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PubMed2001

Architecture of nucleotide excision repair complexes: DNA is wrapped by UvrB before and after damage recognition.

Nucleotide excision repair (NER) is a major DNA repair mechanism that recognizes a broad range of DNA damages. In Escherichia coli, damage recognition in NER is accomplished by the UvrA and UvrB proteins. We have analysed the structural properties of the different protein-DNA complexes formed by UvrA, UvrB and (damaged) DNA using atomic force microscopy. Analysis of the UvrA(2)B complex in search of damage revealed the DNA to be wrapped around the UvrB protein, comprising a region of about seven helical turns. In the UvrB-DNA pre-incision complex the DNA is wrapped in a similar way and this DNA configuration is dependent on ATP binding. Based on these results, a role for DNA wrapping in damage recognition is proposed. Evidence is presented that DNA wrapping in the pre-incision complex also stimulates the rate of incision by UvrC.

Adenosine Triphosphatases↗

PubMed1984

Reaction of myoglobin with phenylhydrazine: a molecular doorstop.

X-ray crystallographic studies of myoglobin do not show an entrance or exit path for potential ligands from the surface to the heme cavity. Efforts to locate such a path have so far centered around dynamic calculations. A structure has now been determined that has a clear opening. Phenylhydrazine reacts with myoglobin in such a way that a phenyl group remains bound to the iron atom. The structure of this complex shows that the side chains of His-64(E7), Arg-45-(CD3), and Val-68(E11) have been forced aside to form an open channel to the surface. Although this may not be the only channel to the iron atom, it seems likely that it is an important one.

Heme↗

PubMed1988

Energy-transfer studies of the distance between the high-affinity metal binding site and the colchicine and 8-anilino-1-naphthalenesulfonic acid binding sites on calf brain tubulin.

The high-affinity metal divalent cation Mg2+, associated with the exchangeable guanosine 5'-triphosphate (GTP) binding site (E site) on purified tubulin, has been replaced by the transition metal ion Co2+ on tubulin as well as on the tubulin-colchicine, tubulin-allocolchicine and tubulin-8-anilino-1-naphthalenesulfonic acid (tubulin-ANS) complexes. While pure native tubulin readily incorporated 0.8 atom of Co2+ per tubulin alpha-beta dimer, incorporation was reduced to 0.4 atom of Co2+ per mole of tubulin when it was complexed with colchicine, indicating that the conformational change induced in tubulin by the binding of colchicine leads to a reduced accessibility of the divalent cation binding site linked to the E site without necessarily changing the intrinsic binding constant. The fluorescence emission spectra of tubulin-bound colchicine, allocolchicine, and ANS displayed a strong overlap with the Co2+ absorption spectrum, identifying these as adequate donor-acceptor pairs. Fluorescence energy-transfer measurements were carried out between tubulin-bound colchicine (or allocolchicine) and ANS as donors and tubulin-complexed Co2+ as acceptor. It was found that the distance between the ANS and the high-affinity divalent cation binding sites is greater than 28 A, while that between the colchicine and the divalent cation binding sites is greater than 24 A.(ABSTRACT TRUNCATED AT 250 WORDS)

Anilino Naphthalenesulfonates↗

PubMed1993

Effects of metal ions, thiamine diphosphate analogues and subunit interactions on the reconstitution behaviour of pyruvate decarboxylase from brewer's yeast.

The reconstitution of pyruvate decarboxylase starts with reversible binding of thiamine diphosphate and Mg2(+)-ions to the apoenzyme, followed by a rate-limiting conformational change to the catalytically active holoenzyme. Investigations with diphospho-esters of 4-methyl-5-(2-hydroxyethyl)thiazolium derivatives have shown that the diphosphate residue of thiamine diphosphate is the most important part of the coenzyme responsible for the first reversible binding step. Methylation of the N1'-atom of the pyrimidine ring of thiamine diphosphate or 4'-oxythiamine diphosphate prevents the coenzyme from binding stably to the apoenzyme, so that the methylated coenzyme displays no coenzyme activity. In contrast, thiamine diphosphate analogues with bulky residues on the neighbouring C2'-atom of the pyrimidine ring form active holoenzyme complexes. This result shows the essential role of the N1'-atom of thiamine diphosphate in stable cofactor binding. The cofactor binding rate to the dimeric and tetrameric apoenzymes indicates that the cofactor is located in the contact regions of the subunits in the tetrameric enzyme.

