Effect of peptide length on the interaction between consensus peptides and DOPC/DOPA bilayers

The effect of peptide length and electrostatics on the interaction between Cardin motif peptides and lipid membranes was investigated for (AKKARA)(n) (n = 1-4) and (ARKAAKKA)(n) (n = 1-3) peptides (A, K, and R refer to alanine, lysine, and arginine, respectively) by fluorescence spectroscopy, circular dichroism, ellipsometry, z potential, and photon correlation spectroscopy measurements. The effect of the peptides regarding leakage induction of both zwitterionic and anionic liposomes increased with increasing peptide length, as did the peptide-induced killing of Enterococcus faecalis and Bacillus subtilis bacteria. The peptides, characterized by a random coil conformation both in buffer and when attached to the liposomes (helix content less than 20%), displayed an increased adsorption with increasing peptide length, and plateau adsorption for the longest peptides corresponded to 1 peptide per 65 and 17 lipid molecules for zwitterionic and anionic membranes, respectively. Control experiments with uncharged peptide analogues as well as experiments at high excess electrolyte concentration showed that peptide charges are important both for peptide adsorption and leakage induction. These observations, together with observations of the liposome z potential at different peptide additions as well as a comparison between the results for zwitterionic and anionic liposomes, suggest that electrostatically affected local packing effects are crucial for the action of these peptides, although pore formation such as that observed for many AMPs cannot be excluded at present.     

Effect of chain length on rates of diffusion-limited small molecule-polymer and polymer-polymer reactions: Phosphorescence quenching studies

Model interactions have been studied by phosphorescence quenching to obtain a better understanding of the chain length dependence of interpolymeric chain end-chain end reactions such as those involved in the termination step of free radical polymerization. For small molecule-polymer interactions in dilute cyclohexane solution, quenching rate constant (k_q) data agree with the Smoluchowski equation prediction that k_q scales as polymer molecular weight (MW) to the -½ power, confirming self-diffusion control. For polymer-polymer interactions in dilute solution, the chain length dependence is weaker than that predicted by translational diffusion control, as described by the Smoluchowski equation, but is stronger than that predicted by renormalization group theory. For interactions between 70000 MW benzil-end-labeled polystyrene and varying MWs of anthracene-end-labeled polystyrene at 300 g/L polymer, k_q decreases by a factor of 10 in going from MWs of 100 to 1000 g/mol; beyond 1000 g/mol, k_q is nearly independent of chain length. Such effects indicate that the importance of oligomeric radical self-diffusion and polymer radical chain-end segmental mobility must be carefully considered in understanding the termination process in free radical polymerization. © 1996 John Wiley & Sons, Inc.     

Kinetics of polyesterification: Effect of diol chain length

Kinetics of polyesterification of maleic anhydride with polyethylene glycol (PEG) of varying molecular weights have been evaluated. The investigations have been carried out by employing heating cycles comparable to those employed in industrial processes and under nonisothermal conditions. The rate of reaction was found to decrease with increase in the chain length of the polyether. The energy of activation was estimated as 26.91, 40.25, and 47.30 Kcal/mol for PEG of molecular weights 200, 300, and 400, respectively. © 1994 John Wiley & Sons, Inc.     

Microemulsions: Effect of alkyl chain length of alcohol and alkane

In microemulsions consisting of four components, i.e. detergent — water — oil — cosurfactant, the free energy of transfer from the continuous oil phase to the interfacial region for the cosurfactant is reported. From the effect of temperature on the free energy, the entropy and the enthalpy values are also reported. The effect of chain length of the alcohol (cosurfactant) is also described. It is further shown, that if the oil phase consists of hexadecane, then the free energy changes as a linear function of the number of carbon atoms in the cosurfactant. On the other hand, if the oil phase is benzene, the cosurfactant chain length has very little effect. These data are analyzed with respect to the microemulsion structure and stability.     

