Solution Structure Of Complex Research Articles

Solution structure of the HIV-2 TAR-argininamide complex

The trans-activating region (TAR) RNA-Tat protein interaction is important for activation of transciption in the human immunodeficiency virus (HIV). A model complex for this interaction composed of the two base bulge HIV-2 TAR and the amide derivative of arginine was studied by multidimensional heteronuclear NMR. Because of the improved spectral properties of the HIV-2 TAR complex, a larger number of NOEs in the bulge region were observed than in earlier studies of the HIV-1 TAR-argininamide complex. A total of 681 NOE distance restraints were collected and used to determine the solution structure of the HIV-2 TAR-argininamide complex. As observed in the previously proposed model from this lab, the two A-form stems co-axially stack and the critical U23 and the argininamide are located in the major groove. Model calculations including non-experimental restraints indicate that U23 is within hydrogen bonding distance to A27 consistent with the formation of a U·A·U base-triple. Base-triple formation helps open the major groove to increase the accessibility of G26 to hydrogen bond donors from the guanidinium group of argininamide. Argininamide binding is stabilized by stacking of the guanidinium group between the bases of A22 and U23, forming an argininamide sandwich.

Synthesis, Structural Diversity, Dynamics, and Acidity of the M(II) and M(IV) Complexes [MH3(PR3)4]+ (M = Fe, Ru, Os; R = Me, Et)

The syntheses of complexes MH2L4 and their protonated analogues [MH3L4]+ (M = Fe (1), Ru (2), Os (3); R = Me (a), Et (b)) are described. The structures of 1a, 1b, and 3a were determined in X-ray diffraction studies. The solution structures of complexes 1−3 were established by detailed NMR investigations. 1a, 2b, and 3a form equilibrium mixtures of two isomers in solution. The iron (1a) and ruthenium (2b) complexes isomerize between six-coordinate M(II) dihydrogen cis-[MH(H2)L4]+ and seven-coordinate M(IV) trihydride [M(H)3L4]+ molecular geometries: the first is a distorted octahedron and the second can be viewed as a hydride-capped M(PR3)4 tetrahedron. Complex 3a is a pentagonal bipyramidal trihydride cis-[Os(H)3(PMe3)4]+ in equilibrium with the hydride-capped tetrahedral structural form. Trihydrides 1b and 3b are exclusively represented by the latter structural type. The cationic molecule 2a corresponds to a dihydrogen complex cis-[RuH(H2)(PMe3)4]+. The metal fragment [MH(PR3)4]+ is thus most reactive toward oxidative addition of H2 for osmium and iron, with a notably lower ability to reduce H2 for ruthenium. This trend and related properties are due to electronic rather than steric factors. All [MH3(PR3)4]+ species (1−3) are fluxional in solution. The intramolecular hydride exchanges and isomerizations were studied between 20 and −140 °C and quantitatively described in terms of their activation parameters. On the basis of these, mechanistic interpretations are provided. Finally the acid/base properties of the [MH3(PR3)4]+/M(H)2(PR3)4 systems were established in a series of NMR experiments in THF-d8. The pKa values range from 10.3 to 12.9 units and increase in the following order: 1a (10.3) < 2b (10.7) < 2a (10.9) < 3a (11.2) < 3b (12.9). This series demonstrates a higher acidity than that of the related [MH(H2)(PP)2]+ molecules with bidentate ligands. The complexes with monodentate phosphine ligands [MH3(PR3)4]+ (1−3) represent a new and distinguished family with structural, dynamic, and acid/base properties remarkably different from most of the other known [MH3L4]+ representatives.

Structure of DNA-cationic liposome complexes: DNA intercalation in multilamellar membranes in distinct interhelical packing regimes.

