Coadsorption of low-molecular weight aromatic and aliphatic alcohols and acids with the cationic surfactant, CTAB, on silica surfaces.

We have investigated the coadsorption of a range of small molecules with the cationic surfactant CTAB to silica surfaces over a range of concentrations and CTAB to solute ratios and compared the coadsorption with adsorption in the presence of the salicylate ion. We find that molecules with aromatic character and molecules with double bonds are most favorably adsorbed, and we attribute this to cation-π bonding between the surfactant headgroups and the π orbitals of the unsaturated bonds of the solute molecules. The adsorption is complex and depends on chemical interactions between the solute molecules and the surfactant, which are highly specific to the structure of the solute. To improve our understanding of the specifics of these interactions, we have performed one-dimensional rotating frame Overhauser spectroscopy (ROESY) nuclear magnetic resonance experiments. These experiments show the complexity of the intermolecular interactions and can be used to determine the position of the solute molecule with regard to the CTAB molecules in the adsorbed aggregates. The ROESY spectrum for the salicylate anion is distinct from those of the other solute molecules and suggests that the anions are dimerizing. Along with the cation-π bonding between the dimers, this provides a model for the strong influence that salicylate has on adsorption, micellar structure, and viscoelasticity. The ROESY data indicate that the catechol molecule interacts with all parts of the surfactant alkane chains such that they wrap around the molecule, but this has little effect on the interfacial curvature or aggregate shape. More intense isophthalic acid-CTAB intermolecular ROEs compared to those of other aromatic solutes are consistent with an interaction between isophthalic acid and the headgroups of two surfactant molecules that slows the intramicellar motion of isophthalic acid. Differences in interactions between solute molecules and the aliphatic surfactant chains do not result in changes in micelle structure.

The flanking sequence contributes to the immobilisation of spermine at the G-quadruplex in the NHE (nuclease hypersensitivity element) III1 of the c-Myc promoter.

Defining the molecular basis of the DNA sequence selectivity of polyamine binding is central to understanding polyamine-dependent gene expression. We have studied, by selective NMR experiments, the variation of spermine mobility and conformation in the presence of G-quadruplexes formed by sequences of the purine-rich strand of the c-Myc promoter, nuclease hypersensitivity element III1 (NHE III1). All the NHE quadruplexes restrict spermine mobility and induce a spermine conformational change but the most effective immobilisation occurs when all five G-tracts of the NHE III1 are present. This suggests structure within the nucleotides flanking the G-quadruplex has a role in immobilising spermine.

Insight into the molecular recognition of spermine by DNA quadruplexes from an NMR study of the association of spermine with the thrombin-binding aptamer.

The preferred residence sites and the conformation of DNA-bound polyamines are central to understanding the regulatory roles of polyamines. To this end, we have used a series of selective (13)C-edited and selective total correlation spectroscopy-edited one-dimensional (1D) nuclear Overhauser effect spectroscopy NMR experiments to determine a number of intramolecular (1)H nuclear Overhauser effect (NOE) connectivities in (13)C-labelled spermine bound to the thrombin-binding aptamer. The results provide evidence that the aptamer-bound spermine adopts a conformation that optimizes electrostatic and hydrogen bond contacts with the aptamer backbone. The distance between the nitrogen atoms of the central aminobutyl is reduced by an increase in the population of gauche conformers at the C6-C7 bonds, which results in either a curved or S-shaped spermine conformation. Molecular modelling contributes insight toward the mode of spermine binding of these spermine structures within the narrow grooves of DNA quadruplexes. In each case, the N5 ammonium group makes hydrogen bonds with two nearby phosphates across the narrow groove. Our results have implications for the understanding of chromatin structure and the rational design of quadruplex-binding drugs.

An investigation of the dynamics of spermine bound to duplex and quadruplex DNA by (13)C NMR spectroscopy.

A detailed analysis of the (13)C relaxation of (13)C-labelled spermine bound to duplex and quadruplex DNA is presented. T(1), T(2) and heteronuclear NOE data were collected at four (13)C frequencies (75.4, 125.7, 150.9 and 201.2 MHz). The data were analyzed in terms of a frequency-dependent order parameter, S (2)(omega), to estimate the generalized order parameter and the contributions to the relaxation from different motional frequencies in the picosecond-nanosecond timescale and from any exchange processes that may be occurring on the microsecond-millisecond timescale. The relaxation data was surprisingly similar for spermine bound to two different duplexes and a linear parallel quadruplex. Analysis of the relaxation data from these complexes confirmed the conclusions of previous studies that the dominant motion of spermine is independent of the macroscopic tumbling of the DNA and has an effective correlation time of approximately 50 ps. In contrast, spermine bound to a folded antiparallel quadruplex had faster relaxation rates, especially R (2). As with the other complexes, a fast internal motion of the order of 50 ps makes a substantial contribution to the relaxation. The generalized order parameter for spermine bound to duplex DNA and the linear quadruplex is small but is larger for spermine bound to the folded quadruplex. In the latter case, there is evidence for exchange between at least two populations of spermine occurring on the microsecond-millisecond timescale.

