Assessment of the ability to model proteins with leucine-rich repeats in light of the latest structural information

The three-dimensional structures of leucine-rich repeat (LRR) -containing proteins from five different families were previously predicted based on the crystal structure of the ribonuclease inhibitor. using an approach that combined homology-based modeling, structure-based sequence alignment of LRRs, and several rational assumptions. The structural models have been produced based on very limited sequence similarity, which, in general. cannot yield trustworthy predictions. Recently, the protein structures from three of these five families have been determined. In this report we estimate the quality of the modeling approach by comparing the models with the experimentally determined structures. The comparison suggests that the general architecture, curvature, interior/exterior orientations of side chains. and backbone conformation of the LRR structures can be predicted correctly. On the other hand. the analysis revealed that, in some cases. it is difficult to predict correctly the twist of the overall super-helical structure. Taking into consideration the conclusions from these comparisons, we identified a new family of bacterial LRR proteins and present its structural model. The reliability of the LRR protein modeling suggests that it would be informative to apply similar modeling approaches to other classes of solenoid proteins.

Crystal structures of free, IMP-, and GMP-bound Escherichia coli hypoxanthine phosphoribosyltransferase

Crystal structures have been determined for free Escherichia coli hypoxanthine phosphoribosyltransferase (HPRT) (2.9 Angstrom resolution) and for the enzyme in complex with the reaction products, inosine 5'-monophosphate (IMP) and guanosine 5-monophosphate (GMP) (2.8 Angstrom resolution). Of the known 6-oxopurine phosphoribosyltransferase (PRTase) structures, E. coli HPRT is most similar in structure to that of Tritrichomonas foetus HGXPRT, with a rmsd for 150 Calpha atoms of 1.0 Angstrom. Comparison of the free and product bound structures shows that the side chain of Phe156 and the polypeptide backbone in this vicinity move to bind IMP or GMP. A nonproline cis peptide bond, also found in some other 6-oxopurine PRTases, is observed between Leu46 and Arg47 in both the free and complexed structures. For catalysis to occur, the 6-oxopurine PRTases have a requirement for divalent metal ion, Usually Mg2+ in vivo. In the free structure, a Mg2+, is coordinated to the side chains of Glu103 and Asp104. This interaction may be important for stabilization of the enzyme before catalysis. E. coli HPRT is unique among the known 6-oxopurine PRTases in that it exhibits a marked preference for hypoxanthine as substrate over both xanthine and guanine. The structures suggest that its substrate specificity is due to the modes of binding of the bases. In E. coli HPRT, the carbonyl oxygen of Asp 163 would likely form a hydrogen bond with the 2-exocyclic nitrogen of guanine (in the HPRT-guanine-PRib-PP-Mg2+ complex). However, hypoxanthine does not have a 2-exocyclic atom and the HPRT-IMP structure suggests that hypoxanthine is likely to occupy a different position in the purine-binding pocket.

The first non-turnover voltammetric response from a molybdenum enzyme: direct electroscopy of dimethylsulfoxide reductase from Rhodobacter capsulatus

The first direct voltammetric response from a molybdenum enzyme under non-turnover conditions is reported. Cyclic voltammetry of dimethylsulfoxide reductase from Rhodobacter capsulatus reveals a reversible Mo-VI/V response at + 161 mV followed by a reversible Mo-V/IV response at -102 mV versus NHE at pH 8. The higher potential couple exhibits a pH dependence consistent with protonation upon reduction to the Mo-V state and we have determined the pK(a) for this semi-reduced species to be 9.0. The lower potential couple is pH independent within the range 5 < pH < 10. The optical spectrum of the Mo chromophore has been investigated with spectroelectrochemistry. At high potential, in its resting state, the enzyme exhibits a spectrum characteristic of the Mo-VI form. This changes significantly following bulk electrolysis (-400 mV versus NHE) at an optically transparent, indium-doped tin oxide working electrode, where a single visible electronic maximum at 632 nm is observed, which is comparable with spectra reported previously for the dithionite-reduced enzyme. This two-electron process is chemically reversible by reoxidizing the enzyme at the electrode in the absence of mediators or promoters. The activity of the enzyme has been established by observation of a catalytic current in the presence of DMSO at pH 8, where a sigmoidal (steady state) voltammogram is seen. Electronic supplementary material to this paper (Fig. S 1) can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00775-002-0374-y.