Cationic liposomes complexed with DNA (CL-DNA) are promising synthetically based nonviral carriers of DNA vectors for gene therapy. The solution structure of CL-DNA complexes was probed on length scales from subnanometer to micrometer by synchrotron x-ray diffraction and optical microscopy. The addition of either linear lambda-phage or plasmid DNA to CLs resulted in an unexpected topological transition from liposomes to optically birefringent liquid-crystalline condensed globules. X-ray diffraction of the globules revealed a novel multilamellar structure with alternating lipid bilayer and DNA monolayers. The lambda-DNA chains form a one-dimensional lattice with distinct interhelical packing regimes. Remarkably, in the isoelectric point regime, the lambda-DNA interaxial spacing expands between 24.5 and 57.1 angstroms upon lipid dilution and is indicative of a long-range electrostatic-induced repulsion that is possibly enhanced by chain undulations.

EXAFS studies of cesium complexation by dibenzo-crown ethers in tri-n-butyl phosphate

Cesium K- and L 3-edge EXAFS (Extended X-ray Absorption Fine Structure) have been evaluated as means of probing the interaction of cesium ions with several dibenzo-crown ethers in tri-n-butyl phosphate (TBP) under conditions proposed for the extraction of radiocesium from acidic nuclear wastes. K-edge EXAFS data are shown to be less satisfactory than the corresponding L 3-edge data, a result of the difficulties inherent in the use of high X-ray energies, the weak spectral contributions of carbon and oxygen at long distances, the disorder characteristic of solution systems, and the low cesium concentrations present. Despite these difficulties, the EXAFS data yield information on the solution structure of the cesium-crown ether complexes that complements results obtained from liquid–liquid extraction studies. Specifically, the coordination of cesium in TBP is shown to differ from that observed in the same solvent upon addition of a dibenzo-crown ether. In addition, cesium coordination by the crown ethers is shown to be unaffected by the presence of water or the identity of the counterion. Finally, the average Cs–O bond length is shown to decrease from 3.23(3) Å in the cesium di-(tert-butylbenzo)-18-crown-6 complex to 3.01(4) Å in the corresponding 21-crown-7 and 24-crown-8 compounds, a result consistent with extraction studies indicating 1:1 complex formation in the 21-crown-7 and 24-crown-8 systems and a mixture of 1:1 and 1:2 complexes for the 18-crown-6.

Specific labeling approaches to guanine and adenine imino and amino proton assignments in the AMP-RNA aptamer complex.

The secondary structure of a recently identified ATP-binding RNA aptamer consists of a purine-rich 11-residue internal loop positioned opposite a single guanine bulge flanked on either side by helical stem segments. The ATP ligand targets the internal loop and bulge domains, inducing a structural transition in this RNA segment on complex formation. Specifically, 10 new slowly exchanging proton resonances in the imino, amino and sugar hydroxyl chemical shift range are observed on AMP-RNA aptamer complex formation. This paper outlines site-specific labeling approaches to identify slowly exchanging imino (guanine) and amino (guanine and adenine) protons in internal loop and bulge segments of compact RNA folds such as found in the AMP-RNA aptamer complex. One approach incorporates 15N-labeled guanine (N1 imino and N2 amino positions) and 15N-labeled adenine (N6 amino position), one residue at a time, in the AMP-binding RNA aptamer, with labeling incorporation through chemical synthesis facilitated by generating the aptamer from two separate strands. The unambiguous assignments deduced from the 15N labeling studies have been verified from an independent labeling strategy where individual guanines in the internal loop have been replaced, one at a time, by inosines and assignments were made on the basis of the large 2 ppm downfield shift of the guanine imino protons on inosine substitution. The strengths and limitations of the inosine-for-guanine substitution approach emerge from our studies on the AMP-RNA aptamer complex. The assignment of the internal loop and bulge imino and amino protons was critical in our efforts to define the solution structure of the AMP-RNA aptamer complex since these slowly exchanging protons exhibit a large number of long-range intramolecular NOEs within the RNA, as well as intermolecular NOEs to the AMP in the complex. The current application of specific 15N and inosine labeling approaches for exchangeable imino and imino proton assignments in the nonhelical segments of an RNA aptamer complex in our laboratory complements selective 2H and 13C approaches to assign nonexchangeable base and sugar protons in RNA and ligand-RNA complexes reported in the literature.

