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PubMed1994

Cholesterol's interfacial interactions with sphingomyelins and phosphatidylcholines: hydrocarbon chain structure determines the magnitude of condensation.

Cholesterol's interfacial interaction with different sphingomyelins and phosphatidylcholines has been investigated using a Langmuir film balance. The average molecular area of cholesterol/sphingomyelin (SM) or cholesterol/phosphatidylcholine (PC) mixed monolayers was determined as a function of film composition from the force-area isotherms measured at 24 degrees C. In contrast to previous results [Lund-Katz, S., Laboda, H. M., McLean, L. R., & Phillips, M. C. (1988) Biochemistry 27, 3416-3423], little difference was observed in equimolar cholesterol's "condensing effect" of SMs compared to PCs when their phase state was similar and when their hydrocarbon structural differences were minimized. For PCs, this meant that one acyl chain had to be long and capable of assuming an extended conformation and thus configurationally similar to the long-chain base of SM. This condition facilitated strong van der Waals attractive interactions with cholesterol's planar steroid ring and was satisfied when the sn-1 acyl chain of PC was either myristate or palmitate. Under these conditions, the structural requirements of the sn-2 chain of PC were mitigated. For instance, at equimolar cholesterol, almost no difference was observed in the apparent molecular area condensations of 1-palmitoyl-2-oleoyl-PC and 1-palmitoyl-2-arachidonoyl-PC at surface pressures between 10 and 40 mN/m. In contrast, the apparent molecular area condensations of dioleoyl-PC and diarachidonoyl-PC were substantially reduced under identical experimental conditions. The results are discussed in terms of the relative importance of phospholipid/sphingolipid hydrocarbon and headgroup structure in determining the extent of interaction with cholesterol.(ABSTRACT TRUNCATED AT 250 WORDS)

Cholesterol↗

PubMed1986

Influence of DNA-binding drugs on chromatin condensation.

We have used transient electric dichroism to study the ability of DNA-binding drugs to affect the folding of chromatin from the 10- to the 30-nm fiber, either by themselves or in conjunction with multivalent cations. Variables considered include the cationic charge of the drug, the comparative influence of intercalation and groove binding as modes of interaction, and the effect of bis-intercalation compared to mono-intercalation. In parallel with our findings with other cations, we observe that a drug must have a charge of 3+ or greater in order to condense chromatin at concentrations substantially lower than the concentration of chromatin, measured in base pairs. Drugs of low charge, whether groove binders or mono-or bis-intercalators, are unable to condense chromatin on their own. Bis-intercalators of high charge, however, are extremely efficient condensers, being able to cross-link chromatin with greater efficiency than polyamines of corresponding charge. When Mg2+ is used in combination with bis-intercalators of high charge, the order of addition of the two determines whether compaction or cross-linking is favored. Finally, the antibiotics actinomycin D, daunomycin, and distamycin, despite varied modes of binding to DNA, all inhibit the compaction of chromatin beyond a critical point in a remarkably similar manner.

Animals↗

PubMed1988

Malate synthase: proof of a stepwise Claisen condensation using the double-isotope fractionation test.