Binding Sites↗

PubMed2006

Syntheses, structures, and photoluminescence properties of metal(II) halide complexes with pyridine-containing flexible tripodal ligands.

Seven coordination compounds, [Zn(L3)Cl2] . MeOH . H2O (1), [Mn(L3)2Cl2] . 0.5EtOH . 0.5H2O (2), [Cu3(L2)2Cl6] . 2DMF (3), [Cu3(L2)2Br6] . 4MeOH (4), [Hg2(L4)Cl4] (5), [Hg2(L4)Br4] (6), and [Hg3(L4)2I6] . H2O (7), were synthesized by the reactions of ligands 1,3,5-tris(3-pyridylmethoxyl)benzene (L3), 1,3,5-tris(2-pyridylmethoxyl)benzene (L2), and 1,3,5-tris(4-pyridylmethoxyl)benzene (L4) with the corresponding metal halides. All the structures were established by single-crystal X-ray diffraction analysis. In complexes 1 and 2, L3 acts as a bidentate ligand using two of three pyridyl arms to link two metal atoms to result in two different 1D chain structures. In complexes 3 and 4, each L2 serves as tridentate ligand and connects three Cu(II) atoms to form a 2D network structure. Complexes 5 and 6 have the same framework structure, and L4 acts as a three-connecting ligand to connect Hg(II) atoms to generate a 3D 4-fold interpenetrated framework, while the structure of complex 7 is an infinite 1D chain. The results indicate that the flexible ligands can adopt different conformations and thus can form complexes with varied structures. In addition, the coordination geometry of the metal atom and the species of the halide were found to have great impact on the structure of the complexes. The photoluminescence properties of the complexes were investigated, and the Zn(II), Mn(II) and Hg(II) complexes showed blue emissions in solid state at room temperature.

Journal Article↗

PubMed2006

Correlation between the 6Li,15N coupling constant and the coordination number at lithium.

The 6Li,15N coupling constants of lithium amide dimers and their mixed complexes with n-butyllithium, formed from five different chiral amines derived from (S)-[15N]phenylalanine, were determined in diethyl ether (Et2O), tetrahydrofuran (THF) and toluene. Results of NMR spectroscopy studies of these complexes show a clear difference in 6Li,15N coupling constants between di-, tri- and tetracoordinated lithium atoms. The lithium amide dimers with a chelating ether group exhibit 6Li,15N coupling constants of approximately 3.8 and approximately 5.5 Hz for the tetracoordinated and tricoordinated lithium atoms, respectively. The lithium amide dimers with a chelating thioether group show distinctly larger 6Li,15N coupling constants of approximately 4.4 Hz for the tetracoordinated lithium atoms, and the tricoordinated lithium atoms have smaller 6Li,15N coupling constants, approximately 4.9 Hz, than their ether analogues. In diethyl ether and tetrahydrofuran, mixed dimeric complexes between the lithium amides and n-butyllithium are formed. The tetracoordinated lithium atoms of these complexes have 6Li,15N coupling constants of approximately 4.0 Hz, and the 6Li,15N coupling constants of the tricoordinated lithium atoms differ somewhat, depending on whether the chelating group is an ether or a thioether; approximately 5.1 and approximately 4.6 Hz, respectively. In toluene, mixed trimeric complexes are formed from two lithium amide moieties and one n-butyllithium. In these trimers, two lithium atoms are tricoordinated with 6Li,15N coupling constants of approximately 4.6 Hz and one lithium is dicoordinated with 6Li,15N coupling constants of approximately 6.5 Hz.

