Role of alkylated residues in the tetrapeptide self-assembly—A molecular dynamics study

Designing peptide sequences that self-assemble into well-defined nanostructures can open a new venue for the development of novel drug carriers and molecular contrast agents. Current approaches are often based on a linear block-design of amphiphilic peptides where a hydrophilic peptide chain is terminated by a hydrophobic tail. Here, a new template for a self-assembling tetrapeptide (YXKX, Y = tyrosine, X = alkylated tyrosine, K = lysine) is proposed with two distinct sides relative to the peptide's backbone: alkylated hydrophobic residues on one side and hydrophilic residues on the other side. Using all-atom molecular dynamics simulations, the self-assembly pathway of the tetrapeptide is analyzed for two different concentrations. At both concentrations, tetrapeptides self-assembled into a nanosphere structure. The alkylated tyrosines initialize the self-assembly process via a strong hydrophobic effect and to reduce exposure to the aqueous solvent, they formed a hydrophobic core. The hydrophilic residues occupied the surface of the self-assembled nanosphere. Ordered arrangement of tetrapeptides within the nanosphere with the backbone hydrogen bonding led to a beta sheet formation. Alkyl chain length constrained the size and shape of the nanosphere. This study provides foundation for further exploration of self-assembling structures that are based on peptides with hydrophobic and hydrophilic moieties located on the opposite sides of a peptide backbone.     

On the magnitude and specificity of medium effects in enzyme-like catalysts for proton transfer

Medium effects are normally studied by comparing the rates of reactions in different solvents. However, medium effects at the active site of enzymes differ dramatically from bulk solvents, both in their diversity (the presence of more than one type of "solvent") and in their spatial arrangement. We describe medium effects in a simple catalytic system, obtained by systematic alkylation of a polymeric scaffold bearing amine groups to give synzymes that catalyze the Kemp elimination of benzisoxazoles with remarkable efficiency. Our analysis indicates that catalysis by these synzymes is driven primarily by specific, localized enzyme-like medium effects, and these effects seem to differ dramatically from the nonspecific medium effects (i.e., desolvation activation) exhibited by solvents. Ligand-binding studies indicate that the synzyme active sites provide localized microenvironments affording a combination of hydrophobic and apolar regions on one hand and dipolar, protic, and positively charged on the other. Such localized microenvironments are not available in bulk solvents. A Br?nsted (leaving group) analysis indicates that, in comparison to solvent catalysis, the efficiency of synzyme catalysis shows little sensitivity to leaving group pK(a). We show that enzyme-like medium effects alone, in the absence of efficient positioning of the catalytic amine base relative to the substrate, can give rise to rate accelerations as high as 10(5), for both activated and nonactivated substrates. Supported by the accidental identification of active sites on the surfaces of noncatalytic proteins and the promiscuous activities found in many enzymes, our findings suggest that the interfaces of protein surfaces and their hydrophobic cores provide a microenvironment that is intrinsically active and may serve as a basis for further evolutionary improvements to give proficient and selective enzymes.     

Solvent controlled self-assembly at the liquid-solid interface revealed by STM

The effect of solvent on the two-dimensional (2D) supramolecular ordering of monodendron 1 at the liquid-solid interface has been systematically investigated by means of scanning tunneling microscopy (STM). Solvents range from those with hydrophilic solvating properties, such as alkylated alcohols and acids, to hydrophobic solvents such as alkylated aromatics and alkanes. Dramatic differences in the 2D ordering are observed depending on the nature of the solvent. Of particular interest is the fact that in hydrophobic solvating solvents, such as aliphatic and aromatic hydrocarbons, solvent molecules are coadsorbed in the 2D molecular network while this is not the case for alkylated alcohols or acids. Furthermore, in the case of the coadsorbing solvents, a striking influence of the alkyl chain length has been observed on the 2D pattern formed. The solvent and alkyl chain length dependences are discussed in terms of molecule-molecule interactions (homo and hetero) and molecule-substrate interactions.     

Self-organization of polymer particles on hydrophobic solid substrates in aqueous media. I. Self-organization of cationic polymer particles on alkylated glass plates

Monodisperse, cationic polymer particles bearing quaternary ammonium groups effectively self-organized on hydrophobic solid substrates such as alkylated glass plates and polymer films to form particle monolayers. With an increase of the particle surface charge density, the surface coverage decreased and the morphology of particle monolayers changed from aggregated type to dispersed type. The dispersed type of particle monolayers having a relatively regular particle distance was formed at higher temperature. The self-organization behaviors on alkylated glass plates were different from those on unmodified glass plates through electrostatic interaction. The formation of particle monolayers on alkylated glass plates occurred only over a certain latex concentration range in contrast with that on unmodified glass plate. The adhesive strength of particle monolayers was enhanced by annealing at temperatures above the glass transition temperature (T _g) of the particles. Lens-shaped particle monolayers were fabricated by annealing the dispersed type of particle monolayers.     