Although aldolase-catalyzed condensations proceed by stepwise mechanisms via the intermediacy of nucleophilic enol(ate)s or enamines, the mechanisms of those enzymes that catalyze Claisen-type condensations are unclear. The reaction pathway followed by an enzyme from this second group, malate synthase, has been studied by the double-isotope fractionation method to determine whether the reaction is stepwise or concerted. In agreement with earlier work, a deuterium kinetic isotope effect D(V/K) of 1.3 +/- 0.1 has been found when [2H3]acetyl-CoA is the substrate. The 13C isotope effect at the aldehydic carbon of glyoxylate has also been measured. For this determination, the malate product (containing the carbon of interest at C-2) was quantitatively transformed into a new sample of malate having the carbon of interest at C-4. This material was decarboxylated by malic enzyme to produce the appropriate CO2 for isotope ratio mass spectrometric analysis. The 13C isotope effect with [1H3]acetyl-CoA [that is, 13(V/K)H] is 1.0037 +/- 0.0004. By use of the known values of the intermolecular and intramolecular deuterium effects and of 13(V/K)H, the value of the 13C isotope effect when deuteriated [2H3]acetyl-CoA is the substrate [that is, 13(V/K)D] can be predicted for three possible mechanisms. If 13(V/K)H is a kinetic isotope effect and the reaction is concerted, the value of the 13C effect on deuteriation of acetyl-CoA will rise to 1.011; if 13(V/K)H is a kinetic isotope effect and the reaction is stepwise, the value of the 13C effect will fall to 1.0025; and if the 13C effect is an equilibrium isotope effect deriving from glyoxylate dehydration, the reaction is necessarily stepwise, and the value of 13(V/K)D will be 1.0037, unchanged from that of 13(V/K)H. Experimentally, the value of 13(V/K)D is 1.0037 +/- 0.0007, which requires that malate synthase follow a stepwise path. It is therefore clear that the two salient characteristics of enzymes that catalyze Claisen-like condensations, namely, the absence of enzyme-catalyzed proton exchange with solvent and the inversion of the configuration at the nucleophilic center, which had been suggestive of a concerted pathway, are not mechanistically diagnostic.

Acetyl Coenzyme A↗

PubMed1981

Kinetic analysis of the malonyl coenzyme A decarboxylation and the condensation reaction of fatty acid synthesis. Application to the study of malonyl coenzyme A inactivated chicken liver fatty acid synthetase.

A kinetic analysis of the decarboxylation of malonyl-CoA and the condensation--CO2 exchange reaction of fatty acid synthesis has been carried out. The analysis supported by experimental evidence defines conditions under which the decarboxylation of malonyl-CoA quantitatively reflects the activity for the condensation reaction between enzyme-bound acyl and malonyl groups. NADP+ decreases the release of 14CO2 from radiolabeled malonyl-CoA by lowering the rates of the processes leading to the formation of triacetic acid lactone. For accurate measurements, the enzyme concentration should be less than 200 micrograms/mL, and malonyl-CoA/enzyme ratios should be 200 or less. Short reaction periods (1 min or less) and inclusion of NADP+ (100 microM) enhance the accuracy of measurements. These analyses have been used to explain the mechanism of malonyl-CoA mediated inactivation of chicken liver fatty acid synthetase and are appropriate for determining the functional condensing site of the polyfunctional polypeptide chains comprising the dimeric enzyme.

Acyl Coenzyme A↗

PubMed2001

Heterocycle formation in vibriobactin biosynthesis: alternative substrate utilization and identification of a condensed intermediate.

The iron-chelating peptide vibriobactin of the pathogenic Vibrio cholerae is assembled by a four-subunit nonribosomal peptide synthetase complex, VibE, VibB, VibH, and VibF, using 2,3-dihydroxybenzoate and L-threonine as precursors to two 2,3-dihydroxyphenyl- (DHP-) methyloxazolinyl groups in amide linkage on a norspermidine scaffold. We have tested the ability of the six-domain VibF subunit (Cy-Cy-A-C-PCP-C) to utilize various L-threonine analogues and found the beta-functionalized amino acids serine and cysteine can function as alternate substrates in aminoacyl-AMP formation (adenylation or A domain), aminoacyl-S-enzyme formation (A domain), acylation by 2,3-dihydrobenzoyl- (DHB-) S-VibB (heterocyclization or Cy domain), heterocyclization to DHP-oxazolinyl- and DHP-thiazolinyl-S-enzyme forms of VibF (Cy domain) as well as transfer to DHB-norspermidine at both N(5) and N(9) positions (condensation or C domain) to make the bis(oxazolinyl) and bis(thiazolinyl) analogues of vibriobactin. When L-threonyl-S-pantetheine or L-threonyl-S-(N-acetyl)cysteamine was used as a small-molecule thioester analogue of the threonyl-S-VibF acyl enzyme intermediate, the Cy domain(s) of a CyCyA fragment of VibF generated DHB-threonyl-thioester products of the condensation step but not the methyloxazolinyl thioesters of the heterocyclization step. This clean separation of condensation from cyclization validates a two-stage mechanism for threonyl, seryl, and cysteinyl heterocyclization domains in siderophore and antibiotic synthetases. Full heterocyclization activity could be restored by providing CyCyA with the substrate L-threonyl-S-peptidyl carrier protein (PCP)-C2, suggesting an important role for the protein scaffold component of the heterocyclization acceptor substrate. We also examined heterocyclization donor substrate specificity at the level of acyl group and protein scaffold and observed intolerance for substitution at either position.