Copper transfer from the Cu(I) chaperone, CopZ, to the repressor, Zn(II)CopY: Metal coordination environments and protein interactions

Extracellular copper regulates the DNA binding activity of the CopY repressor of Enterococcus hirae and thereby controls expression of the copper homeostatic genes encoded by the cop operon. CopY has a CxCxxxxCxC metal binding motif. CopZ, a copper chaperone belonging to a family of metallochaperones characterized by a MxCxxC metal binding motif, transfers copper to CopY. The copper binding stoichiometries of CopZ and CopY were determined by in vitro metal reconstitutions. The stoichiometries were found to be one copper(l) per CopZ and two copper(l) per CopY monomer. X-ray absorption studies suggested a mixture of two- and three-coordinate copper in Cu(1)CopZ, but a purely three-coordinate copper coordination with a Cu-Cu interaction for Cu(1)(2)CopY. The latter coordination is consistent with the formation of a compact binuclear Cu(l)-thiolate core in the CxCxxxxCxC binding motif of CopY. Displacement of zinc, by copper. from CopY was monitored with 2,4-pyridylazoresorcinol. Two copper(l) ions were required to release the single zinc(II) ion bound per CopY monomer. The specificity of copper transfer between CopZ and CopY was dependent on electrostatic interactions. Relative copper binding affinities of the proteins were investigated using the chelator, diethyldithiocarbamic acid (DDC). These data suggest that CopY has a higher affinity for copper than CopZ. However, this affinity difference is not the sole factor in the copper exchange: a charge-based interaction between the two proteins is required for the transfer reaction to proceed. Gain-of-function mutation of a CopZ homologue demonstrated the necessity of four lysine residues on the chaperone for the interaction with CopY. Taken together, these results suggest a mechanism for copper exchange between CopZ and CopY.

Catalytically active Dengue virus NS3 protease forms aggregates that are separable by size exclusion chromatography

An active form of the Dengue virus protease NS3 (CF40.Gly.NS3pro) was expressed in Escherichia coli. This construct consists of a critical 40 amino acid cofactor domain from NS2B fused to the N-terminal 184 amino acid protease domain of NS3 via a flexible, covalent linker (Gly(4)SerGly(4)). The recombinantly produced protein is soluble and has a hexa-histidine tag engineered at the N-terminus for ease of purification using metal affinity chromatography. However, the presence of lower molecular weight impurities after affinity chromatography indicated the need for additional purification steps. The consistent appearance of these impurities suggested that they may be the products of proteolysis and/or auto-proteolysis. The latter possibility was subsequently excluded by the observation of the same impurities in a purified, catalytically inactive form of the recombinant protease (CF40.Gly.NS3pro.SA). Further analysis indicated that these impurities may represent premature translation termination products. Regardless of their origin, they were shown to form various sized aggregates with full-length CF40.Gly.NS3pro that can be separated by size exclusion chromatography, yielding fractions of active protease of sufficient purity for crystallisation trials. The ultimate goal of these studies is to obtain a crystal structure of a catalytically active form of the Dengue virus NS3 protease for structure-based drug design. (C) 2002 Elsevier Science (USA). All rights reserved.

Structure of CcmG/DsbE at 1.14 angstrom resolution: High-fidelity reducing activity in an indiscriminately oxidizing environment

CcmG is unlike other periplasmic thioredoxin (TRX)like proteins in that it has a specific reducing activity in an oxidizing environment and a high fidelity of interaction. These two unusual properties are required for its role in c-type cytochrome maturation. The crystal structure of CcmG reveals a modified TRX fold with an unusually acidic active site and a groove formed from two inserts in the fold. Deletion of one of the groove-forming inserts disrupts c-type cytochrome formation. Two unique structural features of CcmG-an acidic active site and an adjacent groove-appear to be necessary to convert an indiscriminately binding scaffold, the TRX fold, into a highly specific redox protein.

Prolonged retention after aggregation into secretory granules of human R183H-growth hormone (GH), a mutant that causes autosomal dominant GH deficiency type II

Human R183H-GH causes autosomal dominant GH deficiency type II. Because we show here that the mutant hormone is fully bioactive, we have sought to locate an impairment in its progress through the secretory pathway as assessed by pulse chase experiments. Newly synthesized wild-type and R183H-GH were stable when expressed transiently in AtT20 cells, and both formed equivalent amounts of Lubrol-insoluble aggregates within 40 min after synthesis. There was no evidence for intermolecular disulfide bond formation in aggregates of wild-type hormone or the R183H mutant. Both wildtype and R183H-GH were packaged into secretory granules, assessed by the ability of 1 mm BaCl2 to stimulate release and by immunocytochemistry. The mutant differed from wildtype hormone in its retention in the cells after packaging into secretory granules; 50% more R183H-GH than wild-type aggregates were retained in AtT20 cells 120 min after synthesis, and stimulated release of R183H-GH or a mixture of R183H-GH and wild-type that had been retained in the cell was reduced. The longer retention of R183H-GH aggregates indicates that a single point mutation in a protein contained in secretory granules affects the rate of secretory granule release.

