Oligomer formation of the bacterial second messenger c-di-GMP: reaction rates and equilibrium constants indicate a monomeric state at physiological concentrations

Cyclic diguanosine-monophosphate (c-di-GMP) is a bacterial signaling molecule that triggers a switch from motile to sessile bacterial lifestyles. This mechanism is of considerable pharmaceutical interest, since it is related to bacterial virulence, biofilm formation, and persistence of infection. Previously, c-di-GMP has been reported to display a rich polymorphism of various oligomeric forms at millimolar concentrations, which differ in base stacking and G-quartet interactions. Here, we have analyzed the equilibrium and exchange kinetics between these various forms by NMR spectroscopy. We find that the association of the monomer into a dimeric form is in fast exchange (相似文献   

A Blue Light-inducible Phosphodiesterase Activity in the Cyanobacterium Synechococcus elongatus

A blue light-inducible phosphodiesterase (PDE) activity, specific for the hydrolysis of cyclic di-GMP (c-di-GMP), has been identified in a recombinant protein from Synechococcus elongatus. Blue light (BL) activation is accomplished by a light, oxygen, voltage (LOV) domain, found in plant phototropins and bacterial BL photoreceptors. The genome of S. elongatus contains two genes coding for proteins with LOV domains fused to EAL domains (SL1 and SL2). In both cases, a GGDEF motif is placed in between the LOV and the EAL motifs. Such arrangement is frequently found with diguanylate-cyclase (DGC) functions that form c-di-GMP. Cyclic di-GMP acts as a second messenger molecule regulating biofilm formation in many microbial species. Both enzyme activities modulate the intracellular level of this second messenger, although in most proteins only one of the two enzyme functions is active. Both S. elongatus LOV-GGDEF-EAL proteins were expressed in full length or as truncated proteins. Only the SL2 protein, expressed as a LOV-GGDEF-EAL construct, showed an increase of PDE activity upon BL irradiation, demonstrating this activity for the first time in a LOV-domain protein. Addition of GTP or c-di-GMP did not affect the observed enzymatic activity. In none of the full-length or truncated proteins was a DGC activity detected.     

钒酸根、金属离子和腺苷二磷酸的相互作用-ATP及Mg^2^+-ATP类似物的形成

用钒-51核磁共振方法研究钒酸根在不同浓度和离子强度下, 在生理pH水溶液中的物种分配。研究结果表明毫摩尔级浓度的钒酸根主要以中心钒原子为四面体构型的单体、二聚、四聚和五聚体存在。通过比较所得的平衡常数说明在离子强度降低时, 钒酸根的聚合度下降。对于钒酸根-ADP体系, 从所显示的核磁谱变化通过计算得到相应的结合平衡常数, 说明主要发生的反应一是形成ATP类似物ADPV(V代表四面体构型的单体钒酸根); 二是在ADP浓度相对高时, 钒酸根与ADP核糖基上2', 3'-颗位羟基同时作用形成2:2配比的、钒原子为五配位三角双锥构型的配合物。在钒酸根-ADP体系中加入Mn^2^+后, ^5^1V NMR的变化说明ATP的类似物ADPV中β-磷酸根和γ-钒酸根可以协同螯合Mn^2^+, 表明形成了Mg^2^+-ATP的类似物Mn^2^+-ADPV。     

Two-repeat human telomeric d(TAGGGTTAGGGT) sequence forms interconverting parallel and antiparallel G-quadruplexes in solution: distinct topologies, thermodynamic properties, and folding/unfolding kinetics

We demonstrate by NMR that the two-repeat human telomeric sequence d(TAGGGTTAGGGT) can form both parallel and antiparallel G-quadruplex structures in K(+)-containing solution. Both structures are dimeric G-quadruplexes involving three stacked G-tetrads. The sequence d(TAGGGUTAGGGT), containing a single thymine-to-uracil substitution at position 6, formed a predominantly parallel dimeric G-quadruplex with double-chain-reversal loops; the structure was symmetric, and all guanines were anti. Another modified sequence, d(UAGGGT(Br)UAGGGT), formed a predominantly antiparallel dimeric G-quadruplex with edgewise loops; the structure was asymmetric with six syn guanines and six anti guanines. The two structures can coexist and interconvert in solution. For the latter sequence, the antiparallel form is more favorable at low temperatures (<50 degrees C), while the parallel form is more favorable at higher temperatures; at temperatures lower than 40 degrees C, the antiparallel G-quadruplex folds faster but unfolds slower than the parallel G-quadruplex.     

