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PubMed1996

The marine bacterium Pseudoalteromonas haloplanktis has a complex genome structure composed of two separate genetic units.

The genome size of Pseudoalteromonas haloplanktis, a ubiquitous and easily cultured marine bacterium, was measured as a step toward estimating the genome complexity of marine bacterioplankton. To determine total genome size, we digested P. haloplanktis DNA with the restriction endonucleases Notl and Sfil, separated the fragments using pulsed-field gel electrophoresis (PFGE), and summed the sizes of the fragments. The P. haloplanktis genome was 3512 +/- 112 kb by Notl digestion and 3468 +/- 54.1 kb by Sfil digestion. P. haloplanktis is also shown to have a complex genome structure, composed of two large replicons of approximately 2700 and 800 kb. Three pieces of evidence support this conclusion: (1) Two separate bands are always seen in PFGE of undigested P. haloplanktis DNA; (2) restriction digests of the larger band are missing a band of approximately 650 kb compared with restriction digests of total genomic DNA; and (3) a 16S rDNA probe hybridized to the larger replicon but not to the smaller. To our knowledge, P. haloplanktis is the first marine bacterium shown to have a complex genome structure.

DNA, Bacterial↗
PubMed1995

Mercury-199 NMR of the metal receptor site in MerR and its protein-DNA complex.

Structural insights have been provided by mercury-199 nuclear magnetic resonance (NMR) into the metal receptor site of the MerR metalloregulatory protein alone and in a complex with the regulatory target, DNA. The one- and two-dimensional NMR data are consistent with a trigonal planar Hg-thiolate coordination environment consisting only of Cys side chains and resolve structural aspects of both metal ion recognition and the allosteric mechanism. These studies establish 199Hg NMR techniques as useful probes of the metal coordination environment of regulatory proteins, copper enzymes, and zinc transcription factor complexes as large as 50 kilodaltons.

Allosteric Site↗
PubMed2005

Structure determination of GGA-GAE and gamma1-ear in complex with peptides: crystallization of low-affinity complexes in membrane traffic.

Crystallization of protein-protein complexes is an important step in the studies of biological functions of proteins. However, weak and transient, even though specific, interactions often present difficulties in crystallization of protein complexes due to the heterogeneity of the sample mixture. For example, the gamma1-ear domain of the AP-1 complex and the GAE domain of GGA1, responsible for the interaction with accessory proteins involved in vesicular transport, are known to interact with target proteins with affinities of the order of 1-100 microM. Such low affinities have hampered crystallization trials of the complexes. To overcome this problem, the gamma1-ear and GAE domains were first co-crystallized with excess amounts of the peptides. Co-crystals of both domains were obtained and the complex structures were determined at 2.5-2.9 A resolution. Based on the crystal packing of gamma1-ear and the cognate peptide, gamma1-ear fused with a peptide tag at the N-terminus was prepared. The peptide-tagged gamma1-ear readily crystallized and the crystal diffracted far better, 1.9-2.2 A resolution, compared with the co-crystallized complex, giving significantly more details without affecting the overall complex structure.

ADP-Ribosylation Factors↗
PubMed2003

The first coordination complexes of selenones: a structural comparison with complexes of sulfones.

Reactivity of the two classes of very weak donors R(2)XO(2) (X = S, R = Me (1) and Ph (2); X = Se, R = Me (3) and Ph (4)) have been studied. Coordination properties of sulfones and selenones in solution and in the gas phase have been compared for the first time using a model bidentate metal complex, [Rh(2)(O(2)CCF(3))(4)]. Two coordination modes, bridging mu(2)-O,O' and terminal eta(1)-O, have been detected. These types of binding were realized in two series of sulfone and selenone metal complexes, polymeric mono-adducts [Rh(2)(O(2)CCF(3))(4).(R(2)XO(2))]( infinity ) (X = S, R = Me (1a); R = Ph (2a); X = Se, R = Ph (4a)) and discrete bis-adducts [Rh(2)(O(2)CCF(3))(4).(R(2)XO(2))(2)] (X = S, R = Ph (2b); X = Se, R = Me (3b)). The compositions and structures of new compounds have been confirmed by NMR and IR spectroscopy, chemical analyses, and X-ray diffraction studies. Compounds 3b and 4a are the first crystallographically characterized metal complexes having selenone ligands coordinated to the metal centers. Preparation and X-ray study of analogous metal complexes of sulfone and selenone ligands allow, for the first time, tracking the structural changes induced by metal coordination. In addition, the X-ray structure of dimethyl selenone, Me(2)SeO(2) (3), an analogue of Me(2)SO(2), has been determined. Geometries of coordinated sulfone and selenones ligands have been compared with those of the corresponding "free" molecules.

