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PubMed1984

Visualization of drug-nucleic acid interactions at atomic resolution. VII. Structure of an ethidium/dinucleoside monophosphate crystalline complex, ethidium: uridylyl(3'-5') adenosine.

Ethidium forms a crystalline complex with the dinucleoside monophosphate, uridylyl (3'-5') adenosine (UpA). The complex crystallizes in the monoclinic space group P2l with unit cell dimensions, a = 13.704 A, b = 31.674 A, c = 15.131 A, beta = 113.9 degrees. This light atom structure has been solved to atomic resolution and refined by full matrix least squares to a residual of 0.12, using 3,034 observed reflections. The asymmetric unit consists of two ethidium molecules, two UpA molecules and 19 solvent molecules, a total of 145 non-hydrogen atoms. The two UpA molecules are hydrogen-bonded together by Watson-Crick type base pairing. Base-pairs in this duplex are separated by 6.7 A; this reflects intercalative binding by one of the ethidium molecules. The other ethidium molecule stacks on either side of the intercalated base-paired dinucleoside monophosphate, being related by a unit cell translation along the a axis. The conformation of the sugar-phosphate backbone accompanying intercalation has been accurately determined in this analysis, and contains the mixed sugar-puckering pattern: C3' endo (3'-5') C2' endo. This same structural feature has been observed in the ethidium-iodoUpA and ethidium-iodoCpG complexes, and exists in two additional structures containing ethidium-CpG. Taken together, these studies confirm our earlier sugar-puckering assignments and demonstrate that iodine covalently bound to the C5 position on uridine or cytosine does not alter the basic sugar-phosphate geometry or the mode of ethidium intercalation in these model studies. We have proposed this stereochemistry to explain the intercalation of ethidium (as well as other simple intercalators) into both DNA and into double-helical RNA, and discuss this aspect of our work further in this paper and in the accompanying papers.

Binding Sites↗

PubMed1999

An Lrp-type transcriptional regulator from Agrobacterium tumefaciens condenses more than 100 nucleotides of DNA into globular nucleoprotein complexes.

The PutR protein of Agrobacterium tumefaciens positively regulates expression of the putA gene in response to exogenous proline, resulting in the utilization of proline as a source of carbon and nitrogen. PutR activity required a region of DNA extending more than 106 nt upstream of the putA transcription start site. Purified PutR bound to this region with high degree of affinity and repressed expression of the putR promoter in vitro. PutR also activated the putA promoter in vitro in the presence of proline, though less strongly than in whole cells. PutR protected a DNA interval extending from nucleotides -30 to -140, but protected only one helical face over most of this interval, suggesting that it may bind only to this face of the DNA. The addition of proline caused a slight decrease in binding affinity and altered DNase I protection patterns along the entire length of the binding site. PutR-DNA complexes were found by atomic force microscopy to be globular rather than elongated. Although the DNA fragment in these complexes was 190 nm in length, the length of the visible DNA was only 150 nm, indicating that 40 nm of DNA (115 nt) must be condensed with protein. PutR caused a net bend of this binding site, and under some conditions, proline shifted the center of this bend by one helical turn.

Agrobacterium tumefaciens↗

PubMed2004

Atomic force microscopic analysis of the binding of the Schizosaccharomyces pombe origin recognition complex and the spOrc4 protein with origin DNA.

In eukaryotes, the initiation of DNA replication requires the interaction between origin sequences and the origin recognition complex (ORC), which is highly conserved. In this report, atomic force microscopy (AFM) was used to examine the binding of Schizosaccharomyces pombe (sp) ORC and the spOrc4 protein with the sp autonomously replicating sequence 1 (ars1). AFM imaging revealed that spORC binding to ars1 occurred solely through spOrc4p and depended on the N-terminal AT-hook domains present in spOrc4p. At high molar ratios of spORC (or spOrc4p alone) to DNA (6:1), all of the input ars1 was bound in a one protein complex to one plasmid manner. Restriction digestion and AFM analysis of protein-DNA fragments revealed the presence of two binding sites in ars1. One site mapped to a region centered at nucleotide 838 of ars1 previously detected by DNase I protection that was reported to be essential for the autonomously replicating sequence activity of ars1. The second site mapped to a previously uncharacterized region centered at nucleotide 1148. AFM showed that the length of the DNA fragment complexed with either spORC or spOrc4p was shortened by approximately 140 bp, suggesting the wrapping of two turns of the DNA around the spOrc4p alone as well as the spOrc4p in spORC. We also show that treatment of the spORC (spOrc4p)-ars1 complex with topoisomerase I induced a negative shift in the topoisomer distribution. These findings suggest that the binding of spORC to origin DNA alters the structure of the DNA. Thus, in the case of spORC, due to its unusual spOrc4p, at least two factors are likely to influence ars1 activation. These include the selective binding of the complex to A- and T-rich regions and the alteration of the DNA structure due to its wrapping around spOrc4p.