Long-range oxidative damage to DNA: protection of guanines by a nonspecifically bound disulfide

One-electron oxidation of DNA generates a base radical cation ("hole") that migrates through the duplex and causes damage at guanines. Unrepaired damage may lead to mutations. It has been suggested that "sacrificial guanines" in intron regions of DNA might serve to protect genes from damage. We have investigated the ability of a noncovalently bound sacrificial reagent to protect DNA from damage. Irradiation of an anthraquinone (AQ)-linked DNA duplex injects a radical cation into the DNA that causes reactions at GG steps close to and farther from the AQ. Bis[2-(3-(aminopropyl)amino)ethyl]disulfide, an analogue of spermine, binds to duplex DNA. Irradiation of the AQ-linked DNA in the presence of this disulfide suppresses the reaction at both GG steps and protects the DNA from damage. It is suggested that evolutionary pressure for the preservation of genomic integrity would yield disulfide-containing compounds optimized to bind to DNA and neutralize base radical cations.     

Binding of monomeric and dimeric Concanavalin A to mannose-functionalized dendrimers

Because of the central role of Concanavalin A (Con A) in the study of protein-carbohydrate interactions, a thorough understanding of the multivalent functions of Con A is imperative. Here, the association of monomeric and dimeric derivatives of Con A with mannose-functionalized generation two through six PAMAM dendrimers is reported. Hemagglutination assay results indicate relatively low activity of the dendrimers for monomeric Con A, with small increases as the dendrimer generation increases. Isothermal titration microcalorimetry experiments indicate monovalent binding by the dendrimers with monomeric Con A and divalent binding by the dendrimers with dimeric Con A. Continuous (and comparable) but narrowing increases in enthalpy and entropy and the slight increase in association constants with monomeric Con A as the dendrimer generation increases suggest favorable proximity effects on binding. Both the hemagglutination assay and the calorimetry experiments suggest that statistical binding enhancements can be observed with monomeric Con A. The results described here should allow for a more quantitative evaluation of the enhancements that are often observed in protein-carbohydrate interactions for glycosylated frameworks binding to Con A.     

c-di-GMP can form remarkably stable G-quadruplexes at physiological conditions in the presence of some planar intercalators

The ubiquitous bacterial biofilm regulator, c-di-GMP can form G-quadruplexes at physiological conditions in the presence of some aromatic compounds, such as acriflavine and proflavine. The fluorescence of these compounds is quenched upon c-di-GMP binding and some of the formed c-di-GMP G-quadruplexes are stable even at 75 °C.     

The crowded environment of a reverse micelle induces the formation of β-strand seed structures for nucleating amyloid fibril formation

A hallmark of Alzheimer's disease is the accumulation of insoluble fibrils in the brain composed of amyloid beta (Aβ) proteins with parallel in-register cross-β-sheet structure. It has been suggested that the aggregation of monomeric Aβ proteins into fibrils is promoted by "seeds" that form within compartments of the brain that have limited solvent due to macromolecular crowding. To characterize these seeds, a crowded macromolecular environment was mimicked by encapsulating Aβ40 monomers into reverse micelles. Fourier-transform infrared spectroscopy revealed that monomeric Aβ proteins form extended β-strands in reverse micelles, while an analogue with a scrambled sequence does not. This is a remarkable finding, because the formation of extended β-strands by monomeric Aβ proteins suggests a plausible mechanism whereby the formation of amyloid fibrils may be nucleated in the human brain.     