Journal Article↗
PubMed2004

Mammalian protein SCP1 forms synaptonemal complex-like structures in the absence of meiotic chromosomes.

Synaptonemal complexes (SCs) are evolutionary conserved, meiosis-specific structures that play a central role in synapsis of homologous chromosomes, chiasmata distribution, and chromosome segregation. However, it is still for the most part unclear how SCs do assemble during meiotic prophase. Major components of mammalian SCs are the meiosis-specific proteins SCP1, 2, and 3. To investigate the role of SCP1 in SC assembly, we expressed SCP1 in a heterologous system, i.e., in COS-7 cells that normally do not express SC proteins. Notably, under these experimental conditions SCP1 is able to form structures that closely resemble SCs (i.e., polycomplexes). Moreover, we show that mutations that modify the length of the central alpha-helical domain of SCP1 influence the width of polycomplexes. Finally, we demonstrate that deletions of the nonhelical N- or C-termini both affect polycomplex assembly, although in a different manner. We conclude that SCP1 is a primary determinant of SC assembly that plays a key role in synapsis of homologous chromosomes.

Animals↗
PubMed1997

Novel 99mTc aminobisthiolato/monothiolato "3 + 1" mixed ligand complexes: structure-activity relationships and preliminary in vivo validation as brain blood flow imaging agents.

A series of neutral, lipophilic 99mTc mixed-ligand complexes of the general formula 99mTcOL1L2, where L1H2 is an N-substituted bis-(2-mercaptoethyl)amine, [X-CH2CH2N(CH2CH2SH)2], [SNS], and L2H is a monodentate thiol (RSH), [S], has been synthesized and evaluated in rodents for potential use in brain blood flow imaging. The complexes were prepared by ligand exchange reaction using 99mTc(V)O-glucoheptonate as precursor and equimolar quantities of the two ligands. In all cases the syn isomer was formed in a high yield, whereas the anti isomer was not always present. The formation of two isomeric complexes-syn and anti-was expected, since the N-substituent (X-CH2CH2N) can assume syn or anti configuration with respect to the 99mTcO3+ core during complexation. One anti and all syn isomers were isolated by HPLC. Their identity was confirmed by comparative HPLC studies with the analogous 99Tc complexes of established structure. In vivo distribution, in particular brain uptake and retention, greatly depended on the type of either tridentate (L1H2) or monodentate (L2H) ligand. All 99mTc complexes showed significant brain uptake in mice (0.78-4.35% injected dose per organ at 5 min postinjection). This initial uptake remained nearly constant for at least 30 min for most of the complexes. Structure-activity relationships of novel 99mTc(V)O SNS/S complexes in mice are reported and discussed. Selected complexes were further studied in rats. High brain uptake, comparable to that of 99mTc-d,l-HMPAO, and sufficient retention 60 min postinjection were provided with complex 18 [X = (C2H5)2N and R = p-CH3OC6H4CH2].

Animals↗
PubMed2003

Leishmania mexicana glycerol-3-phosphate dehydrogenase showed conformational changes upon binding a bi-substrate adduct.