Journal Article↗

PubMed2006

Crystal structure of the Bowman-Birk Inhibitor from Vigna unguiculata seeds in complex with beta-trypsin at 1.55 A resolution and its structural properties in association with proteinases.

The structure of the Bowman-Birk inhibitor from Vigna unguiculata seeds (BTCI) in complex with beta-trypsin was solved and refined at 1.55 A to a crystallographic R(factor) of 0.154 and R(free) of 0.169, and represents the highest resolution for a Bowman-Birk inhibitor structure to date. The BTCI-trypsin interface is stabilized by hydrophobic contacts and hydrogen bonds, involving two waters and a polyethylene glycol molecule. The conformational rigidity of the reactive loop is characteristic of the specificity against trypsin, while hydrophobicity and conformational mobility of the antichymotryptic subdomain confer the self-association tendency, indicated by atomic force microscopy, of BTCI in complex and free form. When BTCI is in binary complexes, no significant differences in inhibition constants for producing a ternary complex with trypsin and chymotrypsin were detected. These results indicate that binary complexes present no conformational change in their reactive site for both enzymes confirming that these sites are structurally independent. The free chymotrypsin observed in the atomic force microscopy assays, when the ternary complex is obtained from BTCI-trypsin binary complex and chymotrypsin, could be related more to the self-association tendency between chymotrypsin molecules and the flexibility of the reactive site for this enzyme than to binding-related conformational changes.

Amino Acid Sequence↗

PubMed2004

A series of trinuclear Cu(II)Ln(III)Cu(II) complexes derived from 2,6-Di(acetoacetyl)pyridine: synthesis, structure, and magnetism.

A series of trinuclear Cu(II)Ln(III)Cu(II) complexes with the bridging ligand 2,6-di(acetoacetyl)pyridine have been prepared by one-pot reaction with Cu(NO(3))(2).3H(2)O and Ln(NO(3))(3).nH(2)O in methanol. X-ray crystallographic studies for all the complexes indicate that two L(2)(-) ligands selectively sandwich two Cu(II) ions with the 1,3-diketonate entities and one Ln(III) ion with the 2,6-acetylpyridine entity to form a trinuclear CuLnCu core bridged by the enolate oxygen atoms. Cryomagnetic properties of the complexes are studied with respect to the electronic structure of the Ln ion.

Journal Article↗

PubMed2004

Structure-based assembly of protein complexes in yeast.

Images of entire cells are preceding atomic structures of the separate molecular machines that they contain. The resulting gap in knowledge can be partly bridged by protein-protein interactions, bioinformatics, and electron microscopy. Here we use interactions of known three-dimensional structure to model a large set of yeast complexes, which we also screen by electron microscopy. For 54 of 102 complexes, we obtain at least partial models of interacting subunits. For 29, including the exosome, the chaperonin containing TCP-1, a 3'-messenger RNA degradation complex, and RNA polymerase II, the process suggests atomic details not easily seen by homology, involving the combination of two or more known structures. We also consider interactions between complexes (cross-talk) and use these to construct a structure-based network of molecular machines in the cell.

Chaperonins↗

PubMed2006

Supramolecular assembly of cyclodextrin-based nanoparticles on solid surfaces for gene delivery.

In this work, a new approach for surface-mediated gene delivery based on inclusion complex formation between the solid surface and delivery vehicles is presented. beta-Cyclodextrin (CD) molecules form high-affinity inclusion complexes with adamantane. This complexation ability was used to specifically immobilize beta-CD-modified poly(ethylenimine) (CD-PEI) nanoparticles on adamantane- (AD-) modified self-assembled monolayers. To investigate the nanoparticle/surface interaction, CD-PEI-based and PEI-based nanoparticles were passed through a surface plasmon resonance flow cell containing the monolayers. CD-PEI nanoparticles are specifically immobilized on the chip surface by cyclodextrin-adamantane inclusion complex formation. Minimal nanoparticle adsorption was detected with PEI-based nanoparticles or on control surfaces. Competition studies with free cyclodextrins reveal that the multivalent interactions between CD-PEI nanoparticles and the adamantane-modified surface results in significantly higher binding affinity than single cyclodextrin-adamantane complexes. Immobilized nanoparticles were characterized by atomic force microscopy and quantified by fluorescence assay. Thus, the ability of CD-PEI nanoparticles to form inclusion complexes can be exploited to attain specific, high-affinity loading of delivery vehicles onto solid surfaces.