Nuclear magnetic resonance, luminescence and structural studies of lanthanide complexes with octadentate macrocyclic ligands bearing benzylphosphinate groups

The solution and solid-state structures of lanthanide complexes of 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetryltetramethylenetetra(benzylphosphinate), L1a, and of its o-, m- and p-methoxybenzyl analogues (L2, L3, L4) have been investigated by NMR, relaxometry, crystallographic and photophysical methods. It has been shown that the number of proximate water molecules is dependent on the size of the bound lanthanide ion: the complex [LaL1a]– is nine-co-ordinate and adopts a twisted square-antiprismatic structure with one bound water molecule. The analogous [YL1a]–, [YbL1a]–, [GdL1a]– and [EuL1a]– complexes also adopt a twisted square-antiprismatic geometry, but are eight-co-ordinate, with no metal-bound water. Relaxivity studies with the gadolinium complexes showed that they are purely ‘outer-sphere’ contrast agents, but they associate strongly with proteins leading to a pronounced relaxivity enhancement. Detailed biodistribution studies with [GdL1a]– revealed avid biliary uptake at low doses and a well defined tendency for the complex to be cleared more slowly from tumour tissue, allowing tissue differentiation.

Encapsulating an amino acid in a DNA fold.

Here we present the first solution structure of a ligand-DNA aptamer complex. Our NMR-molecular dynamics structural studies of the interaction between argininamide and a DNA stem-loop complex establishes that the hairpin loop DNA binding site undergoes an adaptive conformational transition on complex formation. The tip of the DNA loop folds down towards the stem and sandwiches the bound argininamide between reversed Hoogsteen A.C and Watson-Crick G.C base pairs. The argininamide is encapsulated within the structured DNA loop and is stabilized by an intricate set of intermolecular hydrogen bonds and stacking interactions. The structure of the complex lays out the molecular principles defining both the architecture of the internal cavity and the recognition elements that could contribute to ligand discrimination.

Application of 1H-NOESY NMR Spectroscopy to the Investigation of Ion Pair Solution Structures of Organometallic Complexes by the Detection of Interionic Contacts

The interionic solution structures of trans-[Ru(PMe3)2(CO)(COMe)(pz2-CH2)]BPh4 and trans-[Ru(PMe3)2(CO)(COMe)(η2-pz3-CH)]BPh4 have been “directly” investigated by the detection of interionic contac...

Dissociation Kinetics of Nickel (II), Zinc (II) and Cadmium (II) Complexes of 1,7‐Diaza‐4,10,13‐trioxacyclopentadecane‐N,N′‐diacetic Acid and 1,10‐Diaza‐4,7,13,16‐tetraoxacyclooctadecane‐N,N′‐diacetic Acid

AbstractThe dissociation kinetics of the complexes of nickel(II), zinc(II) and cadmium(II) of 1,7‐diaza‐4,10,13‐trioxacyclopentadecane‐N,N′‐diacetic acid (K21DA) and 1,10‐diaza‐4,7,13,16‐tetraoxacyclooctadecane‐N,N′‐diacetic Acid (K22DA) were studied in constant ionic strength aqueous medium with various [H+]‐range, i.e., (0.88−53.9) × 10−5 M and (0.5−7.5) × 10−3 M. Copper(II) was used as the scavenger of free ligand and the rates of dissociation of these complexes have been found to be independent of (Cu2+]. All the complexes exhibit acid‐independent and acid‐dependent pathways. For NiK21DA, CdK21DA and CdK22DA complexes, the acid‐dependent rates are linear functions of [H+]. For NiK22DA and ZnK21DA complexes, a saturation kinetics is observed, i.e., [H+]‐dependence at low [H+] and [H+]‐independent at high [H+]. The rationalization of such different observations is proposed to be due to difference in complex solution structures rather than the thermodynamic stabilities. Influence of acetate content in the buffer, temperature, and total electrolyte concentration on the rate of dissociation has also been investigated and discussed.