Polyketide chain length control by chain length factor

Bacterial aromatic polyketides are pharmacologically important natural products. A critical parameter that dictates product structure is the carbon chain length of the polyketide backbone. Systematic manipulation of polyketide chain length represents a major unmet challenge in natural product biosynthesis. Polyketide chain elongation is catalyzed by a heterodimeric ketosynthase. In contrast to homodimeric ketosynthases found in fatty acid synthases, the active site cysteine is absent from the one subunit of this heterodimer. The precise role of this catalytically silent subunit has been debated over the past decade. We demonstrate here that this subunit is the primary determinant of polyketide chain length, thereby validating its designation as chain length factor. Using structure-based mutagenesis, we identified key residues in the chain length factor that could be manipulated to convert an octaketide synthase into a decaketide synthase and vice versa. These results should lead to novel strategies for the engineered biosynthesis of hitherto unidentified polyketide scaffolds.     

Small-angle neutron scattering from micelles of alkylpolyoxyethylene sulfate: Effect of chain length

Small-angle neutron scattering (SANS) data have been obtained for (i) a series of solutions of C _m H_2m+1(OCH₂–CH₂)₂SO₄Na, for m=18, 16, and 14; (ii) an approximately 0.07M solution of C₁₄H₂₉(OCH₂–CH₂)₂SO₄Na to which different amounts of NaCl were added; and (iii) a series of solutions of variable concentration of C₁₂H₂₅(OCH₂–CH₂)SO₄Na. The increase of the number of carbon atoms of the hydrocarbon chain produces a noticeable increase of the aggregation number of the micelles, while the salt tolerance decreases with increasing m. All the data can be described in terms of a monodispersed, charged, hard-spheres model interacting via a screened Coulombic potential, except the run at highest salt concentration, for which an ellipsoid model gives better results.     

Effects of chain length and N-methylation on a cation-pi interaction in a beta-hairpin peptide

The effects of N-methylation and chain length on a cation-pi interaction have been investigated within the context of a beta-hairpin peptide. Significant enhancement of the interaction and structural stabilization of the hairpin have been observed upon Lys methylation. Thermodynamic analysis indicates an increased entropic driving force for folding upon methylation of Lys residues. Comparison of lysine to analogues ornithine (Orn) and diaminobutyric acid (Dab) indicates that lysine provides the strongest cation-pi interaction and also provides the most stable beta-hairpin due to a combination of side chain-side chain interactions and beta-sheet propensities. These studies have significance for the recognition of methylated lysine in histone proteins.     

Fragmentation of doubly-protonated peptide ion populations labeled by H/D exchange with CD(3)OD

Doubly-protonated bradykinin (RPPGFSPFR) and an angiotensin III analogue (RVYIFPF) were subjected to hydrogen/deuterium (H/D) exchange with CD(3)OD in a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. A bimodal distribution of deuterium incorporation was present for bradykinin after H/D exchange for 90 s at a CD(3)OD pressure of 4 x 10(-7) Torr, indicating the existence of at least two distinct populations. Bradykinin ion populations corresponding to 0-2 and 5-11 deuteriums (i.e., D(0), D(1), D(2), D(5), D(6), D(7), D(8), D(9), D(10), and D(11)) were each monoisotopically selected and fragmented via sustained off-resonance irradiation (SORI) collision-induced dissociation (CID). The D(0)-D(2) ion populations, which correspond to the slower exchanging population, consistently require lower SORI amplitude to achieve a similar precursor ion survival yield as the faster-reacting (D(5)-D(11)) populations. These results demonstrate that conformation/protonation motif has an effect on fragmentation efficiency for bradykinin. Also, the partitioning of the deuterium atoms into fragment ions suggests that the C-terminal arginine residue exchanges more rapidly than the N-terminal arginine. Total deuterium incorporation in the b(1)/y(8) and b(2)/y(7) ion pairs matches very closely the theoretical values for all ion populations studied, indicating that the ions of a complementary pair are likely formed during the same fragmentation event, or that no scrambling occurs upon SORI. Deuterium incorporation into the y(1)/a(8) pseudo-ion pair does not closely match the expected theoretical values. The other peptide, doubly-protonated RVYIFPF, has a trimodal distribution of deuterium incorporation upon H/D exchange with CD(3)OD at a pressure of 1 x 10(-7) Torr for 600 s, indicating at least three distinct ion populations. After 90 s of H/D exchange where at least two distinct populations are detected, the D(0)-D(7) ion populations were monoisotopically selected and fragmented via SORI-CID over a range of SORI amplitudes. The precursor ion survival yield as a function of SORI amplitude falls into two distinct behaviors corresponding to slower- and faster-reacting ion populations. The slower-reacting population requires larger SORI amplitudes to achieve the same precursor ion survival yield as the faster exchanging population. Total deuterium incorporation into the y(2)/b(5) ion pairs matches closely the theoretical values over all ion populations and SORI amplitudes studied. This result indicates the y(2) and b(5) ions are likely formed by the same mechanism over the SORI amplitudes studied.     