Amines↗

PubMed2002

Biophysical characterization of the DNA binding and condensing properties of adenoviral core peptide mu.

Cationic peptides containing Lys and Arg residues interact with DNA via charge-charge interactions and are known to play an important role in DNA charge neutralization and condensation processes. In this paper, we describe investigations of the interaction of the cationic adenovirus core complex peptide mu with a dodecameric ODN (12 bp) and pDNA (7528 bp) using a combination of fluorescence spectroscopy, circular dichroism spectroscopy, isothermal titration calorimetry, and photon correlation spectroscopy. Comparisons are made with protamine, a cationic peptide well-known for DNA charge neutralization and condensation. Equilibrium dissociation constants are derived independently by both CD and ITC methods for the interaction between protamine or mu with pDNA (K(d) = 0.6-1 microM). Thermodynamic data are also obtained by ITC, indicating strong charge-charge interactions. The interaction of protamine with pDNA takes place with decreasing entropy (-28.7 cal mol(-1) K(-1)); unusually, the interaction of mu with pDNA takes place with increasing entropy (Delta S degrees (bind) = 11.3 cal mol(-1) K(-1)). Although protamine and mu appear to destabilize pDNA double helix character to similar extents, according to CD thermal titration analyses, PCS studies show that interactions between mu and pDNA result in the formation of significantly more size-stable condensed particles than protamine. The enhanced flexibility and size stability of mu-DNA (MD) particles (80-110 nm) compared to protamine counterparts suggest that MD particles are ideal for use as a part of new nonviral gene delivery vectors.

Adenoviridae↗

PubMed2000

Physical constraints in the condensation of eukaryotic chromosomes. Local concentration of DNA versus linear packing ratio in higher order chromatin structures.

The local concentration of DNA in metaphase chromosomes of different organisms has been determined in several laboratories. The average of these measurements is 0.17 g/mL. In the first level of chromosome condensation, DNA is wrapped around histones forming nucleosomes. This organization limits the DNA concentration in nucleosomes to 0. 3-0.4 g/mL. Furthermore, in the structural models suggested in different laboratories for the 30-40 nm chromatin fiber, the estimated DNA concentration is significantly reduced; it ranges from 0.04 to 0.27 g/mL. The DNA concentration is further reduced when the fiber is folded into the successive higher order structures suggested in different models for metaphase chromosomes; the estimated minimum decrease of DNA concentration represents an additional 40%. These observations suggest that most of the models proposed for the 30-40 nm chromatin fiber are not dense enough for the construction of metaphase chromosomes. In contrast, it is well-known that the linear packing ratio increases dramatically in each level of DNA folding in chromosomes. Thus, the consideration of the linear packing ratio is not enough for the study of chromatin condensation; the constraint resulting from the actual DNA concentration in metaphase chromosomes must be considered for the construction of models for condensed chromatin.

Animals↗

PubMed2006

Specific interactions versus counterion condensation. 1. Nongelling ions/polyuronate systems.