Pseudocontact shifts used in the restraint of the solution structures of electron transfer complexes.

The geometry of the ferricytochrome b5-ferricytochrome c complex has been analysed using long-range interprotein paramagnetic dipolar shifts. Heteronuclear filtered NMR spectra of samples containing 15N-labelled cytochrome b5 in complex with unlabelled cytochrome c allowed unambiguous assessment of pseudocontact shifts relative to diamagnetic reference states. Because pseudocontact shifts can be observed for protons as much as 20 A from the paramagnetic centre, this approach allows study of electron transfer proteins in fast exchange. Our findings provide the first physical evidence confirming hypotheses presented in previous theoretical studies. This absence of certain predicted shifts that are expected based on the best fit to a static model of the complex suggests that cytochrome b5 is more dynamic in solution than in the crystal, in agreement with molecular dynamics simulations.

1H NMR and Molecular Modeling Study on the Inclusion Complex β-Cyclodextrin−Indomethacin

The solution structure of the inclusion complex between β-cyclodextrin (2) and the nonsteroidal anti-inflammatory agent indomethacin sodium salt (1) [1-(p-chlorobenzoyl)-5-methoxy-2-methylindoleacetic acid sodium salt] is investigated in D2O solution via 1H NMR spectroscopy. The guest molecule 1 exists in solution as a mixture of E and Z isomers in fast exchange on the NMR time scale, as shown by NOE experiments. Low-temperature 1H NMR spectra on indomethacin methyl ester (3) (soluble in CH2Cl2-d2) showed that the Z isomer is the most thermodynamically stable. Geometrical features of the host−guest inclusion complex between 2 and 1 are inferred from intermolecular dipolar contacts obtained by 1D NOE difference spectra and 2D ROESY experiments. A more detailed picture of the solution structure of the complex is obtained by combining NMR structural information and molecular dynamics and energy calculations on the inclusion complexes. Computations took into account the existence of two diastereomeric forms of the guest (E and Z), the two possible sites of interaction of the guest molecule with the cavity (i.e. the p-chlorobenzoyl ring and the indole ring system), and the different topologies for the entry of the guest into the host's cavity. The main finding that can be obtained from both experimental and theoretical data is that the complexation selectively stabilizes the E isomer with respect to Z. The inclusion complex is characterized by the interaction of the p-chlorobenzoyl moiety of 1E with the lipophilic cavity of the host 2, the entry being through the larger rim of the truncated cone of 2.

Solution Structure of Mithramycin Dimers Bound to Partially Overlapping Sites on DNA

