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Self-association
Selected AbstractsSelf-Association of Bis-Dendritic Organogelators: The Effect of Dendritic Architecture on Multivalent Cooperative InteractionsCHEMISTRY - A EUROPEAN JOURNAL, Issue 8 2010Myungeun Seo Dr. Abstract A series of bis-dendritic gelators consisting of a benzamide dendron and an alkyl dendron were synthesized to investigate the dendritic effect on self-assembly. The gelators with a first-generation benzamide (benzamide- G1) dendron or a first-generation alkyl (alkyl- G1) dendron formed stable gels in most aromatic solvents, and their self-assembled fibrillar networks were imaged by electron microscopy. The unbranched molecule (G0 - G0) or the molecule possessing a second-generation benzamide (benzamide- G2) dendron did not form gels. Differential scanning calorimetry, powder X-ray diffraction, and Fourier transform IR studies revealed that introduction of a dendritic branch strongly affected the molecular packing as well as the strength of intermolecular interactions. Furthermore, concentration-dependent diffusion coefficient measurements and the evaluation of association constants by 1H NMR spectroscopy indicated that bis-dendritic gelators with a benzamide- G1 dendron possessed high association constants and formed large aggregates, whereas molecules with a single benzamide formed dimers in chloroform. The formation of self-assembled fibrillar networks was driven by the multivalent and cooperative hydrogen bonding observed in the benzamide- G1 dendrons. ,,, stacking of aromatic groups and van der Waals interactions between alkyl chains also played roles in the self-assembly process, thus indicating that a spatial balance between two dendrons is important. [source] Using Diffusion NMR To Characterize Guanosine Self-Association: Insights into Structure and MechanismCHEMISTRY - A EUROPEAN JOURNAL, Issue 1 2005Mark S. Kaucher Abstract This paper presents results from a series of pulsed field gradient (PFG) NMR studies on lipophilic guanosine nucleosides that undergo cation-templated assembly in organic solvents. The use of PFG-NMR to measure diffusion coefficients for the different aggregates allowed us to observe the influences of cation, solvent and anion on the self-assembly process. Three case studies are presented. In the first study, diffusion NMR confirmed formation of a hexadecameric G-quadruplex [G,1]16,4,K+,4,pic, in CD3CN. Furthermore, hexadecamer formation from 5,-TBDMS-2,,3,-isopropylidene G,1 and K+ picrate was shown to be a cooperative process in CD3CN. In the second study, diffusion NMR studies on 5,-(3,5-bis(methoxy)benzoyl)-2,,3,-isopropylidene G,4 showed that hierarchical self-association of G8 -octamers is controlled by the K+ cation. Evidence for formation of both discrete G8 -octamers and G16 -hexadecamers in CD2Cl2 was obtained. The position of this octamer,hexadecamer equilibrium was shown to depend on the K+ concentration. In the third case, diffusion NMR was used to determine the size of a guanosine self-assembly where NMR signal integration was ambiguous. Thus, both diffusion NMR and ESI-MS show that 5,- O -acetyl-2,,3,- O -isopropylidene G,7 and Na+ picrate form a doubly charged octamer [G,7]8,2,Na+,2,pic,9 in CD2Cl2. The anion's role in stabilizing this particular complex is discussed. In all three cases the information gained from the diffusion NMR technique enabled us to better understand the self-assembly processes, especially regarding the roles of cation, anion and solvent. [source] Self-Association Based on Interfacial Structured Water Leads to {Mo154},1165 Super Clusters: A Dielectric StudyCHEMPHYSCHEM, Issue 5 2007Alla Oleinikova Dr. Surface water does the job: Molybdenum blue solutions contain unique nanosized wheel-shaped polyoxometalate-type clusters, while structured surface water on the clusters initiates the assembly, leading to the super cluster shown in the figure, which contains an internal "water pool". [source] Self-association of cromolyn sodium in aqueous solution characterized by nuclear magnetic resonance spectroscopyJOURNAL OF PHARMACEUTICAL SCIENCES, Issue 5 2004Xuan Ding Abstract The major objective of this study was to investigate and characterize the solution properties of cromolyn sodium (in D2O or D2O/H2O phosphate buffer at pH 7.5) using nuclear magnetic resonance (NMR) spectroscopy. The self-association of cromolyn molecules was examined primarily via one-dimensional 1H and 13C, and two-dimensional homonuclear NOESY NMR. Significant spectral shifts were observed for a majority of cromolyn 1H and 13C resonances, and are attributed to inter-molecular ring-stacking association accompanied by intra-molecular conformational changes. The critical self-association concentration was determined to be 10 mg/mL at pH 7.5 and 25°C by measuring the chemical shift of a specific cromolyn 1H resonance. The observed magnitude and sign changes of NOESY correlations indicate the formation of cromolyn aggregates with restricted molecular mobility. Mesomorphic liquid crystal formation is suggested by uniformly pronounced line broadening in concentrated cromolyn solutions; the transition concentration was approximately 60 mg/mL at 25°C, which is consistent with literature findings based on other techniques. A stronger tendency toward association was observed at lower temperature but aggregation appeared to be independent of pH. Lastly, it was concluded that self-association of cromolyn is promoted by the presence of monovalent cations as a result of reduced