Effect of length of carbon chain on antioxidation efficiency of o-bisphenols

Conclusions In the oxidation of isotactic polypropylene the highest antioxidant efficiency is shown by an o-bis-phenol, the nuclei of which are linked by a methylene bridge.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 11, pp. 2614–2616, November, 1972.     

Effect of chain length on transfection properties of spermine-based gemini surfactants

The synthesis and associated structure-activity relationships for gene transfection of a series of spermine-derived cationic gemini surfactants incorporating diamino acid headgroups and either identical (symmetrical) or different (unsymmetrical) lipophilic tailgroups is described. Transfection activity is found to depend critically upon the structural elements present.     

Effect of primary radical termination on chain length and initiator efficiency

In polymerization with primary radical termination, when reaction between primary radicals, which escape from solvent cage, is not negligible, a relation between chain length and polymerization rate is found regardless of tractable approximate procedures. Such a relation is applied to the kinetic data obtained in the polymerizations of methyl methacrylate (MMA) and vinyl acetate (VA) initiated by 2,2′-azobis(2,4-valeronitrile) at 50.0°C. Further, when the primary radical termination is high, an initiator efficiency can not be approximated to a ratio of the primary radicals escaping from the cage to the total primary radicals formed in the cage. In the polymerization of MMA, after the primary radicals escapes from the cage, they immediately react with the monomer. Thus, the reaction between the primary radicals is not significant. However, in the polymerization of VA, the rate of reaction between the primary radical and the monomer might be comparable to the rate of reaction between the primary radicals when the initiator concentration is quite high.     

N-methylation of peptides on selected positions during the elongation of the peptide chain in solution phase

[reactions: see text] An efficient and general solution-phase method for the site-specific N-methylation of peptides has been developed. This novel procedure involves synthesis of N-nosyl protected peptides and their subsequent N-methylation with diazomethane. Its efficiency was proved by the successful synthesis of various hindered oligopeptides containing N-methyl amino acid residues with excellent yield and purity. The method is particularly attractive in that the adopted conditions do not cause any detectable racemization of the peptide stereocenters and the process does not require chromatographic purification of the methylated products. A further advantage is the compatibility of this methodology with Fmoc solution-phase peptide synthesis.     

Photopolymerization of methyl methacrylate with azo-containing polydimethylsiloxane as photoinitiator: Effect of siloxane chain length

The kinetics of the free radical photopolymerization of methyl methacrylate (MMA) initiated by azo-containing polydimethylsiloxane (PSMAI) and azobisisobutyronitrile (AIBN) was investigated. The greater polymerization rate R_p in MMA/PSMAI systems may be due to the higher value of the initiation rate R_i and the lower value of the termination rate constant k_t than that in MMA/AIBN system. The reaction orders with respect to initiators PSMAI decreased with an increase in polydimethylsiloxane chain length (SCL) in PSMAI. The observed deviations in polymerization rate from rate equation could be explained in terms of primary radical termination. The photoinitiator efficiency Φ of initiators decreased with increase in SCL, while the ratio of the rate constants for chain termination and chain initiation by primary radical increased with SCL. The fraction β of primary radicals entering into termination in MMA/PSMAI systems were larger than that in MMA/AIBN system. © 1996 John Wiley & Sons, Inc.     