Mithramycin (MTH) is a DNA-binding antitumor agent containing A-B disaccharide and C-D-E trisaccharide segments projecting from opposite ends of an aglycone chromophore. We have previously reported on the solution structure of the MTH-DNA 6-mer complex based on a combined NMR and molecular dynamics study. This study established that the Mg 2+-coordinated mithramycin dimer bound to a widened minor groove centered about the sequence-specific (G-C)·(G-C) site and that the C-D-E trisaccharide segments from individual monomers were directed towards opposite ends of the helix spanning a six base-pair segment. This research is now extended to the binding of mithramycin dimers to partially overlapping sites on the self-complementary d(T-A-G-C-T-A-G-C-T-A) 10-mer duplex. The six base-pair mithramycin dimer footprint centered about (G-C)·(G-C) steps should result in a potential steric clash in the center of the helix involving the inwardly pointing E-sugars of the pair of mithramycin dimers bound to the DNA 10-mer duplex. The MTH-d(T-A-G-C-T-A-G-C-T-A) complex (two MTH dimers per duplex) yields narrow and well-resolved NMR spectra, which have been assigned to identify intramolecular and intermolecular nuclear Overhauser enhancement (NOE) connectivities in the complex. The solution structure of the MTH-DNA 10-mer complex based on distance-restrained molecular dynamics calculations has defined the conformation of the drug and the DNA necessary for accommodation of the pair of mithramycin dimers on the DNA10-mer helix. Specifically, the inwardly pointing E-sugars retain their face-down alignment towards the floor of the minor groove and occupy adjacent binding sites in the center of the duplex. This is achieved, in part, through torsion angle differences in the glycosidic linkage bonds along the length of the inwardly pointing aglycone-C-D-E trisaccharide segment relative to its outwardly pointing aglycone-C-D-E trisaccharide counterpart in the complex. In addition, a pronounced kink at the central (T-A)·(T-A) step opens the minor groove and generates additional space to accommodate the inwardly pointing E-sugars at adjacent sites in the MTH-DNA 10-mer complex. These studies establish conformational plasticity in the C-D-E trisaccharide segment of the mithramycin dimer and deformability of the DNA helix allowing mithramycin dimers to bind to partially overlapping minor groove sites on the DNA helix.

Interactions of nickel(II) with histones. Stability and solution structure of complexes with CH3CO-Cys-Ala-Ile-His-NH2, a putative metal binding sequence of histone H3.

Nickel(II) compounds are established human carcinogens, but the molecular mechanisms underlying their activity are only partially known. One mechanism may include mediation by nickel of promutagenic oxidative DNA damage that depends on Ni(II) binding to chromatin. To characterize such binding at the histone moiety of chromatin, we synthesized the peptide CH3CO-Cys-Ala-Ile-His-NH2 (L), a model of the evolutionarily conserved motif in histone H3 with expected affinity for transition metals, and evaluated its reactivity toward Ni(II). Combined spectroscopic (UV/vis, CD, NMR) and potentiometric measurements showed that, at physiological pH, mixtures of Ni(II) and L yielded unusual macrochelate complexes, NiL and NiL2, in which the metal cation was bound through Cys and His side chains in a square-planar arrangement. Above pH 9, a NiH-3L complex was formed, structurally analogous to typical square-planar nickel complexes. These complexes are expected to catalyze oxidation reactions, and therefore, coordination of Ni(II) by the L motif in core histone H3 may be a key event in oxidative DNA base damage observed in the process of Ni(II)-induced carcinogenesis.

Solution Structure of a Quinomycin Bisintercalator-DNA Complex

A quinomycin antibiotic UK-63052 (designated QN) exhibits a chemical structure related to the antibiotic echinomycin which is known to bisintercalate into DNA. Common features among these antibiotics include two heterocyclic aromatic ring systems propagating from a cross-bridged cyclic octadepsipeptide scaffold. We report on the solution structure of the QN-d(A1-C2-A3-C4-G5-T6-G7-T8) complex (one QN molecule per duplex) based on a combined NMR-molecular dynamics study including intensity-based refinement. The 3-hydroxy quinaldic acid rings bisintercalate into the duplex at (A3-C4)·(G5-T6) steps and stack with flanking Watson-Crick A3·T6 and C4·G5 base-pairs. The intercalation sites at (A3-C4)·(G5-T6) steps are wedge-shaped and unwound, with significant unwinding also observed at the (C4-G5)·(C4-G5) step bracketed between the intercalation sites. The cross-bridged cyclic octadepsipeptide is positioned in the minor groove with the methyl groups on its Ala and NMe-MCp residues directed towards and making van der Waals contacts with the minor groove edge of the duplex. A pair of adjacent intermolecular hydrogen bonds groove edge of the duplex. A pair of adjacent intermolecular hydrogen bonds between the Ala backbone atoms and the G5 minor groove edge (Ala-NH to G5-N (3)and G5-NH 2e to Ala-CO) account for the sequence specificity associated with complex formation. The solution structure of the QN-DNA oligomer complex, which contains only Watson-Crick base-pairs flanking the bisintercalation site, is compared with the crystal structure of the related echinomycin-DNA oligomer complex, which contains Hoogsteen base-pairs on either side of the bisintercalation site.