electrostatic repulsive forces. © 2004 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 93:1351,1358, 2004 [source] Self-association and cyclodextrin solubilization of drugsJOURNAL OF PHARMACEUTICAL SCIENCES, Issue 11 2002Thorsteinn Loftsson Abstract Phase-solubility diagrams are frequently used to calculate stoichiometry of drug/cyclodextrin complexes. Linear diagrams (AL -type systems) are thought to indicate that the complexes are first order with respect to cyclodextrin and first or higher order with respect to the drug. Positive deviation from linearity (AP -type systems) are thought to indicate formation of complexes that are first order with respect to the drug but second or higher order with respect to cyclodextrin. The phase solubility of several different compounds, i.e., cholesterol, ibuprofen, diflunisal, alprazolam, 17,-estradiol and diethylstilbestrol, and various charged and uncharged cyclodextrins was investigated. Phase-solubility diagrams of cholesterol in aqueous cyclodextrin solutions were all of AP type. However, the phase-solubility diagrams obtained with charged cyclodextrins could not be fitted to complexes of second or higher order with respect to cyclodextrin. The phase-solubility diagrams of ibuprofen and diflunisal were of AL type with slope greater than unity indicating formation of 2:1 drug/cyclodextrin complexes. However, Job's plots and space filling docking studies indicated that 1:1 complexes were formed. These and other observations show that stoichiometry of drug/cyclodextrin complexes cannot be derived from simple phase-solubility studies. Furthermore, the results indicate that drug/cyclodextrin complexes can self-associate to form water-soluble aggregates, which then can further solubilize the drug through non-inclusion complexation. © 2002 Wiley-Liss, Inc. and the American Pharmaceutical Association J Pharm Sci 91:2307,2316, 2002 [source] Self-association of EPEC intimin mediated by the ,-barrel-containing anchor domain: a role in clustering of the Tir receptorMOLECULAR MICROBIOLOGY, Issue 1 2004Thierry Touzé Summary Outer membrane intimin directs attachment of enteropathogenic Escherichia coli (EPEC) via its Tir receptor in mammalian target cell membranes. Phosphorylation of Tir triggers local actin polymerization and the formation of ,pedestal-like' pseudopods. We demonstrate that the intimin protein contains three domains, a flexible N-terminus (residues 40,188), a central membrane-integrated ,-barrel (189,549), and a tightly folded Tir-binding domain (550,939). Intimin was shown by electron microscopy to form ring-like structures with a ,7 nm external diameter and an electron dense core, and to form channels of 50picoSiemens conductance in planar lipid bilayers. Gel filtration, multiangle light scattering and cross-linking showed that this central ,-barrel membrane-anchoring domain directs intimin dimerization. Isothermal titration calorimetry revealed a high affinity, single-binding site interaction of 2 : 1 stoichiometry between dimeric intimin and Tir, and modelling suggests that this interaction determines a reticular array-like superstructure underlying receptor clustering. In support of this model, actin rearrangement induced in Tir-primed cultured cells by intimin-containing proteoliposomes was dependent on the concentration of both intimin and Tir, and co-localized with clustered phosphorylated Tir. [source] Self-association of an amphipathic helix peptide inhibitor of HIV-1 integrase assessed by electro spray ionization mass spectrometry in trifluoroethanol/water mixturesRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 5 2001S. Fermandjian Establishing the auto-associative properties of a molecule in solution can be important for determination of its structure and function. EAA26 (VESMNEELKKIIAQVRAQAEHLKTAY) has been designed to inhibit HIV-1 integrase via formation of a stable coiled-coil structure with a nearly homologous segment in the enzyme. The latter catalyzes the permanent incorporation of a DNA copy of the retrovirus genome into host cell DNA, and is thus essential to the life of the retrovirus. This makes integrase an obvious drug target in the therapy of AIDS. The present work has demonstrated, using electrospray ionization mass spectrometry (ESI-MS), that EAA26 is monomeric in pure water, and tetrameric and dimeric at respectively low and medium concentrations of 2,2,2-trifluoroethanol (TFE), and again monomeric at higher TFE concentrations. Thus, the apolar solvent TFE may contribute to either stabilization or disruption of the intermolecular hydrophobic contacts depending on its concentration in aqueous solution. Previous NMR and ultracentifugation results are thus confirmed, indicating the reliability of ESI-MS for defining the self-association state of biologically relevant peptides in both water and organic-water solutions. Copyright © 2001 John Wiley & Sons, Ltd. [source] The absence of inorganic salt is required for the crystallization of the complete oligomerization domain of Salmonella typhimurium histone-like nucleoid-structuring proteinACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 4 2010Paul G. Leonard The histone-like nucleoid-structuring protein (H-NS) plays an important role in both DNA packaging and global gene regulation in enterobacteria. Self-association of the N-terminal domain results in polydisperse oligomers that are critical to the function of the protein. This heterogeneity in oligomer size has so far prevented structure determination of the complete oligomerization