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At least 505 records · Page 28Linked to original sources
PubMed2004

Structural characterization of imazalil/beta-cyclodextrin inclusion complex.

An equimolar inclusion complex between imazalil, a selected fungicide, and beta-cyclodextrin using an aqueous standard solution procedure has been obtained. The complex has been investigated in solution by (1)H and (13)C NMR techniques in combination with computational methods in order to establish a valuable analytical protocol through which to gain insight into the interactions of the inclusion complex in aqueous solution. Intramolecular NMR distance constraints have been detected and used for three-dimensional complex structure determination.

Cyclodextrins↗
PubMed2000

A DNA enzyme with N-glycosylase activity.

In vitro evolution was used to develop a DNA enzyme that catalyzes the site-specific depurination of DNA with a catalytic rate enhancement of about 10(6)-fold. The reaction involves hydrolysis of the N-glycosidic bond of a particular deoxyguanosine residue, leading to DNA strand scission at the apurinic site. The DNA enzyme contains 93 nucleotides and is structurally complex. It has an absolute requirement for a divalent metal cation and exhibits optimal activity at about pH 5. The mechanism of the reaction was confirmed by analysis of the cleavage products by using HPLC and mass spectrometry. The isolation and characterization of an N-glycosylase DNA enzyme demonstrates that single-stranded DNA, like RNA and proteins, can form a complex tertiary structure and catalyze a difficult biochemical transformation. This DNA enzyme provides a new approach for the site-specific cleavage of DNA molecules.

Catalysis↗
PubMed1999

Unexpected modes of PDZ domain scaffolding revealed by structure of nNOS-syntrophin complex.

The PDZ protein interaction domain of neuronal nitric oxide synthase (nNOS) can heterodimerize with the PDZ domains of postsynaptic density protein 95 and syntrophin through interactions that are not mediated by recognition of a typical carboxyl-terminal motif. The nNOS-syntrophin PDZ complex structure revealed that the domains interact in an unusual linear head-to-tail arrangement. The nNOS PDZ domain has two opposite interaction surfaces-one face has the canonical peptide binding groove, whereas the other has a beta-hairpin "finger." This nNOS beta finger docks in the syntrophin peptide binding groove, mimicking a peptide ligand, except that a sharp beta turn replaces the normally required carboxyl terminus. This structure explains how PDZ domains can participate in diverse interaction modes to assemble protein networks.

Amino Acid Sequence↗
PubMed2002

Beyond tandem repeats: complex pattern structures and distant regions of similarity.

MOTIVATION: Tandem repeats (TRs) are associated with human disease, play a role in evolution and are important in regulatory processes. Despite their importance, locating and characterizing these patterns within anonymous DNA sequences remains a challenge. In part, the difficulty is due to imperfect conservation of patterns and complex pattern structures. We study recognition algorithms for two complex pattern structures: variable length tandem repeats (VLTRs) and multi-period tandem repeats (MPTRs). RESULTS: We extend previous algorithmic research to a class of regular tandem repeats (RegTRs). We formally define RegTRs, as well as two important subclasses: VLTRs and MPTRs. We present algorithms for identification of TRs in these classes. Furthermore, our algorithms identify degenerate VLTRs and MPTRs: repeats containing substitutions, insertions and deletions. To illustrate our work, we present results of our analysis for two difficult regions in cattle and human data which reflect practical occurrences of these subclasses in GenBank sequence data. In addition, we show the applicability of our algorithmic techniques for identifying Alu sequences, gene clusters and other distant regions of similarity. We illustrate this with an example from yeast chromosome I.

Algorithms↗
PubMed1997

Copper(II) Complexes of N,N'-Bis((2-substituted-imidazol-4-yl)methylene)-3,3'-diaminodi- propylamine (2-Substituent = H, Me): Delta and Lambda Enantiomorphs of the Protonated Complex and Helical Structure of the Deprotonated Complex Formed by Hydrogen Bonds.

Copper(II) complexes with the quinquedentate ligands H(2)L(n)() (n = 1, 2) of the 1:2 condensation products of 3,3'-diaminodipropylamine and each of 4-formylimidazole and 4-formyl-2-methylimidazole have been synthesized and characterized, where the complexes have the general formula of [Cu(H(2)L(n)())]X(2) and are abbreviated as 1X(2), and 2X(2) (n = 1, 2 for 2-substituent = H, Me; X = ClO(4), NO(3), Cl). X-ray crystal structures of 1(NO(3))(2), and 2(Cl)(2) were determined: 1(NO(3))(2), monoclinic, space group P2(1)/c (No. 14), a = 9.610(4) Å, b = 13.463(5) Å, c = 15.568(5) Å, beta = 98.12(3) degrees, and Z = 4; 2(Cl)(2), monoclinic, space group P2(1)/n (No. 14), a = 9.884(2) Å, b = 15.073(3) Å, c = 15.295(2) Å, beta = 98.57(2) degrees, and Z = 4. The complex assumes Delta or Lambda enantiomorphs due to the spiral arrangement of the quinquedentate ligand around the copper(II) ion, and these Delta and Lambda enantiomorphs of the cation for 1(NO(3))(2) and 2(Cl)(2) coexist as the racemic form in the crystals. When the protonated complexes were treated with NaOH, the mono-deprotonated complexes with the formula [CuHL(n)()]ClO(4), 1'ClO(4) (n = 1) and 2'ClO(4) (n = 2), were obtained. Crystal data for 1'ClO(4): Pbca (No. 61) with a = 13.211(3) Å, b = 25.387(3) Å, c = 10.939(3) Å, and Z = 8.; 2'.ClO(4), Pbca (No. 61) with a = 16.554(4) Å, b = 20.609(4) Å, c = 12.423(3) Å, and Z = 8. The structures consist of an electronically monopositive copper(II) complex involving a deprotonated imidazole moiety and a protonated imidazole moiety per molecular unit and a mononegative anion ClO(4)(-), where an imidazolate nitrogen atom N(2) of the copper(II) complex is hydrogen bonded to the imidazole nitrogen atom N(6) ( denotes the symmetry operation of (1)/(2) + x, (1)/(2) - y, -z) of the adjacent unit with the hydrogen bond distance of N(2).N(6) of 2.842(6) for 1'ClO(4) and 2.815(4) Å for 2'ClO(4) to give a one-dimensional helical structure running along the a-axis. Through the hydrogen bonds, the Delta isomer only aggregates with the Delta isomer and the Lambda isomer only aggregates with the Lambda isomer to give an extended helical chain structure described as DeltaDeltaDeltaDeltaDelta. or LambdaLambdaLambdaLambdaLambda., respectively.

Journal Article↗
PubMed2005

Effects of complexation with 18-crown-6 on the hypernucleofugality of phenyl-lambda3-iodanyl groups. Synthesis of vinyl-lambda3-iodane.18-crown-6 complex.

[structure: see text] 4-tert-Butyl-1-cyclohexenyl(phenyl)(tetrafluoroborato)-lambda(3)-iodane forms a discrete supramolecular complex by the reaction with 18-crown-6. Solvolysis of the cyclohexenyl-lambda(3)-iodane in the presence of 18-crown-6 indicates that the complexation with 18-crown-6 tends to decrease the leaving group ability of hypervalent phenyl-lambda(3)-iodanyl groups.

Journal Article↗
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↗
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↗