ChemInform Abstract: Structures of Complexes in Solution Derived from X‐Ray Diffraction Measurements

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X-ray fluorescent and EXAFS studies of the electronic and spatial structure of dialkyl sulfides and their PdCl2 complexes in extraction systems

SKα, SKβ, ClKβ, ClKβ, and PdLβ2 X-ray fluorescent and PdK EXAFS spectra were obtained for some organic solutions of dialkyl sulfide complexes with palladium chloride. Solvent effects on the electronic and spatial structure of complexes in solution are discussed. In the benzene solution of [PdCl22(C6H13)2S], complex molecules interact with solvent molecules along a coordinate that is perpendicular to the plane of the complex molecule.

The structure of alpha-thrombin inhibited by a 15-mer single-stranded DNA aptamer.

The structure of a complex between human alpha-thrombin and a GGTTGGTGTGGTTGG 15-nucleotide consensus sequence has been solved by x-ray crystallography and refined at 2.9-A resolution to an R value of 0.159. As in solution, in the complex the single-stranded DNA folds into a structure with two G-quartets. The DNA is sandwiched between two different positively charged regions of two symmetry-related thrombin molecules in the crystal structure making ionic and hydrophobic interactions. One region is the fibrinogen recognition exosite and the other, the putative heparin binding site. The lack of inhibition of fibrinogen clotting and platelet activation by the DNA 15-mer with the Arg75-->Glu mutant of thrombin is consistent with the several salt bridges of the DNA in the fibrinogen exosite. The association of DNA with the heparin site of a neighboring molecule appears to simply compensate residual charge. Differences in the 15-mer loop conformations between the complex and NMR solution structures can be attributed to conformational changes upon thrombin binding. Although G-quadruplexes are favored in the presence of monovalent cations, there is no evidence of the latter in the thrombin complex.

Crystal and solution structure of a pendant-armed macrocyclic complex of palladium(II)

The synthesis and X-ray crystal structure of [Pd)py2[9]aneN2S)](BF4)2 (py2[9]aneN2S = 1-thia-4,7-bis(pyridylmethyl)diaza-cyclononane) (P21/n,a = 10.233(4) Å, b = 11.484(5) Å, c = 19.913(6) Å, β = 94.03(4)°, V = 2334(2) Å3, R = 0.0705, Rw = 0.0759 ) are presented. The crystal structure indicates a long range interaction (2.92 Å) between the planar palladium and the apical sulphur atom. Although this distance is longer than the value for a Pd—S bond observed normally there is evidence for a net positive interaction provided by the solution structure as determined by NMR spectroscopy. Comparative analysis of the structural features exhibited by this complex with similar nine-membered chelating ligands emphasizes the presence of an axial Pd—S bond.

Catalysis of allylic substitutions by Pd complexes of oxazolines containing an additional P, S, or Se Center. X-ray crystal structures and solution structures of chiral π-allyl palladium complexes of phosphinoaryloxazolines

Allylic alkylations with Pd complexes of chiral oxazolines with an additional donor P, S, or Se center are reported. Crystal and solution structures of palladium π-allyl complexes of phosphinoaryloxazolines were determined by X-ray crystallography and cross relaxation experiments, respectively. From the results conclusions concerning the steric course of allylic substitutions are drawn.

Solution structure of HIV-1 protease-allophenylnorstatine derivative inhibitor complex obtained from molecular dynamics simulation.

Structures of two enzyme-inhibitor complexes of human immunodeficiency virus-1 protease with allophenylnorstatine derivatives were obtained from molecular dynamics simulation in aqueous solution. The stronger inhibitor gave considerably smaller fluctuation at P3 site, which formed hydrogen bonding with the enzyme flap region.