domain by NMR or X-ray crystallography. In the absence of inorganic salt, the H-NS oligomerization domain is predominantly restricted to an equilibrium between a homodimer and homotetramer, allowing a protein solution to be prepared that is sufficiently homogeneous for successful crystallization. Crystallization was achieved by tailoring the conditions screened to those identified as minimizing the potential disruption of protein-solution homogeneity. This finding provides a significant step towards resolving the structure of this important prokaryotic protein. [source] Structure and chiroptical properties of supramolecular flower pigmentsCHIRALITY, Issue 2 2006George A. EllestadArticle first published online: 30 DEC 200 Abstract Research over the last 30 years has shown that at physiological concentrations of ca. 5 × 10,3 M, flower pigments composed of anthocyanins, either alone or complexed with flavone copigments, and frequently with metals, are self-assembled into non-covalent, chiral supramolecular complexes. This serves several biological functions including color stability, protection against UV radiation and provision for specific colors to attract insects for pollination. Self-association of the monomers takes place under conditions of molecular crowding by precise matching of the ,,, stacking interactions of the aromatic chromophores and intermolecular hydrogen bonding between the attached sugars. The resulting handedness is controlled by the chiral information provided by the sugars joined glycosidically at certain positions around the periphery of the aromatic nuclei. This review gives an overview of (i) the physicochemical evidence including circular dichroism, 1H NMR, and X-ray analysis for the structure and supramolecular chirality of these amphiphilic complexes, (ii) the role of the sugars on directing the chirality of the resulting supramolecules, (iii) the energetics of monomer association, and (iv) the possible influence of stacking chirality on insect pollination. © 2005 Wiley-Liss, Inc. Chirality 18:134,144, 2006. [source] Conformational effects on the performance and selectivity of a polymeric pseudostationary phase in electrokinetic chromatographyELECTROPHORESIS, Issue 4-5 2005Jonathan P. McCarney Abstract The effect of the conformation of a polymeric pseudostationary phase on performance and selectivity in electrokinetic chromatography was studied using an amphiphilic pH-responsive polymer that forms compact intramolecular aggregates (unimer micelles) at low pH and a more open conformation at high pH. The change in conformation was found to affect the electrophoretic mobility, retention, selectivity, and separation efficiency. The low-pH conformer has higher electrophoretic mobility and greater affinity for most solutes. The unimer micelle conformation was also found to provide a solvation environment more like that of micelles and other amphiphilic self-associative polymers studied previously. It was not possible to fully characterize the effect of conformation on efficiency, but very hydrophobic solutes with long alkyl chains appeared to migrate with better efficiency when the unimer micelle conformation was employed. The results imply that polymers with a carefully optimized lipophilic-hydrophilic balance that allow self-association will perform better as pseudostationary phases. In addition, the results show that electrokinetic chromatography is a useful method for determining the changes in solvation environment provided by stimuli-responsive polymers with changes in the conditions. [source] Modulation of glucocorticoid receptor-interacting protein 1 (GRIP1) transactivation and co-activation activities through its C-terminal repression and self-association domainsFEBS JOURNAL, Issue 10 2006Pei-Yao Liu Glucocorticoid receptor-interacting protein 1 (GRIP1), a p160 family nuclear receptor co-activator, possesses at least two autonomous activation domains (AD1 and AD2) in the C-terminal region. AD1 activity appears to be mediated by CBP/p300, whereas AD2 activity is apparently mediated through co-activator-associated arginine methyltransferase 1 (CARM1). The mechanisms responsible for regulating the activities of AD1 and AD2 are not well understood. We provide evidence that the GRIP1 C-terminal region may be involved in regulating its own transactivation and nuclear receptor co-activation activities through primary self-association and a repression domain. We also compared the effects of the GRIP1 C terminus with those of other factors that functionally interact with the GRIP1 C terminus, such as CARM1. Based on our results, we propose a regulatory mechanism involving conformational changes to GRIP1 mediated through its intramolecular and intermolecular interactions, and through modulation of the effects of co-repressors on its repression domains. These are the first results to indicate that the structural components of GRIP1, especially those of the C terminus, might functionally modulate its putative transactivation activities and nuclear receptor co-activator functions. [source] DEGRADATION KINETICS OF ANTHOCYANIN IN ETHANOLIC SOLUTIONSJOURNAL OF FOOD PROCESSING AND PRESERVATION, Issue 5 2006KUO-CHAN TSENG ABSTRACT The objective of this study was to investigate the degradation kinetics of anthocyanin in ethanolic model solutions simulating wine and liqueur in aging or long-term storage. Malvidin-3-glucoside, as the predominant anthocyanin in many cultivars of grape, was chosen to represent anthocyanins. The results from high performance liquid