The characteristics of the interaction between nongelling divalent cations (typically Mg(2+)) and polyuronates have been explored by means of isothermal calorimetry. In particular, three polyuronates mimicking separately guluronan (polyguluronate, polyG), mannuronan (polymannuronate, polyM), and polyalternating (polyMG), the three block-components of natural alginate samples, have been treated with divalent ions, and the enthalpy of mixing was determined for different values of the [M(2+)]/[Polym](rep.unit) ratio. Despite the absence of a site-specific chemical bonding between the two, as confirmed by circular dichroism spectroscopy, a substantial deviation of the experimental enthalpy of mixing from the theoretical behavior, as predicted by the classical counterion condensation (CC) theory, was observed. Such deviation has been interpreted in terms of a "generic" nonbonding affinity of the condensed divalent counterion for the polyelectrolytes. The mathematical formalism of the CC theory was extended to include a contribution to the (reduced) free energy and enthalpy arising from the counterion affinity, g(aff,0) and h(aff,0), and allowed the parametrical calculation of the fraction of divalent counterions condensed as function of the reduced thermodynamic quantity g(aff,0). A best fit procedure of the experimental enthalpy of mixing allowed the g(aff,0) and h(aff,0) pair to be estimated for each of the different polyuronates considered, revealing differences in the three samples. In qualitative terms, the results obtained seem to suggest a notable contribution of the desolvation process (i.e., release of structured water as a consequence of the interaction between the divalent counterion and the uronate group) to the enthalpy of affinity for polyM which is counterbalanced and overcome by an ion pairing term (i.e., partial formation of ion-ion and/or ion-dipole bonds) for polyG and polyMG, respectively.

Cations, Divalent↗

PubMedDate not supplied

Condensed representation of DNA primary sequences.

With rapid reporting of DNA sequences derived from automated DNA sequencing techniques, the problem of reviewing and ordering such information has become acute. We have introduced a condensed representation of primary sequences of DNA that offers an alternative method of registering DNA. The advantage of the condensed codes for DNA is that it not only offers fast, qualitative comparisons of DNA but also allows quantitative comparisons of DNA from different sources. The approach is outlined for a particular human beta globin sequence extract. Using the condensed representation of the primary DNA sequences, comparisons are made between primary sequences for Exon 1 of human beta globin and seven other beta globins.

Animals↗

PubMed2004

Preparation, characterization, and condensation of copper tellurolate clusters in the pores of periodic mesoporous silica MCM-41.

The copper-tellurolate cluster [(Cu(6)(TePh)(6)(PPh(2)Et)(5)] has been loaded into the pores of MCM-41 by solid-state impregnation techniques. It was found that the best loading conditions are 110 degrees C and 10(-)(3) Torr static vacuum. The resulting material was analyzed by powder X-ray diffraction (PXRD), nitrogen adsorption isotherms, thermogravimetric analysis (TGA), (31)P CP MAS NMR spectroscopy, and TEM. It was observed that loading is accompanied by loss of the phosphine shell, with retention of the copper-tellurium core. Condensation of the impregnated material may proceed thermally or photochemically. Thermal condensation results in the formation of Cu(2)Te nanoparticles as demonstrated by PXRD, and TEM data suggests that the process has taken place inside the pores of MCM-41. Photochemical condensation yields larger metal-chalcogen clusters in the pores as suggested by the result of UV-vis diffuse reflectance spectroscopy and TEM measurements.

Journal Article↗

PubMed2005

Condensed two- and three-dimensional aromatic systems: a theoretical study on the relative stabilities of isomers of CB19H16+, B20H15Cl, and B20H14Cl2 and comparison to B12H10Cl22-, C6H4Cl2, C10H7Cl, and C10H6Cl2.

DFT studies (B3LYP/6-31G) on mono- and dichloro derivatives of benzene, naphthalene, B12H12(2-), four-atom-sharing condensed systems B20H16, and monocarborane isomers of B20H16 are used to compare the variation of relative stability and aromaticity between condensed aromatics. The trends in the variation of the relative energies and aromaticity in these two- and three-dimensional systems are similar. Aromaticity, estimated by NICS values, does not change considerably with condensation or substitution. The minor variation in the relative energies of the isomers of chloro derivatives is explained by the topological charge stabilization rule of Gimarc. The compatibility of the cap and ring orbitals decides the relative stability of CB19H16+.

Journal Article↗

PubMed1996

A(15)Tl(27) (A = Rb, Cs): A Structural Type Containing Both Isolated Clusters and Condensed Layers Based on the Tl(11) Fragment. Syntheses, Structure, Properties, and Band Structure.