Adamantane↗

PubMed1998

Differential DNA recognition by the enantiomers of 1-Rh(MGP)2 phi: a combination of shape selection and direct readout.

The enantiomers of the symmetric metallointercalator complex 1-Rh(MGP)2phi5+ [MGP = 4-(guanidylmethyl)-1,10-phenanthroline; phi = phenanthrenequinone diimine] bound to DNA decamer duplexes containing their respective 6 bp recognition sequences have been investigated using 1H NMR. Shape selection due to the chirality of the metal center and hydrogen-bonding contacts of ancillary guanidinium groups to 3'-G N7 atoms define the recognition by complexes which bind by intercalation to duplex DNA. The titration of Lambda-Rh into the self-complementary decamer containing the recognition sequence (5'-GACATATGTC-3', L1) resulted in one symmetric bound conformation observed in the 1H NMR spectrum, indicating that the DNA duplex retains its symmetry in the presence of the metal complex. Upfield chemical shifts of duplex imino protons and the disruption of the NOE base-sugar contacts defined the central T5-A6 intercalation site. The downfield shift of the G8 imino proton supports the conclusion that the pendant guanidinium arms make simultaneous H-bonding contacts to the N7 atoms of 3'-G8 bases on either side of the site. A variable-temperature study of a partially titrated sample (2:3 Lambda-Rh/L1) showed the exchange rate (kobs) at 298 K to be 68 s-1 and the activation barrier to exchange (DeltaG of association) to be 2.7 kcal/mol, a value comparable to the stacking energy of one base step. The results presented coupled with biochemical data are therefore consistent with binding models in which Lambda-1-Rh(MGP)2phi5+ (Lambda-Rh) traps the recognition site 5'-CATATG-3' in an unwound state, permitting intercalation centrally and hydrogen bonding to guanines at the first and sixth base pair positions. The data suggest a different model of binding and recognition by Delta-Rh. The titration of Delta-Rh into a DNA decamer containing the 6 bp recognition site (D1, 5'-CGCATCTGAC-3'; D2, 5'-GTCAGATGCG-3') resulted in two, distinct conformers, in slow exchange on the NMR time scale. The rate of exchange between the two conformers (kobs) at 298 K is 37 s-1, most likely due to partial dissociation between binding modes. The slower rate relative to Lambda-Rh association reflects the relative rigidity of the D1 and/or D2 sequence in comparison to L1. NOE cross-peaks between the intercalating phi ligand and protons of T5-C6, as well as the upfield shifts observed for imino protons at this step, serve to define the central T5-C6 step as the single site of intercalation. The downfield shift of the 3'-G imino protons indicates the complex makes hydrogen bond contacts with these bases. The complex, which is too small to span a 6 bp B-form DNA sequence, nonetheless makes major groove contacts with 3'-G bases to either side of the site. Notably, both 3'-guanine bases are necessary to impart site specificity and slow dissociation kinetics with the 5'-CATCTG-3' site, as evidenced by the extremely exchange-broadened two-dimensional NOESY spectra of Delta-Rh bound to modified duplexes containing N7-deazaguanine at either G8 or G18; the loss of one major groove contact completely abolishes specificity for 5'-CATCTG-3'. DNA chemical shifts upon binding and intermolecular NOE contacts therefore support a model in which Delta-Rh intercalates in one of two canted binding conformations. Within this model, each intercalation mode allows one guanidinium-guanine hydrogen bond at a time, while bringing the other arm close to the phosphate backbone.