chromatography analysis show that the disappearance of malvidin-3-glucoside follows apparent first-order kinetics, and accelerates with the increase in ethanol concentration. The Ea values were found to be 22.80, 24.45, 24.35 and 22.75 kcal/mole at 0, 10, 30 and 50% ethanol concentrations, respectively. We propose that the decreased stability of anthocyanin at an elevated ethanol concentration is a result of a decreased extent of self-association in the solution. [source] The structural organization in aqueous solutions of ionic liquidsAICHE JOURNAL, Issue 1 2009Xiao Zhu Abstract The 1H NMR combined with the local composition (LC) model has been employed to investigate the structural organization of two aqueous solutions of ionic liquids (ILs), namely 1-ethyl-3-methylimidazolium tetrafluoroborate (EmimBF4) and n-butylammonium nitrate (N4NO3). The correlation of chemical shifts using the LC model shows that the self-association of IL plays the leading role, and water prefers to interact with IL rather than self-association in IL-rich region. Instead the network of water molecules is established in water-rich region, because the self-association of water predominates. Furthermore, the difference between the local and the bulk composition presents the turnover at x(IL) (mole fraction of IL) close to 0.6 for EmimBF4/water, which is in accordance with the change of excess function. Accordingly, it could be presumed that the excess properties for N4NO3/water system should behave turnover at x(IL) , 0.55 since the local and the bulk exhibit maximal difference at this composition. © 2008 American Institute of Chemical Engineers AIChE J, 2009 [source] Role of side chains in collagen triple helix stabilization and partner recognition,JOURNAL OF PEPTIDE SCIENCE, Issue 3 2009Rita Berisio Abstract Collagen is a widespread protein family involved in a variety of biological processes. The complexity of collagen and its fibrous nature prevent detailed investigations on the full-length protein. Reductionist approaches conducted by dissecting the protein complexity through the use of model peptides have proved to be quite effective. There are, however, several issues regarding structure,stability relationships, aggregation in higher-order assemblies, and partner recognition that are still extensively investigated. In this review, we discuss the role that side chains play in triple helix stabilization and in partner recognition. On the basis of recent literature data, we show that collagen triple helix stability is the result of the interplay of different factors. As a general trend, interactions established by amino/imino acid side chains within the triple helix scaffold effectively modulate the intrinsic residue propensity for this common structural motif. The use of peptide models has also highlighted the role that side chains play in collagen self-association and in its interactions with receptors. Valuable examples in these fields are illustrated. Finally, future actions required to obtain more detailed information on the structure and the function of this complex protein are also delineated. Copyright © 2008 European Peptide Society and John Wiley & Sons, Ltd. [source] Sequence shuffle controls morphological consequences in a self-assembling tetrapeptide,JOURNAL OF PEPTIDE SCIENCE, Issue 2 2008K. B. Joshi Abstract Peptide and protein self-assembly is a well-studied phenomenon in chemistry and biology, where nanoscopic building blocks exhibit rapid self-association to reveal supramolecular aggregates of defined structural features. These superstructures are stabilized by hydrophobic interactions, hydrogen bonding and a host of other noncovalent interactions. Thus, amino acid side chains in the primary structure hold importance in dictating secondary structures and preference for particular conformational signatures in peptide aggregates. This report describes contrasting nanoscale morphologies in antamanide-derived synthetic tetrapeptide mutants, which are composed by shuffling only two amino acids: phenylalanine and proline. Remarkable differences in ultrastructures in primary sequence-shuffled tetrapeptides suggest dissimilar aggregational pathways due to context-dependent location of proline and phenylalanine residues with respect to one another. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd. [source] Characterizing bathocuproine self-association and subsequent binding to Alzheimer's disease amyloid ,-peptide by NMRJOURNAL OF PEPTIDE SCIENCE, Issue 4 2004Shenggen Yao Abstract Aggregated amyloid ,-peptide (A,) is the primary constituent of the extracellular plaques and perivascular amyloid deposits associated with Alzheimer's disease (AD). Deposition of the cerebral amyloid plaques is thought to be central to the disease progression. One such molecule that has previously been shown to ,dissolve' deposited amyloid in post-mortem brain tissue is bathocuproine (BC). In this paper 1H NMR chemical shift analysis and pulsed field gradient NMR diffusion measurements were used to study BC self-association and subsequent binding to A,. The results show that BC undergoes self-association as its concentration increases. The association constant of BC dimerization, Ka, was estimated to be 0.64 mM,1 at 25°C from 1H chemical shift analysis. It was also found that dimerization of BC appeared to be essential for its binding to A,. From the self-association constant of BC, Ka, the fraction of dimeric BC in the complex was obtained and the dissociation constant, Kd, of BC bound to A,40 peptide