Certain pathogenic trypanosomatids are highly dependent on glycolysis for ATP production, and hence their glycolytic enzymes, including glycerol-3-phosphate dehydrogenase (GPDH), are considered attractive drug targets. The ternary complex structure of Leishmania mexicana GPDH (LmGPDH) with dihydroxyacetone phosphate (DHAP) and NAD(+) was determined to 1.9A resolution as a further step towards understanding this enzyme's mode of action. When compared with the apo and binary complex structures, the ternary complex structure shows an 11 degrees hinge-bending motion of the C-terminal domain with respect to the N-terminal domain. In addition, residues in the C-terminal domain involved in catalysis or substrates binding show significant movements and a previously invisible five-residue loop region becomes well ordered and participates in NAD(+) binding. Unexpectedly, DHAP and NAD(+) appear to form a covalent bond, producing an adduct in the active site of LmGPDH. Modeling a ternary complex glycerol 3-phosphate (G3P) and NAD(+) with LmGPDH identified ten active site residues that are highly conserved among all GPDHs. Two lysine residues, Lys125 and Lys210, that are presumed to be critical in catalysis, were mutated resulting in greatly reduced catalytic activity. Comparison with other structurally related enzymes found by the program DALI suggested Lys210 as a key catalytic residue, which is located on a structurally conserved alpha-helix. From the results of site-directed mutagenesis, molecular modeling and comparison with related dehydrogenases, a catalytic mechanism of LmGPDH and a possible evolutionary scenario of this group of dehydrogenases are proposed.

Amino Acid Sequence↗
PubMed2006

Enantioselective nitrone cycloadditions of alpha,beta-unsaturated 2-acyl imidazoles catalyzed by bis(oxazolinyl)pyridine-cerium(IV) triflate complexes.

[Structure: see text] Enantioselective nitrone cycloadditions with beta-substituted alpha,beta-unsaturated 2-acyl imidazoles catalyzed by bis(oxazolinyl)pyridine-cerium(IV) triflate complexes 1 have been reported. The isoxazolidine products were efficiently transformed into densely functionalized beta'-hydroxy-beta-amino acid derivatives.

Amino Acids↗
PubMed2003

Gold(I) phosphido complexes: synthesis, structure, and reactivity.

Deprotonation of the phosphine complexes Au(PHR(2))Cl with aqueous ammonia gave the gold(I) phosphido complexes [Au(PR(2))](n)() (PR(2) = PMes(2) (1), PCy(2) (2), P(t-Bu)(2) (3), PIs(2) (4), PPhMes (5), PHMes (6); Mes = 2,4,6-Me(3)C(6)H(2), Is = 2,4,6-(i-Pr)(3)C(6)H(2), Mes = 2,4,6-(t-Bu)(3)C(6)H(2), Cy = cyclo-C(6)H(11)). (31)P NMR spectroscopy showed that these complexes exist in solution as mixtures, presumably oligomeric rings of different sizes. X-ray crystallographic structure determinations on single oligomers of 1-4 revealed rings of varying size (n = 4, 6, 6, and 3, respectively) and conformation. Reactions of 1-3 and 5 with PPN[AuCl(2)] gave PPN[(AuCl)(2)(micro-PR(2))] (9-12, PPN = (PPh(3))(2)N(+)). Treatment of 3 with the reagents HI, I(2), ArSH, LiP(t-Bu)(2), and [PH(2)(t-Bu)(2)]BF(4) gave respectively Au(PH(t-Bu)(2))(I) (14), Au(PI(t-Bu)(2))(I) (15), Au(PH(t-Bu)(2))(SAr) (16, Ar = p-t-BuC(6)H(4)), Li[Au(P(t-Bu)(2))(2)] (17), and [Au(PH(t-Bu)(2))(2)]BF(4) (19).

Journal Article↗
PubMed2003

Functional insensitivity of the cytochrome b6f complex to structure changes in the hinge region of the Rieske iron-sulfur protein.