Binding Sites↗

PubMed2000

Evidence of gold-gold intra- and intermolecular interactions gained by laser desorption/ionisation and fast atom bombardment mass spectrometry in the study of some gold(I) coordination compounds

The mass spectrometric behaviour of some two-coordinated linear gold(I) complexes has been studied by fast atom bombardment (FAB) and laser desorption/ionisation (LDI) methods. The results obtained demonstrate some interesting aspects of Au-Au interactions. The detection under FAB conditions of Au(n)(+) clusters, in particular of Au(3)(+) species, can be rationalised by the presence of significant intramolecular Au-Au interactions, while the formation under LDI conditions of Au(n)(+) clusters can be considered indicative of Au(ellipsis)Au intermolecular interactions present in the solid state. Copyright 2000 John Wiley & Sons, Ltd.

Journal Article↗

PubMed2003

The 1.15A crystal structure of the Staphylococcus aureus methionyl-aminopeptidase and complexes with triazole based inhibitors.

Methionyl aminopeptidases (MetAPs) represent a unique class of protease that are responsible for removing the N-terminal methionine residue from proteins and peptides. There are two major classes of MetAPs (type I and type II) described and each class can be subdivided into two subclasses. Eukaryotes contain both the type I and type II MetAPs, whereas prokaryotes possess only the type I enzyme. Due to the physiological importance of these enzymes there is considerable interest in inhibitors to be used as antiangiogenic and antimicrobial agents. Here, we describe the 1.15A crystal structure of the Staphylococcus aureus MetAP-I as an apo-enzyme and its complexes with various 1,2,4-triazole-based derivatives at high-resolution. The protein has a typical "pita-bread" fold as observed for the other MetAP structures. The inhibitors bind in the active site with the N1 and N2 atoms of the triazole moiety complexing two divalent ions. The 1,2,4-triazols represent a novel class of potent non-peptidic inhibitors for the MetAP-Is.

Amino Acid Sequence↗

PubMed2004

The structure of sitting-atop complexes of metalloporphyrins studied by theoretical methods.

The metallation of tetrapyrroles is believed to proceed via a sitting-atop (SAT) complex, in which some of the pyrrole nitrogen atoms are still protonated and the metal ion resides above the ring plane. No crystal structure of such a complex has been presented, but NMR and extended X-ray absorption fine structure (EXAFS) data has been reported for Cu(2+) in acetonitrile. We have used density functional calculations to obtain reasonable models for SAT complexes of porphyrins with Mg(2+), Fe(2+), and Cu(2+). The results show that there are many possible SAT complexes with 1-5 solvent molecules, one or two metal ions, and cis or trans protonation of the porphyrin ring. Many of these have similar energies and their relative stabilities vary with the metal ion. A complex with two cis pyrrolenine nitrogens atoms and 2-4 solvent molecules coordinated to Cu(2+) fits the NMR and EXAFS data best. However, we cannot fully exclude the possibility that what is observed is rather a mixture of a doubly protonated porphyrin and the copper porphyrin. Mg(2+) has a lower affinity for porphyrin and stronger affinity for water, so a complex with five water molecules and only one bond to porphyrin seems to be most stable. For Fe(2+), a cis structure with two first-sphere water molecules and four interactions to the porphyrin seems to be most likely.

Journal Article↗

PubMed2004

Nonoxovanadium(IV) and oxovanadium(V) complexes with mixed O, X, O-donor ligands (X = S, Se, P, or PO).