was then determined to be ,1 mM. Copyright © 2003 European Peptide Society and John Wiley & Sons, Ltd. [source] Self-association of cromolyn sodium in aqueous solution characterized by nuclear magnetic resonance spectroscopyJOURNAL OF PHARMACEUTICAL SCIENCES, Issue 5 2004Xuan Ding Abstract The major objective of this study was to investigate and characterize the solution properties of cromolyn sodium (in D2O or D2O/H2O phosphate buffer at pH 7.5) using nuclear magnetic resonance (NMR) spectroscopy. The self-association of cromolyn molecules was examined primarily via one-dimensional 1H and 13C, and two-dimensional homonuclear NOESY NMR. Significant spectral shifts were observed for a majority of cromolyn 1H and 13C resonances, and are attributed to inter-molecular ring-stacking association accompanied by intra-molecular conformational changes. The critical self-association concentration was determined to be 10 mg/mL at pH 7.5 and 25°C by measuring the chemical shift of a specific cromolyn 1H resonance. The observed magnitude and sign changes of NOESY correlations indicate the formation of cromolyn aggregates with restricted molecular mobility. Mesomorphic liquid crystal formation is suggested by uniformly pronounced line broadening in concentrated cromolyn solutions; the transition concentration was approximately 60 mg/mL at 25°C, which is consistent with literature findings based on other techniques. A stronger tendency toward association was observed at lower temperature but aggregation appeared to be independent of pH. Lastly, it was concluded that self-association of cromolyn is promoted by the presence of monovalent cations as a result of reduced electrostatic repulsive forces. © 2004 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 93:1351,1358, 2004 [source] NMR, solvation and theoretical investigations of conformational isomerism in 2-X-cyclohexanones (X=NMe2, OMe, SMe and SeMe)JOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 11 2003Matheus P. Freitas Abstract The conformational equilibria of 2- N,N -dimethylamino- (1), 2-methoxy- (2), 2-methylthio- (3) and 2-methylselenocyclohexanone (4) were determined in various solvents by measurement of the 3JH-2,H-3 couplings. The observed couplings were analyzed using theoretical and solvation calculations to give both the conformer energies in the solvents studied plus the vapor-phase energies and the coupling constants for the distinct conformers. These gave the conformer energies and couplings of 2,4. The intrinsic couplings for the 2- N,N -dimethylamino compound were determined by the molecular mechanics PCMODEL program. The axial conformation in 1 is the most polar and also more stable in DMSO solution (Eeq,Eax=0.05,kcal,mol,1) and the pure liquid, while the equatorial conformer predominates in the remaining solvents studied (except in CCl4, where self-association is observed). In the methoxy ketone (2) the equatorial conformation is more stable in the vapor (Eeq,Eax=,0.30,kcal,mol,1) and in all solvents. The opposite behavior is shown by 3 and 4, where the axial conformation is the more stable one in the vapor phase (Eeq,Eax=1.60 and 2.95,kcal,mol,1 for 3 and 4, respectively) and is still the prevailing conformer in solution. The axial predominance for 3 and 4 is attributed to hyperconjugation between the electron lone pair of the hetero-substituent and the ,*CO orbital. This interaction is stronger for 3 and 4 than in the case of 1 and 2, where the ,gauche effect' in the equatorial conformation should be more effective in stabilizing this conformation. Copyright © 2003 John Wiley & Sons, Ltd. [source] Solvent dependent study of carbonyl vibrations of 3-phenoxybenzaldehyde and 4-ethoxybenzaldehyde by Raman spectroscopy and ab initio calculationsJOURNAL OF RAMAN SPECTROSCOPY, Issue 8 2009Veerabahu Ramakrishnan Abstract A Raman spectroscopy investigation of the carbonyl stretching vibrations of 3-phenoxybenzaldehye (3Phbz) and 4-ethoxybenzaldeheyde (4Etob) was carried out in binary mixtures with different polar and nonpolar solvents. The purpose of this study was twofold: firstly, to describe the interaction of the carbonyl groups of two solute molecules in terms of a splitting in the isotropic and anisotropic components and secondly, to analyze their spectroscopic signatures in a binary mixture. Changes in wavenumber position, variation in the anisotropic shift and full width half maximum were investigated for binary mixtures with different mole fractions of the reference systems. In binary mixtures, the observed increase in wavenumber with solvent concentration does not show linearity, indicating the significant role of molecular interactions on the occurrence of breaking of the self-association of the solute. In all the solvents, a gradual decrease in the anisotropic shift reflects the progressive separation of the coupled oscillators with dilution. ,i(,c), 3Phbz,solvent mixtures, exhibit a gradual decrease with decrease in the concentration of the solute which is an evidence on the influence of micro viscosity on linewidth. For 4Etob, the carbonyl stretching vibration shows two well-resolved components in the Raman spectra, attributed to the presence of two distinct carbonyl groups: hydrogen-bonded and free carbonyl groups. The intensity ratio of the carbonyl stretching vibration of these two types of carbonyl groups is studied to understand the dynamics of solute/solvent molecules owing to hydrogen bond interactions. Ab initio calculations were employed for predicting relevant molecular structures in the