DNA↗

PubMed2005

Redshift and blueshift of the Ar-H vibrational stretching frequency in complexes of FArH and acetylene.

Two planar hydrogen-bonded complexes of FArH and acetylene were found to be stable using second-order Møller-Plesset perturbation theory (MP2) with 6-311++G(2d,2p) basis sets. The more stable complex involves bonding between the F atom of FArH and a H atom of acetylene, while the other isomer is a T-shaped complex with the H atom of FArH bonded to the center of the CC bond of acetylene; the zero-point energy corrected dissociation energies are 29 and 27 kJ mol(-1), respectively. Interestingly, the Ar-H harmonic vibrational stretching frequency is blueshifted in the more stable isomer and redshifted in the less stable form. The electron density rearrangement of FArH on complexation was investigated and used to explain these unusual findings.

Journal Article↗

PubMed2004

Synthesis of benzannulated N-heterocyclic carbene ligands by a template synthesis from 2-nitrophenyl isocyanide.

The reaction of 2-nitrophenyl isocyanide 2 with [M(CO)5(thf)] (M=Cr, Mo, W) yields the isocyanide complexes [M(CO)5(2)] (3: M=Cr; 4: M=Mo; 5: M=W). Complexes 3-5 react with elemental tin under reduction of the nitro function of the isocyanide ligand to give the complexes with the unstable 2-aminophenyl isocyanide ligand. The coordinated 2-aminophenyl isocyanide ligand in all three complexes reacts spontaneously under intramolecular nucleophilic attack of the primary amine at the isocyanide carbon atom to yield the complexes with the NH,NH-benzimidazol-2-ylidene ligand (6: M=Cr; 7: M=Mo; 8: M=W). An incomplete reduction of the nitro group in 3-5 is observed when hydrazine hydrate is used instead of tin. Here the formation of complexes with a coordinated 2-hydroxylamine-functionalized phenyl isocyanide [(CO)5M-CN-C6H(4-)-2-N(H)-OH] is postulated and this unstable ligand again undergoes intramolecular cyclization to give the NH,NOH-stabilized benzimidazol-2-ylidene complexes 9-11. The tungsten derivative 11 can be allylated stepwise by a deprotonation/alkylation sequence first at the OH and then at the NH position to yield the monoallylated and diallylated species 12 and 13. The molecular structures of 3-5 and 12-13 were established by X-ray crystallography.

Journal Article↗

PubMed2005

Architecture of the native photosynthetic apparatus of Phaeospirillum molischianum.

The ubiquity and importance of photosynthetic organisms in nature has made the molecular mechanisms of photosynthesis a widely studied subject at both structural and functional levels. A current challenge is to understand the supramolecular assembly of the proteins involved in photosynthesis in native membranes. We have used atomic force microscopy to study the architecture of the photosynthetic apparatus and analyze the structure of single molecules in chromatophores of Phaeospirillum molischianum. Core complexes are formed by the reaction center enclosed by an elliptical light harvesting complex 1. LH2 are octameric rings, assembled either with cores or in hexagonally packed LH2 antenna domains. The symmetry mismatch caused by octameric LH2 packing in a hexagonal lattice, that could be avoided in a square lattice, suggests lipophobic effects rather than specific inter-molecular interactions drive protein organization. The core and LH2 complexes are organized to form a supramolecular assembly reminiscent to that found in Rhodospirillum photometricum, and very different from that observed in Rhodobacter sphaeroides, Rb. blasticus, and Blastochloris viridis.

Bacterial Chromatophores↗

PubMed2000

Observation of an unexpected third receptor molecule in the crystal structure of human interferon-gamma receptor complex.