A comparative study of pi-arene-bridged lanthanum arylamide and aryloxide dimers. Solution behavior, exchange mechanisms, and X-ray crystal structures of La2(NH-2,6-iPr2C6H3)6, La(NH-2,6-iPr2C6H3)3(THF)3, and La(NH-2,6-iPr2C6H3)3(py)2

Reaction of 3 equiv of 2,6-diisopropylaniline with La[N(SiMe(3))(2)](3) produces the dimeric species La(2)(NHAr)(6) (1). X-ray crystallography reveals a centrosymmetric structure, where the dimeric unit is bridged by intermolecular eta(6)-arene interactions of a unique arylamide ligand attached to an adjacent metal center. Exposure of 1 to THF results in formation of the monomeric tris-THF adduct La(NHAr)(3)(THF)(3) (2), which was shown by X-ray crystallography to maintain a fac-octahedral structure in the solid state. (1)H NMR spectroscopy illustrates that the binding of THF to 1 to form 2 is reversible and removal of THF under vacuum regenerates dimeric 1. Addition of pyridine to 1 yields the monomeric bis-pyridine adduct La(NHAr)(3)(py)(2) (3), which exhibits a distorted trigonal-bipyramidal La metal center. Solution (1)H NMR, IR, and Raman spectroscopy indicate that the pi-arene-bridged dimeric structure of 1 is maintained in solution. Variable-temperature (1)H NMR spectroscopic investigations of 1 are consistent with a monomer-dimer equilibrium at elevated temperature. In contrast, variable-temperature (1)H NMR spectroscopic investigations of the aryloxide analogue La(2)(OAr)(6) (4) show that the bridging and terminal aryloxide groups exchange by a mechanism in which the dimeric nature of the compound is retained. Density functional theory (DFT) calculations were carried out on model compounds La(2)(OC(6)H(5))(6), La(2)(NHC(6)H(5))(6), and (C(6)H(5)R)La(XC(6)H(5))(3), where X = O or NH and R = H, OH, or NH(2). The formation of eta(6)-arene interactions is energetically favored over monomeric LaX(3) (X = OPh or NHPh) with the aryloxide pi-arene interaction being stronger than the arylamide pi-arene interaction. Calculation of vibrational frequencies reveals the origin of the observed IR spectral behavior of both La(2)(OC(6)H(5))(6) and La(2)(NHC(6)H(5))(6), with the higher energy nu(C=C) stretch due to terminal ligands and the lower energy stretch associated with the bridging ligands.     

Formation of an ion-pair molecule with a single NH(+)...Cl(-) hydrogen bond: Raman spectra of 1,1,3,3-tetramethylguanidinium chloride in the solid state, in solution, and in the vapor phase

Some ionic compounds (salts) form liquids when heated to temperatures in the range of 200-300 degrees C. They may be referred to as moderate temperature ionic liquids. An example of such a compound is the 1,1,3,3-tetramethylguanidinium chloride, [TMGH]Cl, melting at approximately 212 degrees C. The chemistry of this compoundcontaining a dimeric ion-pair "molecule"was investigated in the solid state, in solutions in water and ethanol, and in the vapor phase, based on ab initio molecular orbital density functional theory (DFT)-type calculations with 6-311+G(d,p) basis sets. Calculations on the monomeric [TMGH] (+) ion and the dimeric chloride ion-pair salt converged to give geometries near the established crystal structure of [TMGH]Cl. The structures and their binding energies are given as well as calculated vibrational harmonic normal modes (IR and Raman band wavenumbers and intensities). Experimentally obtained Raman scattering spectra are presented and assigned, by comparing to the quantum mechanical calculations. It is concluded that dimeric molecular ion pairs with four N-H (+)...Cl (-) hydrogen bonds probably exist in the solutions and are responsible for the relatively high solubility of the "salt" in ethanol. It was discovered that the compound can be easily sublimed by heating to about 200-230 degrees C. In the Raman spectrum of the vapor at 225 degrees C, a characteristic strong band at 2229 cm (-1) was found and interpreted to show that the gas phase consists of monomeric ion-pair "molecules" held together by a single N-H (+)...Cl (-) hydrogen bond, the stretching band of which is causing the band.     