binary mixtures arising from intermolecular interactions, and are related to the experimental results. Copyright © 2009 John Wiley & Sons, Ltd. [source] A SERS probe of adenyl residues available for intermolecular interactions.JOURNAL OF RAMAN SPECTROSCOPY, Issue 11 2001Part I, adenyl, fingerprint' This work validated a SERS probe able to compare adenyl reactivity in DNA and RNA. A Creighton silver colloid including adenine (A) [or 2, -deoxyadenosine 5, -phosphate (pdA)] from 2 × 10,3 to 2 × 10,8M is stabilized in the absence or presence of chloride. Concentration-dependent SER spectral profiles reveal how A may interact with (Ag)n+ sites. At concentration ,2 × 10,5M adsorption of (A)n clusters prevents the colloid from undergoing salt effects. Adsorption via N1/N3 is allowed whereas C6NH2 is involved in self-association. At [A] <2 × 10,5M with chloride, hydrogen bonding between chloride and the C6NH2 group enhances C6N electronegativity, which assists C6N/N7 cooperative adsorption. Complex A(Cl,) entities compete with individual chloride ions for adsorption on silver. Very similar C6N/N7 adenyl adsorption occurs for pdA but only above 2 × 10,5M. Chloride,adenyl bonding is reduced and pdA self-association is weaker than adenine self-association. Steric factors, repulsive electrostatic forces and phosphate competitive reactivity with respect to chloride may explain the much higher pdA concentration needed to saturate the silver surface compared with A. Mg2+,phosphate complexation entails concentration-dependent opposite effects on adenyl reactivity with (Ag)n+ sites. Cytosine, thymine and guanine base or corresponding nucleotides deliver weaker SER spectra and much higher SERS responses for chloride adsorption compared with A or pdA. This reveals a weaker adsorption of the oxo bases, assumed to result from alternative oxo and nitrogen interactions with the (Ag)n+ sites. Copyright © 2001 John Wiley & Sons, Ltd. [source] The von Willebrand factor self-association is modulated by a multiple domain interactionJOURNAL OF THROMBOSIS AND HAEMOSTASIS, Issue 3 2005H. ULRICHTS Summary.,Background:,Platelet adhesion and aggregation at sites of vascular injury exposed to rapid blood flow require von Willebrand factor (VWF). VWF becomes immobilized by binding to subendothelial components or by a self-association at the interface of soluble and surface-bound VWF. Objectives:,As this self-association has been demonstrated only under shear conditions, our first goal was to determine whether the same interaction could be observed under static conditions. Furthermore, we wanted to identify VWF domain(s) important for this self-association. Results:,Biotinylated VWF (b-VWF) interacted dose-dependently and specifically with immobilized VWF in an enzyme-linked immunosorbent assay (ELISA) assay, showing that shear is not necessary to induce the VWF self-association. Whereas anti-VWF monoclonal antibodies (mAbs) had no effect on the self-association, the proteolytic VWF-fragments SpII(1366,2050) and SpIII(1,1365) inhibited the b-VWF,VWF interaction by 70 and 80%, respectively. Moreover, a specific binding of b-VWF to immobilized Sp-fragments was demonstrated. Finally, both biotinylated SpII and SpIII were able to bind specifically to both immobilized SpII and SpIII. Similar results were observed under flow conditions, which confirmed the functional relevance of our ELISA system. Conclusion:,We have developed an ELISA binding assay in which a specific VWF self-association under static conditions can be demonstrated. Our results suggest a multiple domain interaction between immobilized and soluble VWF. [source] Elucidation of spermidine interaction with nucleotide ATP by multiple NMR techniquesMAGNETIC RESONANCE IN CHEMISTRY, Issue 2 2010Zhiyan Song Abstract Interaction of polyamines with nucleotides plays a key role in many biological processes. Here we use multiple NMR techniques to characterize interaction of spermidine with adenosine 5,-triphosphate (ATP). Two-dimensional 1H- 15N spectra obtained from gs-HMBC experiments at varied pH show significant shift of N-1 peak around pH 2.0,7.0 range, suggesting that spermidine binds to N-1 site of ATP base. The binding facilitates N-1 deprotonation, shifting its pKa from 4.3 to 3.4. By correlating 15N and 31P chemical shift data, it is clear that spermidine is capable of concurrently binding to ATP base and phosphate sites around pH 4.0,7.0. The self-diffusion constants derived from 1H PFG-diffusion measurements provide evidence that binding of spermidine to ATP is in 1:1 ratio, and pH variations do not induce significant nucleotide self-association in our samples. 31P spectral analysis suggests that at neutral pH, Mg2+ ion competes with spermidine and shows stronger binding to ATP phosphates. From 31P kinetic measurements of myosin-catalyzed ATP hydrolysis, it is found that binding of spermidine affects the stability and reactivity of ATP. These NMR results are important for advancing the studies on nucleotide,polyamine interaction and its impact on nucleotide structures and activities under varied conditions. Copyright © 2009 John Wiley & Sons, Ltd. [source] Monitoring the non-specific interactions of catechin through diffusion measurements based on pulsed-field gradientsMAGNETIC RESONANCE IN CHEMISTRY, Issue 13 2002C. Monteiro Abstract The self-association of aqueous catechin as a function of concentration was monitored through variations in 1H chemical shifts, proton T1 and T2 data and translational diffusion coefficients obtained with the pulsed-field