Alkylated glass partition allows formation of solvent-free lipid bilayer by Montal-Mueller technique

Formation of bilayer lipid membrane (BLM) by Montal-Mueller technique across a small aperture in a partition film traditionally requires coating of the aperture with a hydrophobic substance, often just an organic solvent. However, we demonstrate here that the most effective coating is not strictly hydrophobic but rather provides water/oil repellent properties. BLM were formed from diphytanoylphosphatidylcholine (DPhPC) on small 0.1-0.8 mm apertures made in specially prepared alkylated glass coverslips. The coverslips were either fluorosiliconized by 3,3,3-Trifluoropropyl-trimethoxysilane, which reduces adsorption of DPhPC in addition to creation of hydrophobic surface, or silanized, which promote adsorption of DPhPC. At fluorosiliconized surfaces stable BLM were formed. Specific capacitance of these BLM was 0.86 microF/cm(2)+/-5%, while their lateral tension was estimated as 4.3+/-0.4 mN/m. BLM were stable for hours under moderate voltage applied. At silanized surfaces stable BLM were formed only in acidic medium (3 相似文献   

Catalytic deprotection of protected alcohols in water using low-loading and alkylated polystyrene-supported sulfonic acid

Catalytic deprotection of various protected alcohols was efficiently conducted using a hydrophobic low-loading and alkylated polystyrene-supported sulfonic acid (LL-ALPS-SO3H) in water as the sole solvent. Transprotection of an alcohol from a silyl ether to the corresponding benzylic ether or ester also proceeded smoothly in water.     

Synthesis of nitrogen and sulfur macrocycles with cis exogenous oxygen and sulfur donor atoms

A series of new N4 and N8 macrocycles has been prepared, that includes cis-exogenous O2, S2 and S/O atoms to allow chelation to a metal external to the macrocyclic ring. We found that thioamide units within the macrocycles were unstable to attack by secondary amines and thus alkylated precursors containing only tertiary amines could lead to exogenous-S2 macrocycles. Cyclisation of alkylated tetraamine precursors with dimethyloxalate or dithiooxamide led to both N4 and N8 macrocycles via 1 + 1 and 2 + 2 cyclisation reactions with exogenous-O2 or S2 respectively. Alkylation of preformed exogenous-O2 macrocycles was explored and led to alkyl substitution at the secondary amine nitrogens in the ring, however synthesis of these species was overall lower yielding than cyclisation using alkylated tetraamine precursors. Thionation of an exo-O2 macrocycle using an analogue of Lawesson's Reagent led to formation of the analogous exogenous-S2 and exogenous-O,S macrocycles. Related S2N2 macrocycles with exogenous-O2 were prepared by a cyclisation route but could not be isolated free of larger ring analogues.     

Spectroscopic studies of STZ-induced methylated-DNA in both in vivo and in vitro conditions

Alkylating agents after formation of DNA adduct not only possess their harmful role on living cells but also can transfer this information to the next generation. Different techniques have been introduced to study the alkylated DNA, most of which are specific and designed for investigation of specific target DNA. But the exact differences between spectroscopic and functional properties of alkylated DNA are not seen in the literature. In the present study DNA was methylated using streptozotocin (STZ) by both in vitro and in vivo protocols, then methylated-DNA was investigated by various techniques. Our results show that (1) the binding of ethidium bromide as an intercalating dye decreases to methylated-DNA in comparison with normal DNA, (2) CD spectra of methylated-DNA show changes including a decrease in the positive band at 275 nm and a shift from 258 nm crossover to a longer wavelength, which is caused by reduction of water around it, due to the presence of additional hydrophobic methyl groups, (3) the stability of methylated-DNA against DTAB as a denaturant is decreased and (4) the enzyme-like activity of methylated-DNA in an electron transfer reaction is reduced. In conclusion, additional methyl groups not only protrude water around DNA, but also cause the loss of hydrogen bonding, loosening of conformation, preventing desired interactions and thus normal function of DNA.     