Disaggregation of amphotericin B by sodium deoxycholate micellar aggregates

Amphotericin B (AmB) is present as aggregates in aqueous media. Sodium deoxycholate (NaDC) is known to cause disaggregation of AmB and to form monomers, as is observed by the increase of absorbance at 414 nm. By following the fluorescence intensity at 472 nm (lambda(ex) 335 nm), it was found that with increasing NaDC concentration there is a progressive disaggregation of AmB leading to increase in both monomeric and dimeric forms. Although the presence of dimeric AmB form in NaDC micellar media is known, observation of the growth of the dimeric species is novel. Studies in fluorescence lifetime and steady state fluorescence anisotropy also support this conclusion. As NaDC (at ca. 10 mM) is the preferred choice of medium for AmB delivery and AmB aggregation has been implicated for its toxicity, the observation of dimeric AmB at these NaDC concentrations assumes significance.     

Structural and vibrational characterisation of 3-amino-1-propanol a concerted SCF-MO ab initio, Raman and infrared (matrix isolation and liquid phase) spectroscopy study

Results obtained for the isolated and liquid 3-amino-1-propanol by a concerted molecular orbital and vibrational spectroscopic approach are reported. The relative energies and both structural and vibrational data of the different conformers of the studied compound were calculated using the extended 6-31G* basis set both at the HF-SCF and MP2 ab initio levels of theory and the theoretical results used to interpret Raman and infrared experimental data. In the gaseous phase and for the molecule isolated in an Argon matrix, monomeric 3-amino-1-propanol exists as a mixture of conformers, the first and second lowest energy forms corresponding to conformers which exhibit an intramolecular OH-N hydrogen bond (forms I and II). On the other hand, in the pure liquid, where intermolecular H-bonding occurs, the monomeric unit within the aggregates assumes a conformation similar to that of the third most stable form found for the isolated molecule situation (form III), which is characterised by having a weak intramolecular NH-O bond. The experimental data obtained for the pure liquid also reveals the presence of monomeric form I in this phase, a result that is in consonance with the strongly stabilizing OH-N intramolecular hydrogen bond that is present in this conformer.     

Cleavable cationic antibacterial amphiphiles: synthesis, mechanism of action, and cytotoxicities

The development of novel antimicrobial agents having high selectivity toward bacterial cells over mammalian cells is urgently required to curb the widespread emergence of infectious diseases caused by pathogenic bacteria. Toward this end, we have developed a set of cationic dimeric amphiphiles (bearing cleavable amide linkages between the headgroup and the hydrocarbon tail with different methylene spacers) that showed high antibacterial activity against human pathogenic bacteria (Escherichia coli and Staphylococcus aureus) and low cytotoxicity. The Minimum Inhibitory Concentrations (MIC) were found to be very low for the dimeric amphiphiles and were lower or comparable to the monomeric counterpart. In the case of dimeric amphiphiles, MIC was found to decrease with the increase in the spacer chain length (n = 2 to 6) and again to increase at higher spacer length (n > 6). It was found that the compound with six methylene spacers was the most active among all of the amphiphiles (MICs = 10-13 μM). By fluorescence spectroscopy, fluorescence microscopy, and field-emission scanning electron microscopy (FESEM), it was revealed that these cationic amphiphiles interact with the negatively charged bacterial cell membrane and disrupt the membrane integrity, thus killing the bacteria. All of the cationic amphiphiles showed low hemolytic activity (HC(50)) and high selectivity against both gram-positive and gram-negative bacteria. The most active amphiphile (n = 6) had a 10-13-fold higher HC(50) than did the MIC. Also, this amphiphile did not show any cytotoxicity against mammalian cells (HeLa cells) even at a concentration above the MIC (20 μM). The critical micellar concentration (CMC) values of gemini surfactants were found to be very low (CMC = 0.30-0.11 mM) and were 10-27 times smaller than the corresponding monomeric analogue (CMC = 2.9 mM). Chemical hydrolysis and thermogravimetric analysis (TGA) proved that these amphiphiles are quite stable under both acidic and thermal conditions. Collectively, these properties make the newly synthesized amphiphiles potentially superior disinfectants and antiseptics for various biomedical and biotechnological applications.     