Structure analysis of the cytochrome bc1 complex in the presence and absence of Qp quinol analog inhibitors implied that a large amplitude motion of the Rieske iron-sulfur protein (ISP) is required to mediate electron transfer from ubiquinol to cytochrome c1. Studies of the functional consequences of mutagenesis of an 8-residue ISP "hinge" region in the bc1 complex showed it to be sensitive to structure perturbation, implying that optimum flexibility and length are required for the large amplitude motion. Mutagenesis-function analysis carried out on the ISP hinge region of the cytochrome b6 f complex using the cyanobacterium Synechococcus sp. PCC 7002 showed the following. (i) Of three petC genes, only that in the petCA operon codes for functional ISP. (ii) The function of the complex was insensitive to changes in the hinge region that increased flexibility, decreased flexibility by substitutions of 4-6 Pro residues, shortened the hinge by a 1-residue deletion, or elongated it by insertion of 4 residues. The latter change increased sensitivity to Qp inhibitors, whereas deletion of 2 residues resulted in a loss of inhibitor sensitivity and a decrease in activity, indicating a minimum hinge length of 7 residues required for optimum binding of ISP at the Qp site. Thus, in contrast to the bc1 complex, the function of the b6 f complex was insensitive to sequence changes in the ISP hinge that altered its length or flexibility. This implies that either the barriers to motion or the amplitude of ISP motion required for function is smaller than in the bc1 complex.

Amino Acid Sequence↗
PubMed2000

Syntheses and characterization of anti-inflammatory dinuclear and mononuclear zinc indomethacin complexes. Crystal structures of [Zn2(indomethacin)4(L)2] (L = N,N-dimethylacetamide, pyridine, 1-methyl-2-pyrrolidinone) and [Zn(indomethacin)2(L1)2] (L1 = ethanol, methanol).

The syntheses and spectral and structural characterizations of Zn(II) indomethacin [1-(4-chlorobenzoyl)-5-methoxy-2-methyl-1H-indole-3-acetic acid = IndoH] complexes, as different solvent adducts, have been studied. The complexes are unusual in that both monomeric and dimeric complexes are formed and that this is the first example of the same carboxylato ligand binding via both carboxylate oxygen atoms in monomeric and dimeric Zn(II) complexes. The crystal structures of Zn-Indo complexes with N,N-dimethylacetamide (DMA), pyridine (Py), 1-methyl-2-pyrrolidinone (NMP), EtOH, and MeOH as solvent ligands, [Zn2(Indo)4(DMA)2].2DMA, 1, [Zn2(Indo)4(Py)2].2H2O, 2b, [Zn2(Indo)4(NMP)2], 3, cis-[Zn(Indo)2(EtOH)2], 4, and cis-[Zn(Indo)2(MeOH)2], 5, were determined. Complexes 1, 2b, and 3 crystallize in the triclinic space group P1 (No. 2): a = 13.628(2) A, b = 17.462(2) A, c = 11.078(1) A, alpha = 99.49(1) degrees, beta = 108.13(1) degrees, gamma = 110.10(1) degrees for 1; a = 13.347(3) A, b = 16.499(5) A, c = 10.857(1) A, alpha = 99.48(2) degrees, beta = 108.25(2) degrees, gamma = 106.24(2) degrees for 2; a = 14.143(3) A, b = 14.521(2) A, c = 11.558(2) A, alpha = 109.07(1) degrees, beta = 90.80(2) degrees, gamma = 116.40(1) degrees for 3. The three complexes exhibit dinuclear paddle-wheel structures with a Zn...Zn distance of 2.9686(6) A, Zn-ORCOO distances of 2.035(2)-2.060(2) A, and a Zn-ODMA distance of 1.989(2) A in 1, a Zn...Zn distance of 2.969(1) A, Zn-ORCOO distances of 2.020(3)-2.049(3) A, and a Zn-NPy distance of 2.036(3) A in 2, and a Zn...Zn distance of 2.934(1) A, Zn-ORCOO distances of 2.009(3)-2.051(3) A, and a Zn-ONMP distance of 1.986(3) A in 3. In these cases, the zinc ions are offset along the z direction such that the L-Zn...Zn-L moiety is nonlinear, unlike the Cu analogues. Each Zn has a square-pyramidal geometry bridged by four carboxylato ligands in the basal plane with the solvent ligands containing an O- or N-donor atom at the apex. Complexes 4 and 5 are isostructural, with space group C2/c (No. 15). For 4, a = 30.080(2) A, b = 5.3638(6) A, c = 24.739(2) A, beta = 90.342(7) degrees, and for 5, a = 29.419(2) A, b = 5.320(2) A, c = 24.461(2) A, beta = 90.840(4) degrees. The Zn resides on a 2-fold axis and the complexes have a distorted cis octahedral structure with Zn-ORCOO bond lengths of 2.183(3) and 2.169(3) A, a Zn-OEtOH bond length of 2.015(3) A in 4, Zn-ORCOO bond lengths of 2.195(2) and 2.151(2) A, and a Zn-OMeOH bond length of 2.022(3) A in 5.