gradient spin-echo method. The latter approach is very efficient and it is not restricted to aromatic compounds. Equilibrium constants were estimated for various models of self-association and the apparent enthalpy of dissociation was measured with isothermal titration calorimetry. Comparison of the latter parameter with thermodynamic data reported for various types of non-specific interactions suggests that such phenomena could be studied using this approach. Copyright © 2002 John Wiley & Sons, Ltd. [source] Role of the N-terminal Region in the Function of the Photosynthetic Bacterium Transcription Regulator PpsR,PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 4 2008Yoichi Yamazaki PpsR is a transcription repressor for the gene cluster encoding photosystem genes in Rhodobacter sphaeroides. Repression activity is accomplished by DNA binding on the promoter regions of the photosystem gene clusters, and depends on both the redox potential and the presence of antirepressor protein AppA. To understand DNA repression regulation by PpsR, we investigated the function of PpsR domains in self-association for DNA binding. We constructed domain-deletion mutants and verified DNA-binding activity and dimer formation. Gel shift assay for measuring the DNA-binding activity of three sequential N-terminal deletion mutants revealed that N-terminal deletions (of minimum 121 residues) caused loss of binding activity. Size-exclusion gel chromatography revealed that deletion mutant which lacks the N-terminal 121-amino acid deletion mutant to exist as a dimer, although it was less stable than the intact PpsR. The mutants lacking the adjacent regions, Q-linker region and the first Per-Ant-Sim domain, did not form dimers, suggesting the involvement of the N-terminal region in dimer formation. This region is thus considered to be a functional domain in self-association, although not yet identified as a structural domain. Circular dichroism spectrum of the N-terminal region fragment exhibited a ,/, structure. We conclude that this region is a structural and functional domain, contributing to PpsR repression through dimer stabilization. [source] Fluorescence Lifetimes Study of ,-Tocopherol and Biological Prenylquinols in Organic Solvents and Model MembranesPHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 5 2006Jerzy Kruk ABSTRACT We have found that for biological prenyllipids, such as plastoquinol-9, ,-tocopherol quinol, and ,-tocopherol, the shortest fluorescence lifetimes were found in aprotic solvents (hexane, ethyl acetate) whereas the longest lifetimes were those of ubiquinonol-10 in these solvents. For all the investigated prenyllipids, fluorescence lifetime in alcohols increased along with an increase in solvent viscosity. In a concentrated hexane solution, the lifetimes of prenylquinols considerably decreased. This contrasts with methanol solutions, which is probably due to the self-association of these compounds in aprotic solvents. We have also found a correlation of the Stokes shift of prenyllipids fluorescence with the orientation polarizability of the solvents. Based on data obtained in organic solvents, measurements of the fluorescence lifetimes of prenyllipids in liposomes allowed an estimation of the relative distance of their fluorescent rings from the liposome membrane surface, and was found to be the shortest for ,-tocopherol quinol in egg yolk phosphatidyl-choline liposomes, and increased in the following order: ,-tocopherol in dipalmitoyl phosphatidylcholine liposomes < ,-tocopherol < plastoquinol-9 < ubiquinol-10 in egg-yolk phosphatidylcholine liposomes. [source] N15 Cro and , Cro: Orthologous DNA-binding domains with completely different but equally effective homodimer interfacesPROTEIN SCIENCE, Issue 5 2008Matthew S. Dubrava Abstract Bacteriophage Cro proteins bind to target DNA as dimers but do not all dimerize with equal strength, and differ in fold in the region of the dimer interface. We report the structure of the Cro protein from Enterobacteria phage N15 at 1.05 Å resolution. The subunit fold contains five ,-helices and is closely similar to the structure of P22 Cro (1.3 Å backbone room mean square difference over 52 residues), but quite different from that of , Cro, a structurally diverged member of this family with a mixed ,-helix/,-sheet fold. N15 Cro crystallizes as a biological dimer with an extensive interface (1303 Å2 change in accessible surface area per dimer) and also dimerizes in solution with a Kd of 5.1 ± 1.5 ,M. Its dimerization is much stronger than that of its structural homolog P22 Cro, which does not self-associate detectably in solution. Instead, the level of self-association and interfacial area for N15 Cro is similar to that of , Cro, even though these two orthologs do not share the same fold and have dimer interfaces that are qualitatively different in structure. The common Cro ancestor is thought to be an all-helical monomer similar to P22 Cro. We propose that two Cro descendants independently developed stronger dimerization by entirely different mechanisms. [source] Protein self-association in solution: The bovine , -lactoglobulin dimer and octamerPROTEIN SCIENCE, Issue 11 2003Michael Gottschalk Abstract We have used proton magnetic relaxation dispersion (MRD) to study the self-association of bovine , -lactoglobulin variant A (BLG-A) as a function of temperature at pH 4.7 (dimer,octamer equilibrium) and as a function of NaCl concentration at pH 2.5 (monomer,dimer equilibrium). The MRD method identifies coexisting oligomers from