The enantioselectivity of modified cyclodextrins: Studies on interaction mechanisms

The separation of enantiomers of rather simple molecules, such as alkanes and alkanoic acid esters substituted at the 2-position, has been investigated on alkylated β-cyclodextrin stationary phases. By observing the effect of varying the substrate and the cyclodextrin alkylating agent it has been possible to propose a mechanism for the separation. The most important factors seem to be hydrophobic interactions and the ability of the cyclodextrin to change its conformation to accept the guest molecule.     

A Transformation of N‐Alkylated Anilines to N‐Aryloxamates

Transformation of N‐alkylated anilines to N‐aryloxamates was studied using ethyl 2‐diazoacetoacetate as an alkylating agent and dirhodium tetraacetate (Rh₂(OAc)₄) as the catalyst. The general applicability of the reaction as a synthetic method for N‐aryloxamates was studied with a number of substituted N‐alkylated anilines. The results revealed that the oxamate was formed by a radical reaction with molecular O₂ and Rh₂(OAc)₄ as initiator.     

Efficient intracellular siRNA delivery by ethyleneimine-modified amphiphilic macromolecules

New materials that can bind and deliver oligonucleotides such as short interfering RNA (siRNA) without toxicity are greatly needed to fulfill the promise of therapeutic gene silencing. Amphiphilic macromolecules (AMs) were functionalized with linear ethyleneimines to create cationic AMs capable of complexing with siRNA. Structurally, the parent AM is formed from a mucic acid backbone whose tetra-hydroxy groups are alkylated with 12-carbon aliphatic chains to form the hydrophobic component of the macromolecule. This alkylated mucic acid is then mono-functionalized with poly(ethylene glycol) (PEG) as a hydrophilic component. The resulting AM contains a free carboxylic acid within the hydrophobic domain. In this work, linear ethyleneimines were conjugated to the free carboxylic acid to produce an AM with one primary amine (1N) or one primary amine and four secondary amines (5N). Further, an AM with amine substitution both to the free carboxylic acid in the hydrophobic domain and also to the adjacent PEG was synthesized to produce a polymer with one primary amine and eight secondary amines (9N), four located on each side of the AM hydrophobic domain. All amine-functionalized AMs formed nanoscale micelles but only the 5N and 9N AMs had cationic zeta potentials, which increased with increasing number of amines. All AMs exhibited less inherent cytotoxicity than linear polyethyleneimine (L-PEI) at concentrations of 10 μM and above. By increasing the length of the cationic ethyleneimine chain and the total number of amines, successful siRNA complexation and cellular siRNA delivery was achieved in a malignant glioma cell line. In addition, siRNA-induced silencing of firefly luciferase was observed using complexes of siRNA with the 9N AM and comparable to L-PEI, yet showed better cell viability at higher concentrations (above 10 μM). This work highlights the promise of cationic AMs as safe and efficient synthetic vectors for siRNA delivery. Specifically, a novel polymer (9N) was identified for efficient siRNA delivery to cancer cells and will be further evaluated.     

Synthesis of New Furo[2,3‐d]pyrimidines and Pyrimido[4′,5′:4,5]furo[2,3‐d]pyrimidines

Sodium salt of 4‐hydroxy‐6‐methyl‐2‐phenylpyrimidine‐5‐carbonitrile ( 3 ) was subjected to alkylation with different a‐halo compounds, where the corresponding O‐alkylated products 4_a‐g were obtained. Ring closure of the O‐alkylated product 4_a‐c performed using sodium ethoxide in refluxing ethanol afforded furo[2,3‐d]pyrimidines 5_a‐c The latter compounds on reaction with a variety of reagents gave other new furopyrimidines as well as a number of furodipyrimidines.     

Alternative procedure for the purification of the heat-stable enterotoxin of enterotoxigenic Escherichia coli pathogenic for calves

A method for purification of the heat-stable enterotoxin (ST) of enterotoxigenic Escherichia coli (ETEC) strains (C1444 and B41) pathogenic for calves and some physiochemical properties of the ST are described. The method involved ultrafiltration on PM-10 and UM-2 Diaflo membranes, acetone fractionation, ion-exchange chromatography on AG 1-X2, chromatofocusing and a combination of hydrophobic interaction chromatography on octyl-Sepharose CL-4B and gel-permeation on Bio-Gel P-2. Polyacrylamide gel electrophoresis in sodium dodecyl sulphate of fluorescamine-labeled purified, reduced and alkylated ST preparations revealed a single band with approximate molecular masses of 2500 and 2200 for the C1444 and B41 STs, respectively. For the C1444 ST, the final purification achieved was approximately 27,000-fold on the basis of absorbance at 280 nm per mouse effective dose. However, it was 2000-fold when calculated on the basis of mg protein per effective dose (5 ng). Amino acid composition of the C1444 ST was found to be different from that of the B41 ST suggesting that the ST produced by bovine isolates may be heterogeneous in their structure.     