The isomorphous title compounds (and the ordered substitutional Rb(14)CsTl(27)) are obtained directly from reactions of the elements in sealed Ta below approximately 330 degrees C. Refinements of single-crystal data for the three established a structure with alternate layers of isolated pentacapped trigonal prismatic Tl(11)(7)(-) (D(3)(h)()) ions and condensed [Tl(16)(8-)] networks that are separated by cations. The condensed layer consists of Tl(11) units that share prismatic edges and are interbridged through waist-capping atoms (Tl(6/2)Tl(3)Tl(2)). (Rb(15)Tl(27): P&sixmacr;2m, Z = 1, a = 10.3248(6) Å, c = 17.558(2) Å.) The rubidium phase is a poor metal (rho(293) approximately 34 &mgr;Omega.cm) and is Pauli-paramagnetic. Extended Hückel band calculations indicate partially filled bands and a non-zero DOS at E(F), consistent with the observed metallic behavior, although appropriate cation tuning or modest anion doping should provide a Zintl phase. The band structure and COOP curves are also used to rationalize the distortion of the Tl(11) unit on condensation and the critical role of the interfragment bonds between waist-capping atoms in stabilizing the layer.

Journal Article↗

PubMed1999

Magic Electron Counts for Networks of Condensed Octahedral Niobium Clusters in Oxoniobates.

Chemical bonding in networks of octahedral oxoniobate clusters condensed through vertex-sharing is analyzed at the extended Hückel level of theory. Crystal or molecular orbitals of the condensed cluster networks are derived from the Nb-Nb bonding molecular orbitals of the monomeric Nb(6)O(18) cluster. Extended networks are treated by considering crystal orbitals at special points of the corresponding Brillouin zones. We find that cluster electron counts corresponding to optimal bonding in these networks decrease from 14 for the Nb(6)O(18) cluster to 12 per Nb octahedron for a dimer, 11 for a linear chain of clusters, 10-10(1)/(2) for a square network of clusters, and 7(3)/(4)-8(1)/(2) for cubic NbO in which all cluster vertices are shared. These results are in good agreement with both the counts derived from the experimentally observed structures and a previously devised counting scheme. The loss of Nb-Nb bonding at the shared cluster vertices and the Nb-O-Nb pi antibonding involving Nb atoms of neighboring octahedra are the reasons for the reduction of the magic cluster electron counts in the considered networks. It is proposed that similar counting schemes can be developed for other condensed cluster networks.

Journal Article↗

PubMed2005

Ti-crossed-Claisen condensation between carboxylic esters and acid chlorides or acids: a highly selective and general method for the preparation of various beta-keto esters.

Ti-crossed-Claisen condensation between a 1:1 mixture of carboxylic esters and acid chlorides promoted by TiCl4-Bu3N-N-methylimidazole proceeded successfully to give various beta-keto esters in good yields with excellent selectivities (19 examples, approximately 48-95% yield; cross/self-selectivity = approximately 96/4-99/1). The present method was extended to the condensation between a 1:1 mixture of carboxylic acids and carboxylic esters (six examples, approximately 70-92% yield; cross/self-selectivity = approximately 91/9-99/1). To demonstrate the utility of the present two Ti-crossed-Claisen condensations, we performed a couple of efficient short-step syntheses of two natural, representative, and useful perfumes, cis-jasmone and (R)-muscone.

Carboxylic Acids↗

PubMed2006

Monitoring temporal evolution of silicate species during hydrolysis and condensation of silicates using mass spectrometry.

The first stages of solid-state formation from solution can be crucial in determining the properties of the resulting solids. We are trying to approach prenucleation reactions of silicates from an aqueous solution containing tetraalkylammoniumhydroxides (TAAOH) and tetraalkoxysilanes (TAOS) by analyzing hydrolysis and condensation using electrospray mass spectrometry (ESI MS). Time-resolved measurements were performed using different reactor systems to show the stepwise hydrolysis of the silanes and subsequent condensation of silicate monomers via oligomers to form larger units. We approached the precipitation point by varying the pH and the concentrations of the reactants. The results show the evolution of different silicate species occurring during condensation. No defined molecular entities were identified at pH values close to precipitation, which suggests that under the conditions used, solids are probably not formed from defined building blocks.

Journal Article↗

PubMed2006

Photoreversible DNA condensation using light-responsive surfactants.