Novel sesquiterpenes from the fungus lactarius piperatus

Four novel sesquiterpenes, namely 7alpha,8beta,13-trihydroxy-5,13-marasmanolide (2), isoplorantinone (5), 4,8,14-trihydroxyilludala-2,6,8-triene (6), and 8-hydroxy-8,9-secolactara-1,6-dien-5,13-olide (10), together with six known ones, 7alpha,8beta-dihydroxy-5,13-marasmanolide (1), 7alpha,8alpha-dihydroxy-5,13-marasmanolide (3), isolactarorufin (4), blennin A (7), blennin D (8), and lactarorufin (9), were isolated from the ethanolic extract of Lactarius piperatus. The structures of these sesquiterpenes, representing diversified structural types, were determined mainly by spectroscopic methods, especially 2D-NMR techniques. The structure of 6 was further confirmed by a single-crystal X-ray-diffraction determination.

Cytotoxic iron chelators: Characterization of the structure, solution chemistry and redox activity of ligands and iron complexes of the di-2-pyridyl ketone isonicotinoyl hydrazone (HPKIH) analogues

Di-2-pyridyl ketone isonicotinoyl hydrazone (HPKIH) and a range of its analogues comprise a series of monobasic acids that are capable of binding iron (Fe) as tridentate (N,N,O) ligands. Recently, we have shown that these chelators are highly cytotoxic, but show selective activity against cancer cells. Particularly interesting was the fact that cytotoxicity of the HPKIH analogues is maintained even after complexation with Fe. To understand the potent anti-tumor activity of these compounds, we have fully characterized their chemical properties. This included examination of the solution chemistry and X-ray crystal structures of both the ligands and Fe complexes from this class and the ability of these complexes to mediate redox reactions. Potentiometric titrations demonstrated that all chelators are present predominantly in their charge-neutral form at physiological pH (7.4), allowing access across biological membranes. Keto-enol tautomerism of the ligands was identified, with the tautomers exhibiting distinctly different protonation constants. Interestingly, the chelators form low-spin (diamagnetic) divalent Fe complexes in solution. The chelators form distorted octahedral complexes with Fe-II, with two tridentate ligands arranged in a meridional fashion. Electrochemistry of the Fe complexes in both aqueous and non-aqueous solutions revealed that the complexes are oxidized to their ferric form at relatively high potentials, but this oxidation is coupled to a rapid reaction with water to form a hydrated (carbinolamine) derivative, leading to irreversible electrochemistry. The Fe complexes of the HPKIH analogues caused marked DNA degradation in the presence of hydrogen peroxide. This observation confirms that Fe complexes from the HPKIH series mediate Fenton chemistry and do not repel DNA. Collectively, studies on the solution chemistry and structure of these HPKIH analogues indicate that they can bind cellular Fe and enhance its redox activity, resulting in oxidative damage to vital biomolecules.

Variation of the crystalline structure of coal char during gasification

The variation of the crystallite structure of several coal chars during gasification in air and carbon dioxide was studied by high-resolution transmission electron microscopy (HRTEM) and X-ray diffraction (XRD) techniques. The XRD analysis of the partially gasified coal chars, based on two approaches, Scherrer's equation and Alexander and Sommer's method, shows a contradictory trend of the variation of the crystallite height with carbon conversion, despite giving a similar trend for the crystallite width change. The HRTEM fringe images of the partially gasified coal chars indicate that large and highly ordered crystallites exist at conversion levels as high as 86%. It is also demonstrated that the crystalline structure of chars can be very different although their pore structures are similar, suggesting a combination of crystalline structure analysis with pore structure analysis in studies of carbon gasification.

Novel Scorpionate and Pyrazole Dioxovanadium Complexes, Catalysts for Carboxylation and Peroxidative Oxidation of Alkanes