BACKGROUND: Molecular interactions among cytokines and cytokine receptors form the basis of many cell-signaling pathways relevant to immune function. Interferon-gamma (IFN-gamma) signals through a multimeric receptor complex consisting of two different but structurally related transmembrane chains: the high-affinity receptor-binding subunit (IFN-gammaRalpha) and a species-specific accessory factor (AF-1 or IFN-gammaRbeta). In the signaling complex, the two receptors probably interact with one another through their extracellular domains. Understanding the atomic interactions of signaling complexes enhances the ability to control and alter cell signaling and also provides a greater understanding of basic biochemical processes. RESULTS: The crystal structure of the complex of human IFN-gamma with the soluble, glycosylated extracellular part of IFN-gammaRalpha has been determined at 2.9 A resolution using multiwavelength anomalous diffraction methods. In addition to the expected 2:1 complex, the crystal structure reveals the presence of a third receptor molecule not directly associated with the IFN-gamma dimer. Two distinct intermolecular contacts, involving the edge strands of the C-terminal domains, are observed between this extra receptor and the 2:1 receptor-ligand complex thereby forming a 3:1 complex. CONCLUSIONS: The observed interactions in the 2:1 complex of the high-affinity cell-surface receptor with the IFN-gamma cytokine are similar to those seen in a previously reported structure where the receptor chains were not glycosylated. The formation of beta-sheet packing interactions between pairs of IFN-gammaRalpha receptors in these crystals suggests a possible model for receptor oligomerization of Ralpha and the structurally homologous Rbeta receptors in the fully active IFN-gamma signaling complex.

Binding Sites↗

PubMed2006

Dicoordinate copper(I) silanechalcogenolates.

The copper silanechalcogenolates tBu3PCuESiPh3 (1, E = O; 2, E = S; 3, E = Se) were prepared from the reaction of [tBu3PCu(CH3CN)3]BF4 with [Ph3SiELi(THF)2]2 in acetonitrile. The compounds were obtained as colorless, crystalline, but thermally labile solids. X-ray crystallography shows that complexes 1-3 are monomeric in the solid state with no Cu...Cu interactions. The Cu atoms have either a linear or a near-linear coordination geometry in all three complexes. Interestingly, the O atom in complex 1 is also linear, which is in contrast to the highly bent S (2) and Se analogues (3). Density functional theory calculations suggest that both the linear geometry of 1 and an associated extremely short Cu-O distance [1.769(4) A] are not the result of pi delocalization but are the result of a fine balance of electrostatic interaction and Pauli repulsion.

Chalcogens↗

PubMed2005

Parallel transformations of cyclohexene mediated by the Cp*W(NO) fragment.

Hydrogenolysis of Cp*W(NO)(CH2CMe3)2 at room temperature in cyclohexene results in the formation of the intermediate 16e organometallic complex, [Cp*W(NO)(eta2-cyclohexene)]. This intermediate leads to three parallel transformations of cyclohexene, namely (a) C-H activation of cyclohexene to form an eta3-cyclohexenyl hydrido complex, (b) combination of cyclohexene and H2 to form a cyclohexyl hydrido complex, and (c) coupling of two molecules of cyclohexene with concomitant loss of two hydrogen atoms to form a complex containing a novel eta1,eta3-(cyclohexyl)cyclohexenyl ligand. Single-crystal X-ray crystallographic analyses of products resulting from transformations (b) and (c) have been effected.

Journal Article↗

PubMed2003

Chiral organometallic half-sandwich complexes with defined metal configuration.

Chiral organometallic half-sandwich complexes with stereogenic metal atoms are close relatives of chiral organic compounds with stereogenic carbon atoms. Similarities and differences between these two classes of compounds are outlined. Some representative metal complexes are discussed in an introductory section followed by a more detailed treatment of the available strategies to control the metal configuration by means of chiral auxiliaries. Special sections are devoted to the discussion of the configurational stability of chiral-at-metal complexes and their applications in stoichiometric and catalytic stereoselective reactions.

Journal Article↗

PubMed2005

Chromatic adaptation of photosynthetic membranes.

Many biological membranes adapt in response to environmental conditions. We investigated how the composition and architecture of photosynthetic membranes of a bacterium change in response to light, using atomic force microscopy. Despite large modifications in the membrane composition, the local environment of core complexes remained unaltered, whereas specialized paracrystalline light-harvesting antenna domains grew under low-light conditions. Thus, the protein mixture in the membrane shows eutectic behavior and can be mimicked by a simple model. Such structural adaptation ensures efficient photon capture under low-light conditions and prevents photodamage under high-light conditions.