A means to control DNA compaction with light illumination has been developed using the interaction of DNA with a photoresponsive cationic surfactant. The surfactant undergoes a reversible photoisomerization upon exposure to visible (trans isomer, more hydrophobic) or UV (cis isomer, more hydrophilic) light. As a result, surfactant binding to DNA and the resulting DNA condensation can be tuned with light. Dynamic light scattering (DLS) measurements were used to follow lambda-DNA compaction from the elongated-coil to the compact globular form as a function of surfactant addition and light illumination. The results reveal that compaction occurs at a surfactant-to-DNA base pair ratio of approximately 7 under visible light, while no compaction is observed up to a ratio of 31 under UV light. Upon compaction, the measured diffusion coefficient increases from a value of 0.6 x 10(-8) cm2/s (elongated coil with an end-to-end distance of 1.27 microm) to a value of 1.7 x 10(-8) cm2/s (compact globule with a hydrodynamic radius of 120 nm). Moreover, the light-scattering results demonstrate that the compaction process is completely photoreversible. Fluorescence microscopy with T4-DNA was used to further confirm the light-scattering results, allowing single-molecule detection of the light-controlled coil-to-globule transition. These structural studies were combined with absorbance and fluorescence spectroscopy of crystal violet in order to elucidate the binding mechanism of the photosurfactant to DNA. The results indicate that both electrostatic and hydrophobic forces are important in the compaction process. Finally, a DNA-photosurfactant-water phase diagram was constructed to examine the effects of both DNA and surfactant concentration on DNA compaction. The results reveal that precipitation, which occurs during the latter stages of condensation, can also be reversibly controlled with light illumination. The combined results clearly show the ability to control the interaction between DNA and the complexing agent and, therefore, DNA condensation with light.

Chemical Precipitation↗

PubMed2006

DNA condensation and cell transfection properties of guanidinium calixarenes: dependence on macrocycle lipophilicity, size, and conformation.

Calix[n]arenes functionalized with guanidinium groups at the upper rim and alkyl chains at the lower rim bind to DNA, condense it, and in some cases, promote cell transfection depending on their structure and lipophilicity. Atomic force microscopy (AFM) studies indicate that upon DNA binding the hydrophobic association of the lipophilic chains of cone guanidinium calix[4]arenes drives the formation of intramolecular DNA condensates, characterized by DNA loops emerging from a dense core. Furthermore, hexyl and octyl chains confer to these calixarenes cell transfection capabilities. Conversely, larger and conformationally mobile calix[6]- and calix[8]arene methoxy derivatives form intermolecular aggregates characterized by "gorgonlike" structures composed of multiple plectomenes. These adducts, in which interstrand connections are dominated by electrostatic interactions, fail to promote cell transfection. Finally, calix[4]arenes in a 1,3-alternate conformation show an intermediate behavior because they condense DNA, but the process is driven by charge-charge interactions.

Calixarenes↗

PubMed2000

A DFT theoretical analysis of aldehyde condensation pathways onto methyllithium, lithium dimethylamide, and their aggregates

A DFT analysis of the condensation of monomeric methyllithium and lithium dimethylamide (LMA), as well as their homo and hetero dimers, on formaldehyde and acetaldehyde is reported. A stable complex, exhibiting a directional interaction between a lone pair of the oxygen on the aldehyde and a lithium, is first found. At this stage, the aldehyde carbonyl and the Li-X (X = C or N) bonds lie in the same plane. To proceed, the condensation reaction has to go through a transition state that mainly consists of a rotation of the aldehyde plane, placing it perpendicular to the C-C or C-N forming bond. The reaction then leads, in a strongly exothermic final step, to the addition product that is a lithium alcoholate or alpha-amino alcoholate, associating into an hetero-aggregate with the remaining moiety of the initial dimer. From the relative heights of the activation barriers, it appears that, for the heterodimer MeLi-LMA, the formation of the C-N bond should be kinetically favored over the C-C one, while the lithium ethylate resulting from the C-C binding is the thermodynamic product. A decomposition of the activation energy barriers has been carried out in order to determine the physicochemical forces responsible for the variation of the condensation activation barriers with the structure of the final species formed. The results obtained are discussed in relation with corresponding experimental data.

Journal Article↗