Large-Scale Production of the Immunomodulator c-di-GMP from GMP and ATP by an Enzymatic Cascade

(3'-5')-Cyclic diguanylate (c-di-GMP) is a bacterial second messenger with immunomodulatory activities in mice suggesting potential applications as a vaccine adjuvant and as a therapeutic agent. Clinical studies in larger animals or humans will require larger doses that are difficult and expensive to generate by currently available chemical or enzymatic synthesis and purification methods. Here we report the production of c-di-GMP at the multi-gram scale from the economical precursors guanosine monophosphate (GMP) and adenosine triphosphate by a "one-pot" three enzyme cascade consisting of GMP kinase, nucleoside diphosphate kinase, and a mutated form of diguanylate cyclase engineered to lack product inhibition. The c-di-GMP was purified to apparent homogeneity by a combination of anion exchange chromatography and solvent precipitation and was characterized by reversed phase high performance liquid chormatography and mass spectrometry, nuclear magnetic resonance spectroscopy, and further compositional analyses. The immunomodulatory activity of the c-di-GMP preparation was confirmed by its potentiating effect on the lipopolysaccharide-induced interleukin 1β, tumor necrosis factor α, and interleukin 6 messenger RNA expression in J774A.1 mouse macrophages.     

Interaction between dyes and polyelectrolytes. XI. Photoreduction of methylene blue bound to potassium polystyrenesulfonate

The effect of potassium polystyrenesulfonate (PSSK) on the quantum yield (Φ) in the photoreduction of methylene blue (MB) by allylthiourea was investigated. MB was bound to PSSK in monomeric, dimeric, or slightly aggregated form, depending on the polyanion–dye ratio (P/D). At a relatively lower P/D in which most MB molecules were bound to PSSK in dimeric or slightly aggregated form, the value of Φ was smaller than that at a P/D of zero. On the other hand, at a higher P/D, in which most MB molecules were bound to PSSK in monomeric form, the value of Φ was larger than that at a P/D of zero. It was suggested that the lower reactivity of dimeric or slightly aggregated MB on PSSK was caused by the length of its lifetime which is shorter than that of the monomeric form. It was also suggested that the increase in Φ at higher P/D was caused by the decreased deactivation of the triplet excited MB by the ground-state MB.     

The Preorganization Effect of the Calix[4]arene Platform on the Extraction Properties of Acetylhydrazide Groups with Transition Metal Ions

The binding properties of the cone conformer of O,O,O,O-tetrakis[hydrazinocarbonylmethyl]-4-tert-butylcalix[4]arene, the cone and the 1,3-alternate conformers of the corresponding thia analogue have been evaluated by means of liquid–liquid extraction for a large variety of metal ions. The extraction constants and the stoichiometries of the complexes formed have been determined. Comparison of the extraction properties of calix[4]arenes with their acyclic monomeric analogue clearly demonstrated, that the preorganization of acetylhydrazide groups on the calix[4]arene platform is the cause for a significant improvement of its binding properties. The presence of additional “soft” nitrogen binding sites in acetylhydrazide derivatives of calix[4]arenes compared to their amide derivatives leads to a shift from their classical selectivity for alkali and alkaline earth cations to transition metals. The cone conformer of tetrathiacalix[4]arene shows higher selectivity in a series of d-metal ions compared with its “classical” analogue. The 1,3-alternate conformer exhibits an excellent extraction selectivity for Cu²⁺ and Hg²⁺.     

Monomer–Dimer Equilibrium for the 5′–5′ Stacking of Propeller‐Type Parallel‐Stranded G‐Quadruplexes: NMR Structural Study

Guanine‐rich sequence motifs, which contain tracts of three consecutive guanines connected by single non‐guanine nucleotides, are abundant in the human genome and can form a robust G‐quadruplex structure with high stability. Herein, by using NMR spectroscopy, we investigate the equilibrium between monomeric and 5′–5′ stacked dimeric propeller‐type G‐quadruplexes that are formed by DNA sequences containing GGGT motifs. We show that the monomer–dimer equilibrium depends on a number of parameters, including the DNA concentration, DNA flanking sequences, the concentration and type of cations, and the temperature. We report on the high‐definition structure of a simple monomeric G‐quadruplex containing three single‐residue loops, which could serve as a reference for propeller‐type G‐quadruplex structures in solution.     

