the compounds and SePA and SeCys exhibited a protective effect on DNA, while SeM and MSeCys did not lead to any protection. The in vitro cytotoxicity studies in normal and tumor cells revealed that MSeCys and SeM were not cytotoxic to lymphocytes and EL4 tumor cells at the concentrations employed. In contrast, SeCys was toxic, with a higher effect on tumor cells than lymphocytes. Our studies suggest that the non-toxic diselenides like SePA should be explored as protective agents against gamma-irradiation induced damage.

A description of the structural determination procedures of a gap junction channel at 3.5 A resolution

Intercellular signalling is an essential characteristic of multicellular organisms. Gap junctions, which consist of arrays of intercellular channels, permit the exchange of ions and small molecules between adjacent cells. Here, the structural determination of a gap junction channel composed of connexin 26 (Cx26) at 3.5 A resolution is described. During each step of the purification process, the protein was examined using electron microscopy and/or dynamic light scattering. Dehydration of the crystals improved the resolution limits. Phase refinement using multi-crystal averaging in conjunction with noncrystallographic symmetry averaging based on strictly determined noncrystallographic symmetry operators resulted in an electron-density map for model building. The amino-acid sequence of a protomer structure consisting of the amino-terminal helix, four transmembrane helices and two extracellular loops was assigned to the electron-density map. The amino-acid assignment was confirmed using six selenomethionine (SeMet) sites in the difference Fourier map of the SeMet derivative and three intramolecular disulfide bonds in the anomalous difference Fourier map of the native crystal.

Purification, crystallization and preliminary X-ray diffraction analysis of the FeoB G domain from Methanococcus jannaschii

The transmembrane protein FeoB plays a key role in ferrous iron acquisition in prokaryotes. The N-terminal domain of FeoB from Methanococcus jannaschii was overproduced, purified to homogeneity and crystallized in the presence of GTP and magnesium. The native protein crystallized in a tetragonal space group and the crystals diffracted to beyond 2.2 A resolution, with unit-cell parameters a = b = 84.77, c = 137.90 A. The Matthews coefficient and the solvent content were estimated to be 2.65 A(3) Da(-1) and 53.64%, respectively, which corresponds to the presence of two molecules per asymmetric unit. To obtain initial phases, selenomethionyl-substituted protein was overproduced, purified and crystallized.

Crystallization and preliminary X-ray analysis of three dUTPases from Gram-positive bacteria

All organisms examined to date possess a dUTPase that performs the important function of efficiently hydrolyzing dUTP to dUMP in order to prevent the incorporation of dUTP into DNA. Three putative dUTPases from Gram-positive bacteria have been studied in this work. Two dUTPase-encoding genes, yncF and yosS, have been identified in Bacillus subtilis. The gene dut, encoding dUTPase from the dental pathogen Streptococcus mutans, was amplified from S. mutans genomic DNA. The three genes were cloned into expression vectors and overexpressed at high levels in Escherichia coli. Each protein was purified in two steps using chromatographic methods. Crystals of the YosS and YncF proteins and of S. mutans dUTPase were obtained using the vapour-diffusion method. X-ray diffraction data sets were collected from crystals of selenomethionine-labelled YosS and S. mutans dUTPase to resolutions of 2.3 and 1.7 A, respectively. The crystal of native YncF diffracted to 2.7 A resolution.

Purification, crystallization and preliminary X-ray diffraction analysis of human Gadd45gamma

Gadd45, MyD118 and CR6 (also termed Gadd45alpha, Gadd45beta and Gadd45gamma, respectively) comprise a family of proteins that play important roles in negative growth control, maintenance of genomic stability, DNA repair, cell-cycle control and apoptosis. Recombinant human Gadd45gamma and its selenomethionine derivative were expressed in an Escherichia coli expression system and purified; they were then crystallized using the hanging-drop vapour-diffusion method. Diffraction-quality crystals were grown at 291 K using PEG 3350 as precipitant. Using synchrotron radiation, the best diffraction data were collected to 2.3 A resolution for native crystals at 100 K; selenomethionyl derivative data were collected to 3.3 A resolution. All the crystals belonged to space group I2(1)3, with approximate unit-cell parameters a = b = c = 126 A.

Expression, purification, crystallization and preliminary X-ray studies of histamine dehydrogenase from Nocardioides simplex

Histamine dehydrogenase (HADH) from Nocardioides simplex catalyzes the oxidative deamination of histamine to produce imidazole acetaldehyde and an ammonium ion. HADH is functionally related to trimethylamine dehydrogenase (TMADH), but HADH has strict substrate specificity towards histamine. HADH is a homodimer, with each 76 kDa subunit containing two redox cofactors: a [4Fe-4S] cluster and an unusual covalently bound flavin mononucleotide, 6-S-cysteinyl-FMN. In order to understand the substrate specificity of HADH, it was sought to determine its structure by X-ray crystallography. This enzyme has been expressed recombinantly in Escherichia coli and successfully crystallized in two forms. Diffraction data were collected to 2.7 A resolution at the SSRL synchrotron with 99.7% completeness. The crystals belonged to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 101.14, b = 107.03, c = 153.35 A.

Crystallization and preliminary X-ray diffraction analysis of the cytosolic domain of a cation diffusion facilitator family protein

The cation diffusion facilitator (CDF) family proteins are ubiquitously distributed in the three domains of life and transport metals such as zinc and various heavy metals. Prokaryotic CDF proteins consists of an N-terminal putative six-transmembrane domain followed by a C-terminal cytosolic domain. The cytosolic domain of the CDF-family protein from Thermotoga maritima has been overexpressed, purified and crystallized. The selenomethionine-substituted crystals diffracted X-rays to 2.5 A resolution using synchrotron radiation, belonged to space group R32, with unit-cell parameters a = b = 97.7, c = 83.4 A, and are expected to contain one molecule in each asymmetric unit.

Crystal Structure of the VP4 Protease from Infectious Pancreatic Necrosis Virus Reveals the Acyl-Enzyme Complex for an Intermolecular Self-cleavage Reaction

Infectious pancreatic necrosis virus (IPNV), an aquatic birnavirus that infects salmonid fish, encodes a large polyprotein (NH(2)-pVP2-VP4-VP3-COOH) that is processed through the proteolytic activity of its own protease, VP4, to release the proteins pVP2 and VP3. pVP2 is further processed to give rise to the capsid protein VP2 and three peptides that are incorporated into the virion. Reported here are two crystal structures of the IPNV VP4 protease solved from two different crystal symmetries. The electron density at the active site in the triclinic crystal form, refined to 2.2-A resolution, reveals the acyl-enzyme complex formed with an internal VP4 cleavage site. The complex was generated using a truncated enzyme in which the general base lysine was substituted. Inside the complex, the nucleophilic Ser(633)Ogamma forms an ester bond with the main-chain carbonyl of the C-terminal residue, Ala(716), of a neighboring VP4. The structure of this substrate-VP4 complex allows us to identify the S1, S3, S5, and S6 substrate binding pockets as well as other substrate-VP4 interactions and therefore provides structural insights into the substrate specificity of this enzyme. The structure from the hexagonal crystal form, refined to 2.3-A resolution, reveals the free-binding site of the protease. Three-dimensional alignment with the VP4 of blotched snakehead virus, another birnavirus, shows that the overall structure of VP4 is conserved despite a low level of sequence identity ( approximately 19%). The structure determinations of IPNV VP4, the first of an acyl-enzyme complex for a Ser/Lys dyad protease, provide insights into the catalytic mechanism and substrate recognition of this type of protease.