Ligating properties of four potentially tridentate bisphenol ligands containing [O, X, O] donor atoms (X = S 1, Se 2, P 3, or P=O 4) toward the vanadium ions in +IV or +V oxidation states have been studied. Each ligand with different heterodonor atoms yields as expected nonoxovanadium(IV) complexes, V(IV)L(2), whose structures have been determined by X-ray diffraction methods as having six-coordinate V(IV), VO(4)X(2), core. Compounds 1-4 have also been studied with electrochemical methods, variable-temperature (2-295 K) magnetic susceptibility measurements, X-band electron paramagnetic resonance (EPR) (2-60 K) spectroscopy, and magnetic circular dichroism (MCD) (5 K) measurements. Electrochemical results suggest metal-centered oxidations to V(V) (i.e., no formation of phenoxyl radicals from the coordinated phenolates). A combination of density functional theory calculations and experimental EPR investigations indicates a dramatic effect of the heteroatoms on the electronic structure of 1-4 with consequent reordering of the energy levels; 1 and 3 possess a trigonal ground state (d(z)()(2))(1), but 4 with the phosphoryl oxygen as the heterodonor atom in contrast exhibits a tetragonal ground state, (d(xy)())(1). On the basis of the intense electronic transitions in absorption spectra, all electronic transitions observed for 4 have been assigned to ligand-to-metal charge-transfer transitions, which have been confirmed by preliminary resonance Raman measurements and C/D ratios obtained from low-temperature MCD spectroscopy. Moreover, diamagnetic complexes 5 and 6 containing mononuclear and dinuclear oxovanadium(V) units have also been synthesized and structurally and spectroscopically ((51)V NMR) characterized.

Journal Article↗

PubMed2004

Tetrakis(tetrahydrofuran-kappaO)lithium mer-tris(carbazolyl-kappaN)-trans-dichloro(tetrahydrofuran-kappaO)zirconate.

In the title compound, [Li(C(4)H(8)O)(4)][ZrCl(2)(C(12)H(8)N)(3)(C(4)H(8)O)], the environment of the Zr atom is pseudo-octahedral, with the three carbazolyl ligands in a mer configuration. The counter-ion of the zirconium complex is composed of an Li atom surrounded by four tetrahydrofuran (THF) molecules. The THF molecule attached to the Zr atom is disordered over two sites, as are two of the THF molecules in the lithium moiety. All bond distances and angles are consistent with those in complexes with similar structural entities. The Zr-N bond distances are 2.2185 (18) and 2.167 (3) A.

Journal Article↗

PubMed1978

Atomic absorption spectroscopic determination of lead extracted from acid-solubilized tissues.

A method is presented for determining lead in a variety of tissues. Lyophilized samples are solubilized with nitric acid at room temperature in glass screw-cap culture tubes. Following neutralization with sodium hydroxide and sodium bicarbonate, the lead is extracted into methyl isobutyl ketone as the pyrrolidine dithiocarbamate complex and analyzed by flame atomic absorption spectrophotometry. Brain, heart, liver, lung, and spleen gave recoveries ranging from 92 to 102% with standard deviations of less than 8%. Aorta, kidney, and rib were unsuitable for analysis by this method. A large number of samples can be analyzed without specialized equipment or intricate experimental steps. The detection limit is 35 ng/g tissue (wet weight) and sensitivity is approximately 140 ng/g tissue (wet weight).

Brain Chemistry↗

PubMed1992

New conformationally restricted 99mTc N2S2 complexes as myocardial perfusion imaging agents.

In developing 99mTc complexes as potential myocardial imaging agents, a new series of ligands based on a conformationally restricted N2S2 system were investigated. Using piperazine or homopiperazine as the starting material, two N2S2 ligands (4a and 4b) with additional conformation restriction between the two nitrogen donor atoms were synthesized. The 99mTc complexes were prepared by a direct labeling method with tin(II) tartrate as the reducing agent for [99mTc]pertechnetate. The resulting 99mTc complexes were purified through a sulfonpropyl Sephadex column and further purified by HPLC with a reverse-phase column eluting with a solvent system of acetonitrile/buffer. Biodistribution studies in rats showed initial uptake in the heart (0.21%, 0.42% dose/order for [99mTc]4a and 4b at 2 min postinjection). Carrier-added preparation of [99mTc]4b was successful. NMR, IR, UV, crystallographic, and elemental analysis of the [99Tc]4b complex suggest that it contains a TcVO3+ center core and is 1+ charged. The results suggest that this series of 1+ charged 99mTc complexes may have potential as myocardial imaging agents, and further study of the complexes is warranted.

Animals↗