Adsorption and thermal reactions of alkanethiols on pt(111): Dependence on the length of the alkyl chain

The adsorption and thermal decomposition of alkanethiols (R-SH, where R = CH3, C2H5, and C4H9) on Pt(111) were studied with temperature-programmed desorption (TPD) and X-ray photoelectron spectroscopy (XPS) with synchrotron radiation. Dissociation of sulfhydryl hydrogen (RS-H) of alkanethiol results in the formation of alkanethiolate; the extent of dissociation at an adsorption temperature of 110 K depends on the length of the alkyl chain. At small exposure, all chemisorbed CH3SH, C2H5SH, and C4H9SH decompose to desorb hydrogen below 370 K and yield carbon and sulfur on the surface. Desorption of products containing carbon is observed only at large exposure. In thermal decomposition, alkanethiolate is proposed to undergo a stepwise dehydrogenation: R'-CH2S --> R'-CHS --> R'-CS, R' = H, CH3, and C3H7. Further decomposition of the R'-CS intermediate results in desorption of H2 at 400-500 K and leaves carbon and sulfur on the surface. On the basis of TPD and XPS data, we conclude that the density of adsorption of alkanethiol decreases with increasing length of the alkyl chain. C4H9SH is proposed to adsorb mainly with a configuration in which its alkyl group interacts with the surface; this interaction diminishes the density of adsorption of alkanethiols but facilitates dehydrogenation of the alkyl group.     

Effect of chain length on thermal conversion of alkoxy-substituted copper phthalocyanine precursors

A series of dialkoxy-substituted copper phthalocyanine (CuPc) precursors (4a-4d) have been prepared by treating phthalonitrile with the corresponding lithium alkoxide under mild conditions. The precursors exhibited high solubilities in common organic solvents, including acetone, toluene, tetrahydrofuran (THF), CH(2)Cl(2), and CHCl(3). Elongation of the alkoxy chains improved the solubilities of the precursors effectively, and accordingly, the butoxy-substituted derivative (4d) showed the highest solubility among 4a-4d. X-ray crystallography clarified that the conjugated skeletons of 4a-4d are all isostructural, and have two alkoxy groups in a syn-conformation fashion, leading to highly bent structures. Thermal conversions of the precursors examined by thermogravimetry (TG) and differential thermal analysis (DTA) demonstrate that 4a was converted into CuPc via two distinct exothermic processes in the 200-250 °C temperature range, while 4d exhibits only one exothermic signal in the DTA. In the field emission scanning electron microscopy (FESEM) images of 4a, the presence of two types of distinct crystal morphology (prismatic and plate-like crystals) can be recognized, implying that the two observed exothermic processes in the DTA can be attributed to the different crystal morphologies of the samples rather than the step-by-step elimination of the alkoxy groups. The thermal formation of CuPc from the precursors has been unambiguously confirmed by X-ray powder diffraction, UV-vis spectroscopy, and elemental analysis. The precursors were converted into CuPc at lower temperature with increasing chain length, presumably because of the increased void volume in the crystals. Thermal conversion performed in the solution phase results in a bright blue-colored solution with prominent absorption bands in the 650-700 nm region, strongly supporting the formation of CuPc.     

Effect of chain length and asymmetry on material properties of bilayer membranes

Dissipative particle dynamics is used to extract the material parameters (bending and area stretch moduli) of a bilayer membrane patch. Some experiments indicate that the area stretch modulus of lipid vesicles varies little as the chain length of the lipids composing the bilayer increases. Here we show that making the interactions between the hydrophilic head groups of the model amphiphiles proportional to the hydrophobic tail length reproduces the above result for the area stretch modulus. We also show that the area stretch modulus of bilayers composed of amphiphiles with the same number of tail beads but with asymmetric chains is less than that of bilayers with symmetric chains. The effects on the bilayer density and lateral stress profiles of changes to the amphiphile architecture are also presented.     