Adaptation, Biological↗

PubMed2000

Structure of an EF-Tu complex with a thiazolyl peptide antibiotic determined at 2.35 A resolution: atomic basis for GE2270A inhibition of EF-Tu.

The structure of a 1:1 molar complex between Escherichia coli elongation factor (EF) Tu-GDP and the cyclic thiazolyl peptide antibiotic, GE2270A, has been determined by X-ray diffraction analysis to a resolution of 2.35 A and refined to a crystallographic refinement factor of 20.6%. The antibiotic binds in the second domain of EF-Tu-GDP, making contact with three segments of amino acids (residues 215-230, 256-264, and 273-277). The majority of the protein-antibiotic contacts are van der Waals interactions. A striking feature of the antibiotic binding site is the presence of a salt bridge, not previously observed in other EF-Tu complexes. The ionic interaction between Arg 223 and Glu 259 forms over the antibiotic and probably accounts for the strong affinity observed between EF-Tu and GE2270A. Arg 223 and Glu 259 are highly conserved, but not invariant throughout the prokaryotic EF-Tu family, suggesting that the antibiotic may bind EF-Tu from some organisms better than others may. Superposition of the antibiotic binding site on the EF-Tu-GTP conformation reveals that one region of the antibiotic would form steric clashes with the guanine nucleotide-binding domain in the GTP, but not the GDP, conformation. Another region of the antibiotic binds to the same site as the aminoacyl group of tRNA. Together with prior biochemical studies, the structural findings confirm that GE2270A inhibits protein synthesis by blocking the GDP to GTP conformational change and by directly competing with aminoacyl-tRNA for the same binding site on EF-Tu. In each of the bacterial strains that are resistant to GE2270A, the effect of a site-specific mutation in EF-Tu could explain resistance. Comparison of the GE2270A site in EF-Tu with sequence homologues, EF-G and EF-1alpha, suggests steric clashes that would prevent the antibiotic from binding to translocation factors or to the eukaryotic equivalent of EF-Tu. Although GE2270A is a potent antibiotic, its clinical efficacy is limited by its low aqueous solubility. The results presented here provide the details necessary to enhance the solubility of GE2270A without disrupting its inhibitory properties.

Anti-Bacterial Agents↗

PubMed1981

Crystallographic refinement and atomic models of a human Fc fragment and its complex with fragment B of protein A from Staphylococcus aureus at 2.9- and 2.8-A resolution.

The model of human Fc fragment was refined at 2.9-A resolution. Two different automated procedures for crystallographic refinement were used [Deisenhofer, J., & Steigemann, W. (1975) Acta Crystallogr., Sec. B B31, 238; Jack, A., & Levitt, M. (1978) Acta Crystallogr., Sect. A A34, 931]. The final R value is 0.22. The dimer of CH3 domains closely resembles the CH1-CL aggregate in Fab fragments. There is no contact between CH2 domains. The contact between CH2 and CH3 domains has about one-third of the size of the CH3-CH3 contact. The carbohydrate, a branched chain of nine hexose units, covers parts of the C-contact face of the CH2 domain, shielding hydrophobic residues on this surface. Six atoms of the carbohydrate are within hydrogen-bonding distance of atoms in the CH2 domain. Crystallographic refinement of the complex between Fc fragment and fragment B of protein A from Staphylococcus aureus reduced the R value of the model is 0.24. A major part of the structure of fragment B consists of two alpha helics; the rest of the polypeptide chain is folded irregularly. In the crystal, fragment B forms two contacts with Fc fragment molecules. Contact 1 involves residues from both helices of fragment B, and residues from the CH2 and CH3 domains of FC, and is predominantly hydrophobic. Contact 2 is smaller than contact 1. Residues from the second helix and adjacent residues of fragment B and residues only from the CH3 domain of Fc contribute to contact 2. The nature of contact 2 is mainly polar and includes a sulfate ion. There are strong arguments that contact 1 is the fragment B-Fc contact formed in solution under physiological conditions, while contact 2 is a crystal contact.

Humans↗

PubMed2001

Viewing of complex molecules of ethidium bromide and plasmid DNA in solution by atomic force microscopy.

Tertiary structure changes in plasmid DNA, induced by ethidium bromide intercalation, have been observed in aqueous solutions by the use of an atomic force microscope. A relaxed closed circular pBR322 molecule became a positively supercoiled complex on the drug binding. The supercoiling always resulted in an interwound (or a plectonemic) form, but never a solenoidal (or a toroidal) form. A quantitative analysis of the compactness of such supercoiled complexes has been carried out.