Anti-Inflammatory Agents↗
PubMed2006

Mitochondrial protein import: convergent solutions for receptor structure.

Complex machinery has evolved to recognise and import nuclear-encoded proteins into mitochondria. Recent work now shows that the plant Tom20 mitochondrial protein import receptor has a similar tertiary structure to animal Tom20, although the proteins are evolutionarily distinct, representing an elegant example of convergent evolution.

Animals↗
PubMed1999

Crystal structures of complexes of PcrA DNA helicase with a DNA substrate indicate an inchworm mechanism.

We have determined two different structures of PcrA DNA helicase complexed with the same single strand tailed DNA duplex, providing snapshots of different steps on the catalytic pathway. One of the structures is of a complex with a nonhydrolyzable analog of ATP and is thus a "substrate" complex. The other structure contains a bound sulphate ion that sits in a position equivalent to that occupied by the phosphate ion produced after ATP hydrolysis, thereby mimicking a "product" complex. In both complexes, the protein is monomeric. Large and distinct conformational changes occur on binding DNA and the nucleotide cofactor. Taken together, these structures provide evidence against an "active rolling" model for helicase action but are instead consistent with an "inchworm" mechanism.

Adenylyl Imidodiphosphate↗
PubMed2005

3D QSAR studies on GSK-3 inhibition by aloisines.

GSK-3 is involved in various physiological processes and its inhibitors have been evaluated as promising drug candidates for a lot of unmet pathologies. In this paper, inhibition of GSK-3 by aloisines is investigated by 3D QSAR studies. Two alignment rules were applied to check the influence of spatial alignment of the compounds. Both the CoMFA and CoMSIA techniques were carried out and ASS procedure was applied for CoMFA to find a satisfactory model. The best QSAR model obtained is a CoMSIA model characterized with r(2) of 0.938 and q(2) of 0.673 including steric, electrostatic and hydrophobic fields, possessing good predicting ability. To get a better understanding of the relationship between chemical structure and biological activity, a complex structure of aloisine with GSK-3 was obtained by superimposing GSK-3 into the known cocrystal structure of aloisine-CDK2, and then factors that affect the inhibition activity were investigated further, combining the QSAR study with the complex structure, the results of which are in good accordance and complementary to each other.

Binding Sites↗
PubMed2003

An empirical approach for structure-based prediction of carbohydrate-binding sites on proteins.

A computer program system was developed to predict carbohydrate-binding sites on three-dimensional (3D) protein structures. The programs search for binding sites by referring to the empirical rules derived from the known 3D structures of carbohydrate-protein complexes. A total of 80 non-redundant carbohydrate-protein complex structures were selected from the Protein Data Bank for the empirical rule construction. The performance of the prediction system was tested on 50 known complex structures to determine whether the system could detect the known binding sites. The known monosaccharide-binding sites were detected among the best three predictions in 59% of the cases, which covered 69% of the polysaccharide-binding sites in the target proteins, when the performance was evaluated by the overlap between residue patches of predicted and known binding sites.

Animals↗