Solution structure of Domains IVa and V of the tau subunit of Escherichia coli DNA polymerase III and interaction with the alpha subunit.

The solution structure of the C-terminal Domain V of the tau subunit of E. coli DNA polymerase III was determined by nuclear magnetic resonance (NMR) spectroscopy. The fold is unique to tau subunits. Amino acid sequence conservation is pronounced for hydrophobic residues that form the structural core of the protein, indicating that the fold is representative for tau subunits from a wide range of different bacteria. The interaction between the polymerase subunits tau and alpha was studied by NMR experiments where alpha was incubated with full-length C-terminal domain (tau(C)16), and domains shortened at the C-terminus by 11 and 18 residues, respectively. The only interacting residues were found in the C-terminal 30-residue segment of tau, most of which is structurally disordered in free tau(C)16. Since the N- and C-termini of the structured core of tau(C)16 are located close to each other, this limits the possible distance between alpha and the pentameric deltatau2gammadelta' clamp-loader complex and, hence, between the two alpha subunits involved in leading- and lagging-strand DNA synthesis. Analysis of an N-terminally extended construct (tau(C)22) showed that tau(C)14 presents the only part of Domains IVa and V of tau which comprises a globular fold in the absence of other interaction partners.

Structure of the theta subunit of Escherichia coli DNA polymerase III in complex with the epsilon subunit.

The catalytic core of Escherichia coli DNA polymerase III contains three tightly associated subunits, the alpha, epsilon, and theta subunits. The theta subunit is the smallest and least understood subunit. The three-dimensional structure of theta in a complex with the unlabeled N-terminal domain of the epsilon subunit, epsilon186, was determined by multidimensional nuclear magnetic resonance spectroscopy. The structure was refined using pseudocontact shifts that resulted from inserting a lanthanide ion (Dy3+, Er3+, or Ho3+) at the active site of epsilon186. The structure determination revealed a three-helix bundle fold that is similar to the solution structures of theta in a methanol-water buffer and of the bacteriophage P1 homolog, HOT, in aqueous buffer. Conserved nuclear Overhauser enhancement (NOE) patterns obtained for free and complexed theta show that most of the structure changes little upon complex formation. Discrepancies with respect to a previously published structure of free theta (Keniry et al., Protein Sci. 9:721-733, 2000) were attributed to errors in the latter structure. The present structure satisfies the pseudocontact shifts better than either the structure of theta in methanol-water buffer or the structure of HOT. satisfies these shifts. The epitope of epsilon186 on theta was mapped by NOE difference spectroscopy and was found to involve helix 1 and the C-terminal part of helix 3. The pseudocontact shifts indicated that the helices of theta are located about 15 A or farther from the lanthanide ion in the active site of epsilon186, in agreement with the extensive biochemical data for the theta-epsilon system.

Lanthanide labeling offers fast NMR approach to 3D structure determinations of protein-protein complexes.

A novel nuclear magnetic resonance (NMR) strategy based on labeling with lanthanides achieves rapid determinations of accurate three-dimensional (3D) structures of protein-protein complexes. The method employs pseudocontact shifts (PCS) induced by a site-specifically bound lanthanide ion to anchor the coordinate system of the magnetic susceptibility tensor in the molecular frames of the two molecules. Simple superposition of the tensors detected in the two protein molecules brings them together in a 3D model of the protein-protein complex. The method is demonstrated with the 30 kDa complex between two subunits of Escherichia coli polymerase III, comprising the N-terminal domain of the exonuclease subunit epsilon and the subunit theta. The 3D structures of the individual molecules were docked based on a limited number of PCS observed in 2D 15N-heteronuclear single quantum coherence spectra. Degeneracies in the mutual orientation of the protein structures were resolved by the use of two different lanthanide ions, Dy3+ and Er3+.

Fast structure-based assignment of 15N HSQC spectra of selectively 15N-labeled paramagnetic proteins.

A novel strategy for fast NMR resonance assignment of (15)N HSQC spectra of proteins is presented. It requires the structure coordinates of the protein, a paramagnetic center, and one or more residue-selectively (15)N-labeled samples. Comparison of sensitive undecoupled (15)N HSQC spectra recorded of paramagnetic and diamagnetic samples yields data for every cross-peak on pseudocontact shift, paramagnetic relaxation enhancement, cross-correlation between Curie-spin and dipole-dipole relaxation, and residual dipolar coupling. Comparison of these four different paramagnetic quantities with predictions from the three-dimensional structure simultaneously yields the resonance assignment and the anisotropy of the susceptibility tensor of the paramagnetic center. The method is demonstrated with the 30 kDa complex between the N-terminal domain of the epsilon subunit and the theta subunit of Escherichia coli DNA polymerase III. The program PLATYPUS was developed to perform the assignment, provide a measure of reliability of the assignment, and determine the susceptibility tensor anisotropy.