DNA↗

PubMed2002

Tetrakis(dimethyl sulfide)palladium(II) bis(tetrafluoroborate) and tetrakis(1,4-oxathiane-kappaS)palladium(II) bis(tetrafluoroborate).

Tetrakis(dimethyl sulfide)palladium(II) bis(tetrafluoroborate), [Pd(C(2)H(6)S)(4)](BF(4))(2), (I), and tetrakis(1,4-oxathiane-kappaS)palladium(II) bis(tetrafluoroborate), [Pd(C(4)H(8)OS)(4)](BF(4))(2), (II), both crystallize as mononuclear square-planar complexes with tetrafluoroborate as the counter-ions. The Pd atom accepts four S-donor atoms and is positioned at an inversion centre in both compounds. The two unique S atoms in the dimethyl sulfide complex, (I), are disordered. The Pd-S distances are in the range 2.3338(12)-2.3375(12)A in (I), and the corresponding distances in the thioxane complex, (II), are 2.3293(17) and 2.3406(17)A. The anions in both compounds interact weakly with the Pd atom.

Journal Article↗

PubMed2005

Formation and characterization of thorium methylidene CH2=ThHX complexes.

Laser-ablated thorium atoms react with methyl fluoride to give the CH2=ThHF molecule as the major product observed and trapped in solid argon. Infrared spectroscopy, isotopic substitution, and density functional theoretical frequency calculations confirm the identification of this methylidene complex. The four strongest computed absorptions (Th-H stretch, Th=C stretch, CH2 wag, and Th-F stretch) are the four vibrational modes observed. The CH2=ThHCl and CH2=ThHBr species formed from methyl chloride and methyl bromide exhibit the first three of these modes in the infrared spectra. The computed structures (B3LYP and CCSD) show considerable agostic interaction, similar to that observed for the Group 4 CH2=MHX (M = Ti, Zr, Hf) methylidene complexes, and the agostic angle and C=Th bond length decrease slightly in the CH2=ThHX series (X = F, Cl, Br).

Journal Article↗

PubMed1997

Evaluation of Distribution Constants of Lanthanoid(III) Acetylacetonates between Sodium Dodecyl Sulfate Micelles and Water by Micellar Capillary Electrophoresis

The solubilization behavior of acetylacetonate complexes of lanthanoids(III) (Nd, Sm, Tb, and Tm) in sodium dodecyl sulfate micelles has been quantitatively evaluated by means of micellar capillary electrophoresis. From analysis of the migration times of the lanthanoid complexes, assuming incorporation of the cationic bis-acetylacetonates as well as the neutral tris-acetylacetonates into the anionic micelles, the distribution constant of each species between the micelles and water (Kmc/w) was determined. The distribution constants obtained were compared with those of the tris-acetylacetonates between heptane and water (Khep/w). The Kmc/w value of the neutral complex is smaller than that of the cationic one but much larger than the Khep/w value. The Kmc/w and Khep/w values of the neutral complex increase with increasing atomic number of the lanthanoid, whereas the opposite tendency was observed for Kmc/w of the cationic complex. Copyright 1997 Academic Press. Copyright 1997Academic Press

Journal Article↗

PubMed1993

Atomic structures of the human immunophilin FKBP-12 complexes with FK506 and rapamycin.

High resolution structures for the complexes formed by the immunosuppressive agents FK506 and rapamycin with the human immunophilin FKBP-12 have been determined by X-ray diffraction. FKBP-12 has a novel fold comprised of a five-stranded beta-sheet wrapping around a short alpha-helix with an overall conical shape. Both FK506 and rapamycin bind in the cavity defined by the beta-sheet, alpha-helix and three loops. Both FK506 and rapamycin bind in similar fashions with a set of hydrogen bonds and an unusual carbonyl binding pocket. Bound FK506 has a different conformation than free (crystalline) FK506 while rapamycin's bound conformation is virtually identical to that of unbound rapamycin. FKBP-12 is a peptidyl-prolyl isomerase (PPIase), and the structures of the complexes suggest ways in which this catalytic activity could operate. The different complexes are active in suppressing different steps of T cell activation, an activity seemingly unconnected with the PPIase activity.

Amino Acid Sequence↗