Pyridinium salt liquid crystals Effect of mesogen extension and alkyl chain length

The thermotropism of 1-n-alkyl-(4-methyl and 4-tolyl)pyridinium bromides were compared for alkyl chain lengths ranging from n = 12 to 22 carbons. A smectic A mesophase is present in both series for the longer chain compounds, n ≥ 16, with the clearing temperature being similar for both series but increasing rapidly with chain length. The series with the elongated mesogen also possesses an ordered mesophase identified as smectic G. The transition between this mesophase and the S_A or isotropic phase in the 4-tolyl series, and the transition to and from the crystalline phase in both series, are affected relatively little by the alkyl chain length. It seems that the S_A mesophase is governed primarily by the amphiphilic character of the substances, whereas elongation of the ionic head group is responsible for the appearance of a more ordered mesophase at intermediate temperatures.     

Mechanisms for the selective gas-phase fragmentation reactions of methionine side chain fixed charge sulfonium ion containing peptides

To enable the development of improved tandem mass spectrometry based methods for selective proteome analysis, the mechanisms, product ion structures, and other factors influencing the gas-phase fragmentation reactions of methionine side-chain derivatized "fixed-charge" phenacylsulfonium ion containing peptide ions have been examined. Dissociation of these peptide ions results in the exclusive characteristic loss of the derivatized side chain, thereby enabling their selective identification. The resultant product ion(s) are then subjected to further dissociation to obtain sequence information for subsequent protein identification. Molecular orbital calculations (at the B3LYP/6-31 + G (d,p) level of theory) performed on a simple peptide model, together with experimental evidence obtained by multistage dissociation of a regioselectively deuterated methionine derivatized sulfonium ion containing tryptic peptide, indicate that fragmentation of the fixed charge containing peptide ions occurs via SN2 reactions involving the N- and C-terminal amide bonds adjacent to the methionine side chain, resulting in the formation of stable cyclic five- and six-membered iminohydrofuran and oxazine product ions, respectively. These studies further indicate that the rings formed via these neighboring group reactions are stable to further dissociation by MS3. As a consequence, the formation of b- or y-type sequence ions are "skipped" at the site of cyclization. Despite this, complete sequence information is still obtained because of the presence of both cyclic products.     

Fragmentation of doubly-protonated Pro-His-Xaa tripeptides: Formation of b 2 2+ ions

When ionized by electrospray from acidic solutions, the tripeptides Pro-His-Xaa (Xaa=Gly, Ala, Leu) form abundant doubly-protonated ions, [M+2H]²⁺. Collision-induced dissociation (CID) of these doubly-protonated species results, in part, in formation of b ₂ ²⁺ ions, which fragment further by loss of CO to form a ₂ ²⁺ ions; the latter fragment by loss of CO to form the Pro and His iminium [immonium is commonly used in peptide MS work] ions. Although larger doubly-charged b ions are known, this represents the first detailed study of b ₂ ²⁺ ions in CID of small doubly protonated peptides. The most abundant CID products of the studied doubly-protonated peptides arise mainly in charge separation involving two primary fragmentation channels, formation of the b ₂ /y ₁ pair and formation of the a ₁ /y ₂ pair. Combined molecular dynamics and density functional theory calculations are used to gain insight into the structures and fragmentation pathways of doubly-protonated Pro-His-Gly including the energetics of potential protonation sites, backbone cleavages, post-cleavage charge-separation reactions and the isomeric structures of b ₂ ²⁺ ions. Three possible structures are considered for the b ₂ ²⁺ ions: the oxazolone, diketopiperazine, and fused ring isomers. The last is formed by cleavage of the His-Gly amide bond on a pathway that is initiated by nucleophilic attack of one of the His side-chain imidazole nitrogens. Our calculations indicate the b ₂ ²⁺ ion population is dominated by the oxazolone and/or fused ring isomers.