The dioxovanadium(V) complexes [VO2(3,5-Me(2)Hpz)(3)][BF4] (1) (pz = pyrazolyl), [VO2{SO3C(pz)(3)}] (2), [VO2{HB(3,5-Me(2)pz)(3)}] (3) and [VO2{HC(pz)(3)}][BF4] (4), bearing pyrazole or scorpionate ligands, were obtained by reaction of triethyl vanadate [VO(OEt)(3)] with hydrotris(3,5-dimethyl-1-pyrazolyl)methane [HC(3,5-Me(2)pz)(3)] or 3,5-dimethylpyrazole (3,5-Me(2)Hpz; 1), lithium tris(1-pyrazolyl)methanesulfonate {Li[SO3C(pz)(3)], 2}, potassium hydrotris(3,5-dimethyl-1-pyrazolyl)borate {K[HB(3,5-Me(2)pz)(3)], 3} and hydrotris(1-pyrazolyl)methane [HC(pz)(3), 4], respectively. Treatment of [VO(OEt)(3)] with potassium hydrotris(1-pyrazolyl)borate {K[HB(pz)(3)]} led to the mixed eta(3)-tris(pyrazolyl)borate and eta(2)-bis(pyrazolyl)borate oxovanadium(IV) complex [VO{HB(pz)(3)}{H2B(pz)(2)}, 5]. The compounds were characterized by elemental analyses, IR, NMR and EPR spectroscopy, FAB and ESI mass spectrometry, cyclic voltammetry and, for 5, also by single crystal X-ray diffraction analysis. All complexes exhibit catalytic activity in the single-pot carboxylation [in trifluoroacetic acid/potassium peroxodisulfate (CF3COOH/K2S2O8)] of gaseous alkanes (methane and ethane) to carboxylic acids (yields up to 40%. TONs up to 157) and in the peroxidative oxidation [in water/acetonitrile (H2O/NCMe)] of liquid alkanes (cyclohexane and cyclopentane) to the corresponding alcohols and ketones (yields up to 24%, TONs up to 117), under mild conditions.

Synthesis, characterization and redox behaviour of benzoyldiazenido- and oxorhenium complexes bearing N,N- and S,S-type ligands

The reactions of [ReCl2{eta(2)-N2C(O)Ph}(PPh3)(2)](1) with 2-aminopyrimidine (H(2)Npyrm), 2,2'-bipyridine (bpy) and tetraethylthiuram disulfide (tds), in MeOH upon reflux, lead to the new eta(1)-(benzoyldiazenido)-rhenium(III) complexes [ReCl{eta(1)-N2C(O)Ph}(HNpyrm)(PPh3)(2)](2)and [ReCl2{eta(1)-N2C(O)Ph}(bpy)(PPh3)] (3), and the known oxo(diethyldithiocarbamato)dirhenium(v)complex [Re2O2(mu O){Et2NC(S)S}(4)](4), respectively. The Et2NC(S)S ligands in 4 result from S-S bond rupture of tds molecules. The obtained compounds have been characterized by IR, H-1, P-31{H-1} and C-13{H-1} NMR spectroscopies, FAB(+)-MS, elemental and single-crystal X-ray diffraction (for 2 and 4)analyses. Complex 2 represents the first structurally characterized Re compound derived from 2-aminopyrimidine. Besides, the redox behaviour of 2-4 in CH2Cl2 solution has been studied by cyclic voltammetry, and the Lever electrochemical ligand parameter (E-L)has been estimated, for the first time, for HNpyrm. The electrochemical results are discussed in terms of electronic properties of the Re centres and the ligands.

The condensation and ordering of models of empty liquids

We consider a simple model consisting of particles with four bonding sites ("patches"), two of type A and two of type B, on the square lattice, and investigate its global phase behavior by simulations and theory. We set the interaction between B patches to zero and calculate the phase diagram as the ratio between the AB and the AA interactions, epsilon(AB)*, varies. In line with previous work, on three-dimensional off-lattice models, we show that the liquid-vapor phase diagram exhibits a re-entrant or "pinched" shape for the same range of epsilon(AB)*, suggesting that the ratio of the energy scales - and the corresponding empty fluid regime - is independent of the dimensionality of the system and of the lattice structure. In addition, the model exhibits an order-disorder transition that is ferromagnetic in the re-entrant regime. The use of low-dimensional lattice models allows the simulation of sufficiently large systems to establish the nature of the liquid-vapor critical points and to describe the structure of the liquid phase in the empty fluid regime, where the size of the "voids" increases as the temperature decreases. We have found that the liquid-vapor critical point is in the 2D Ising universality class, with a scaling region that decreases rapidly as the temperature decreases. The results of simulations and theoretical analysis suggest that the line of order-disorder transitions intersects the condensation line at a multi-critical point at zero temperature and density, for patchy particle models with a re-entrant, empty fluid, regime. (C) 2011 American Institute of Physics. [doi: 10.1063/1.3657406]

Complexes of copper(II) with 3-(ortho-substituted phenylhydrazo)pentane-2,4-diones: syntheses,properties and catalytic activity for cyclohexane oxidation