Diastereoselectivity and molecular recognition in the self-assembly of double-stranded dinuclear metal complexes of the type [M2[(R,S)-tetraphos]2](PF6)2 (M = Ag and Au).

The ligand (R,S)-Ph(2)PCH(2)CH(2)P(Ph)CH(2)CH(2)P(Ph)CH(2)CH(2)PPh(2), (R,S)-tetraphos, combines with silver(I) and gold(I) ions in the presence of hexafluorophosphate to diastereoselectively self-assemble the head-to-head (H,H) diastereomers of the double-stranded, dinuclear metal complexes [M(2)[(R,S)-tetraphos](2)](PF(6))(2) in which the two chiral metal centers in the complexes have M (R end of phosphine) and P (S end of phosphine) configurations. The crystal and molecular structures of the compounds have been determined: (H,H)-(M,P) -[Ag(2)[(R,S)-tetraphos](2)](PF(6))(2), monoclinic, P2(1)/c, a = 10.3784(2), b = 47.320(1), c = 17.3385(4) A, beta = 103.8963(5) degrees, Z = 4; (H,H)-(M,P)-[Au(2)[(R,S)-tetraphos](2)](PF(6))(2), monoclinic, P.2(1) (No. 4, c unique axis), a = 24.385(4), b = 46.175(3), c = 14.820(4) A, Z = 8. The complexes crystallize as racemic compounds in which the unit cell in each case contains equal numbers of enantiomorphic molecules of the cation and associated anions. The cations in both structures have similar side-by-side structures of idealized C(2) symmetry, the bulk helicity of each molecule in the solid state being due solely to the twist of the central ten-membered ring containing the two metal ions of opposite configuration, which has the chiral twist-boat-chair-boat conformation. When 1 equiv each of (R,S)-tetraphos, (R,R)-(+/-)-tetraphos, (S,S)-(+)-tetraphos, 2 equiv of Ph(2)PCH(2)CH(2)PPh(2) (dppe), and 7 equiv of [AuCl(SMe(2))] in dichloromethane are allowed to react for several minutes in the presence of an excess of ammonium hexafluorophosphate in water (two phases), the products are the double-stranded digold(I) complexes in which each ligand strand has recognized itself by stereoselective self-assembly, together with [Au(dppe)(2)]PF(6).

A comparison of the association of spermine with duplex and quadruplex DNA by NMR.

The association of [1',1"-(13)C(2)]spermine ([1',1"-(13)C(2)]N,N'-bis(3-aminopropyl)-1,4-butanediamine) with duplex and quadruplex DNA has been studied by nuclear magnetic resonance spectroscopy. 1D NOESY experiments using two-way selective cross-polarization (ISI-SCP-NOESY) showed spermine intramolecular NOEs are either weakly positive or weakly negative when spermine is complexed to duplex B-DNA and linear four-stranded quadruplex DNA. In contrast, large negative intramolecular NOEs are observed when spermine is complexed to two distinct forms of folded quadruplex DNA suggesting greater immobilization of spermine on these folded DNA quadruplexes. No changes in the quadruplex stem structure are observed but there are minor changes to the loop structure of a two-stranded folded quadruplex on binding spermine.

Structural investigation of the hedamycin:d(ACCGGT)2 complex by NMR and restrained molecular dynamics.

Hedamycin, a member of the pluramycin family of drugs, displays a range of biological responses including antitumor and antimicrobial activity. The mechanism of action is via direct interaction with DNA through intercalation between the bases of the oligonucleotide and alkylation of a guanine residue at 5'-PyG-3' sites. There appears to be some minor structural differences between two earlier studies on the interaction of hedamycin with 5'-PyG-3' sites. In this study, a high-resolution NMR analysis of the hedamycin:d(ACCGGT)2 complex was undertaken in order to investigate the effect of replacing the thymine with a guanine at the preferred 5'-CGT-3' site. The resultant structure was compared with earlier work, with particular emphasis placed on the drug conformation. The structure of the hedamycin:d(ACCGGT)2 complex has many features in common with the two previous NMR structures of hedamycin:DNA complexes but differed in the conformation and orientation of the N,N-dimethylvancosamine saccharide of hedamycin in one of these structures. The preferential binding of hedamycin to 5'-CG-3' over 5'-TG-3' binding sites is explained in terms of the orientation and location of the N,N-dimethylvancosamine saccharide in the minor groove.