Synthesis of DOTA-conjugated multivalent cyclic-RGD peptide dendrimers via 1,3-dipolar cycloaddition and their biological evaluation: implications for tumor targeting and tumor imaging purposes

This report describes the design and synthesis of a series of alpha(V)beta(3) integrin-directed monomeric, dimeric and tetrameric cyclo[Arg-Gly-Asp-d-Phe-Lys] dendrimers using "click chemistry". It was found that the unprotected N-epsilon-azido derivative of cyclo[Arg-Gly-Asp-d-Phe-Lys] underwent a highly chemoselective conjugation to amino acid-based dendrimers bearing terminal alkynes using a microwave-assisted Cu(I)-catalyzed 1,3-dipolar cycloaddition. The alpha(V)beta(3) binding characteristics of the dendrimers were determined in vitro and their in vivoalpha(V)beta(3) targeting properties were assessed in nude mice with subcutaneously growing human SK-RC-52 tumors. The multivalent RGD-dendrimers were found to have enhanced affinity toward the alpha(V)beta(3) integrin receptor as compared to the monomeric derivative as determined in an in vitro binding assay. In case of the DOTA-conjugated (111)In-labeled RGD-dendrimers, it was found that the radiolabeled multimeric dendrimers showed specifically enhanced uptake in alpha(V)beta(3) integrin expressing tumors in vivo. These studies showed that the tetrameric RGD-dendrimer had better tumor targeting properties than its dimeric and monomeric congeners.     

A Rhizavidin Monomer with Nearly Multimeric Avidin‐Like Binding Stability Against Biotin Conjugates

Developing a monomeric form of an avidin‐like protein with highly stable biotin binding properties has been a major challenge in biotin‐avidin linking technology. Here we report a monomeric avidin‐like protein—enhanced monoavidin—with off‐rates almost comparable to those of multimeric avidin proteins against various biotin conjugates. Enhanced monoavidin (eMA) was developed from naturally dimeric rhizavidin by optimally maintaining protein rigidity during monomerization and additionally shielding the bound biotin by diverse engineering of the surface residues. eMA allowed the monovalent and nonperturbing labeling of head‐group‐biotinylated lipids in bilayer membranes. In addition, we fabricated an unprecedented 24‐meric avidin probe by fusing eMA to a multimeric cage protein. The 24‐meric avidin and eMA were utilized to demonstrate how artificial clustering of cell‐surface proteins greatly enhances the internalization rates of assembled proteins on live cells.     

Computational study of pH-dependent oligomerization and ligand binding in Alt a 1, a highly allergenic protein with a unique fold

Alt a 1 is a highly allergenic protein from Alternaria fungi responsible for several respiratory diseases. Its crystal structure revealed a unique β-barrel fold that defines a new family exclusive to fungi and forms a symmetrical dimer in a butterfly-like shape as well as tetramers. Its biological function is as yet unknown but its localization in cell wall of Alternaria spores and its interactions in the onset of allergy reactions point to a function to transport ligands. However, at odds with binding features in β-barrel proteins, monomeric Alt a 1 seems unable to harbor ligands because the barrel is too narrow. Tetrameric Alt a 1 is able to bind the flavonoid quercetin, yet the stability of the aggregate and the own ligand binding are pH-dependent. At pH 6.5, which Alt a 1 would meet when secreted by spores in bronchial epithelium, tetramer-quercetin complex is stable. At pH 5.5, which Alt a 1 would meet in apoplast when infecting plants, the complex breaks down. By means of a combined computational study that includes docking calculations, empirical pKa estimates, Poisson–Boltzmann electrostatic potentials, and Molecular Dynamics simulations, we identified a putative binding site at the dimeric interface between subunits in tetramer. We propose an explanation on the pH-dependence of both oligomerization states and protein–ligand affinity of Alt a 1 in terms of electrostatic variations associated to distinct protonation states at different pHs. The uniqueness of this singular protein can thus be tracked in the combination of all these features.