Reactions of copper(II) with 3-phenylhydrazopentane-2,4-diones X-2-C6H4-NHN = C{C(= O)CH3}(2) bearing a substituent in the ortho-position [X = OH (H2L1) 1, AsO3H2 (H3L2) 2, Cl (HL3) 3, SO3H (H2L4) 4, COOCH3 (HL5) 5, COOH (H2L6) 6, NO2 (HL7) 7 or H (HL8) 8] lead to a variety of complexes including the monomeric [CuL4(H2O)(2)]center dot H2O 10, [CuL4(H2O)(2)] 11 and [Cu(HL4)(2)(H2O)(4)] 12, the dimeric [Cu-2(H2O)(2)(mu-HL2)(2)] 9 and the polymeric [Cu(mu-L-6)](n)] 13 ones, often bearing two fused six-membered metallacycles. Complexes 10-12 can interconvert, depending on pH and temperature, whereas the Cu(II) reactions with 4 in the presence of cyanoguanidine or imidazole (im) afford the monomeric compound [Cu(H2O)(4){NCNC(NH2)(2)}(2)](HL4)(2)center dot 6H(2)O 14 and the heteroligand polymer [Cu(mu-L-4)(im)](n) 15, respectively. The compounds were characterized by single crystal X-ray diffraction (complexes), electrochemical and thermogravimetric studies, as well as elemental analysis, IR, H-1 and C-13 NMR spectroscopies (diones) and ESI-MS. The effects of the substituents in 1-8 on the HOMO-LUMO gap and the relative stability of the model compounds [Cu(OH)(L-8)(H2O)]center dot H2O, [Cu(L-1)(H2O)(2)]center dot H2O and [Cu(L-4)(H2O)(2)]center dot H2O are discussed on the basis of DFT calculations that show the stabilization follows the order: two fused 6-membered > two fused 6-membered/5-membered > one 6-membered metallacycles. Complexes 9, 10, 12 and 13 act as catalyst precursors for the peroxidative oxidation (with H2O2) of cyclohexane to cyclohexanol and cyclohexanone, in MeCN/H2O (total yields of ca. 20% with TONs up to 566), under mild conditions.

Synthesis, Antimicrobial and Antiproliferative Activity of Novel Silver(I) Tris(pyrazolyl)methanesulfonateand 1,3,5-Triaza-7-phosphadamantane Complexes

Five new silver(I) complexes of formulas [Ag(Tpms)] (1), [Ag(Tpms)-(PPh3)] (2), [Ag(Tpms)(PCy3)] (3), [Ag(PTA)][BF4] (4), and [Ag(Tpms)(PTA)] (5) {Tpms = tris(pyrazol-1-yl)methanesulfonate, PPh3 = triphenylphosphane, PCy3 = tricyclohexylphosphane, PTA = 1,3,5-triaza-7-phosphaadamantane) have been synthesized and fully characterized by elemental analyses, H-1, C-13, and P-31 NMR, electrospray ionization mass spectrometry (ESI-MS), and IR spectroscopic techniques. The single crystal X-ray diffraction study of 3 shows the Tpms ligand acting in the N-3-facially coordinating mode, while in 2 and 5 a N2O-coordination is found, with the SO3 group bonded to silver and a pendant free pyrazolyl ring. Features of the tilting in the coordinated pyrazolyl rings in these cases suggest that this inequivalence is related with the cone angles of the phosphanes. A detailed study of antimycobacterial and antiproliferative properties of all compounds has been carried out. They were screened for their in vitro antimicrobial activities against the standard strains Enterococcus faecalis (ATCC 29922), Staphylococcus aureus (ATCC 25923), Streptococcus pneumoniae (ATCC 49619), Streptococcus pyogenes (SF37), Streptococcus sanguinis (SK36), Streptococcus mutans (UA1S9), Escherichia coli (ATCC 25922), and the fungus Candida albicans (ATCC 24443). Complexes 1-5 have been found to display effective antimicrobial activity against the series of bacteria and fungi, and some of them are potential candidates for antiseptic or disinfectant drugs. Interaction of Ag complexes with deoxyribonucleic acid (DNA) has been studied by fluorescence spectroscopic techniques, using ethidium bromide (EB) as a fluorescence probe of DNA. The decrease in the fluorescence of DNA EB system on addition of Ag complexes shows that the fluorescence quenching of DNA EB complex occurs and compound 3 is particularly active. Complexes 1-5 exhibit pronounced antiproliferative activity against human malignant melanoma (A375) with an activity often higher than that of AgNO3, which has been used as a control, following the same order of activity inhibition on DNA, i.e., 3 > 2 > 1 > 5 > AgNO3 >> 4.