their rotational correlation times and determines their relative populations from the associated dispersion amplitudes. From MRD-derived correlation times and hydrodynamic model calculations, we confirm that BLG-A dimers associate to octamers below room temperature. The tendency for BLG-A dimers to assemble into octamers is found to be considerably weaker than in previous light scattering studies in the presence of buffer salt. At pH 2.5, the MRD data are consistent with an essentially complete transition from monomers in the absence of salt to dimers in 1 M NaCl. Because of an interfering relaxation dispersion from nanosecond water exchange, we cannot determine the oligomer populations at intermediate salt concentrations. This nanosecond dispersion may reflect intersite exchange of water molecules trapped inside the large binding cavity of BLG-A. [source] Modern analytical ultracentrifugation in protein science: A tutorial reviewPROTEIN SCIENCE, Issue 9 2002Jacob Lebowitz Abstract Analytical ultracentrifugation (AU) is reemerging as a versatile tool for the study of proteins. Monitoring the sedimentation of macromolecules in the centrifugal field allows their hydrodynamic and thermodynamic characterization in solution, without interaction with any matrix or surface. The combination of new instrumentation and powerful computational software for data analysis has led to major advances in the characterization of proteins and protein complexes. The pace of new advancements makes it difficult for protein scientists to gain sufficient expertise to apply modern AU to their research problems. To address this problem, this review builds from the basic concepts to advanced approaches for the characterization of protein systems, and key computational and internet resources are provided. We will first explore the characterization of proteins by sedimentation velocity (SV). Determination of sedimentation coefficients allows for the modeling of the hydrodynamic shape of proteins and protein complexes. The computational treatment of SV data to resolve sedimenting components has been achieved. Hence, SV can be very useful in the identification of the oligomeric state and the stoichiometry of heterogeneous interactions. The second major part of the review covers sedimentation equilibrium (SE) of proteins, including membrane proteins and glycoproteins. This is the method of choice for molar mass determinations and the study of self-association and heterogeneous interactions, such as protein,protein, protein,nucleic acid, and protein,small molecule binding. [source] Poly[[{,4 -3-[(1H -1,2,4-triazol-1-yl)methyl]benzoato}zinc(II)] hemihydrate]: a novel two-dimensional framework formed by self-association of zinc(II) sulfate with 3-[(1H -1,2,4-triazol-1-yl)methyl]benzoic acidACTA CRYSTALLOGRAPHICA SECTION C, Issue 6 2010Li Duan The title novel two-dimensional coordination polymer, {[Zn2(C10H8N3O2)4]·H2O}n, features a {Zn2L2} bimetallic ring repeat unit {L is the 3-[(1H -1,2,4-triazol-1-yl)methyl]benzoate ligand}. Each ZnII cation of the bimetallic ring is further bonded to two other L ligands, resulting in a novel infinite two-dimensional network structure with two channels of different sizes. The crystallographically unique ZnII atom is thus six-coordinated in a distorted octahedral environment of four carboxylate O atoms and two triazole N atoms. Two of these networks interpenetrate in an orthogonal arrangement to form the full three-dimensional framework, with disordered water molecules located in the channels. [source] Hexamer oligonucleotide topology and assembly under solution phase NMR and theoretical modeling scrutinyBIOPOLYMERS, Issue 12 2010Maxim P. Evstigneev Abstract The entire family of noncomplementary hexamer oligodeoxyribonucleotides d(GCXYGC) (X and Y = A, G, C, or T) were assessed for topological indicators and equilibrium thermodynamics using a priori molecular modeling and solution phase NMR spectroscopy. Feasible modeled hairpin structures formed a basis from which solution structure and equilibria for each oligonucleotide were considered. 1H and 31P variable temperature-dependent (VT) and concentration-dependent NMR data, NMR signal assignments, and diffusion parameters led to d(GCGAGC) and d(GCGGGC) being understood as exceptions within the family in terms of self-association and topological character. A mean diffusion coefficient D298 K = (2.0 ± 0.07) × 10,10 m2 s,1 was evaluated across all hexamers except for d(GCGAGC) (D298 K = 1.7 × 10,10 m2 s,1) and d(GCGGGC) (D298 K = 1.2 × 10,10 m2 s,1). Melting under VT analysis (Tm = 323 K) combined with supporting NMR evidence confirmed d(GCGAGC) as the shortest tandem sheared GA mismatched duplex. Diffusion measurements were used to conclude that d(GCGGGC) preferentially exists as the shortest stable quadruplex structure. Thermodynamic analysis of all data led to the assertion that, with the exception of XY = GA and GG, the remaining noncomplementary oligonucleotides adopt equilibria between monomer and duplex, contributed largely by monomer random-coil forms. Contrastingly, d(GCGAGC) showed preference for tandem sheared GA mismatch duplex formation with an association constant K = 3.9 × 105M,1. No direct evidence was acquired for hairpin formation in any instance although its potential existence is considered possible for d(GCGAGC) on the basis of molecular modeling studies. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 1023,1038, 2010. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] | ||||||||||||||||||||||||||||