Alkylations of Resorcarenes and Calix[4]pyrroles in Phase Transfer Catalytic Systems

Calixlnlarenesarecyclicoligomersmadeupofphenolsandformaldehyde.Thisversatileclassofcompoundshasbeenextensivelystudiedinthelastdecademainlyinordertoobtainnewcomplexingagentsbyappropriatefuntionalizationoftheparentmoleculel.ResorcarenesZandcall-c[4]pyrroles'aretwosubgroupmembersofthefamilyofcalixarensandalsoattractedincreasinginterests.Aspartofaprogrammeaimedatthesynthesisofneweasy-to-makecalixarenemolecules,wedecidedtoinvestigatethealkylationofsomecalixarensinPhaseTransferCatalysis(PTC)condi…     

Self-generation of tiered surfactant superstructures for one-pot synthesis of Co3O4 nanocubes and their close- and non-close-packed organizations

Self-generation of ionic organic capping from nonionic surfactant polyoxyethylene (20) sorbitan trioleate (Tween-85) has been realized for the controlled synthesis of single crystalline Co(3)O(4) quantum dots (3.0-5.7 nm) in cubic morphology from related layered hydroxide precursors at 80-95 degrees C. With chemical modification of hydrophobic functional groups on the surface of Co(3)O(4) nanocubes; furthermore, various nanocube-containing micellar superstructures can be further assembled through hydrophobic interactions between Tween-85 molecules and the surface coating under "one-pot" conditions. In particular, square arrangements, spherical domains, and line-assemblies of the prepared Co(3)O(4) nanocubes and their inter-transformations have been attained for the first time by manipulating intersurfactant-interactions. Hydrolysis of Tween-85 and the resultant tiered surfactant superstructures have been investigated with FTIR/UV-vis/EA/TGA/DTA/XPS methods, and the capping species has been identified to be alkylated oleic carboxylate anions derived from Tween-85. Pronounced quantum confinement effects have been observed with the prepared Co(3)O(4) nanocubes, and the optical band gap energies determined are 3.95 and 2.13 eV, respectively, for O(2-)--> Co(2+) and O(2-)--> Co(3+) charge-transfer processes.     

Polyethylene imine derivatives ('synzymes') accelerate phosphate transfer in the absence of metal

The efficient integration of binding, catalysis, and multiple turnovers remains a challenge in building enzyme models. We report that systematic derivatization of polyethylene imine (PEI) with alkyl (C(2)-C(12)), benzyl, and guanidinium groups gives rise to catalysts ('synzymes') with rate accelerations (k(cat)/k(uncat)) of up to 10(4) for the intramolecular transesterification of 2-hydroxypropyl-p-nitrophenyl phosphate, HPNP, in the absence of metal. The synzymes exhibit saturation kinetics (K(M) approximately 250 microM, k(cat) approximately 0.5 min(-1)) and up to 2340 turnovers per polymer molecule. Catalysis can be specifically and competitively inhibited by anionic and hydrophobic small molecules. The efficacy of catalysis is determined by the PEI derivatization pattern. The derivatization reagents exert a synergistic effect, i.e., their combinations increase catalysis by more than the sum of each single modification. The pH-rate profile for k(cat)/K(M) is bell shaped with a maximum at pH 7.85 and can be explained as a combination of two effects that both have to be operative for optimal activity: K(M) increases at high pH due to deprotonation of PEI amines that bind the anionic substrate and kcat decreases as the availability of hydroxide decreases at low pH. Thus, catalysis is based on substrate binding by positively charged amine groups and the presence of hydroxide ion in active sites in an environment that is tuned for efficient catalysis. Inhibition studies suggest that the basis of catalysis and multiple turnovers is differential molecular recognition of the doubly negatively charged transition state (over singly charged ground state and product): this contributes a factor of at least 5-10-fold to catalysis and product release.     

Synthesis of imidazoles as novel emivirine and S‐DABO analogues

5‐Alkyl‐4‐benzyl‐1,3‐dihydroimidazol‐2‐ones ( 3a‐d ) and 5‐alkyl‐4‐benzyl‐1,3‐dihydroimidazole‐2‐thiones (7a‐d) were prepared via Dakin West reaction on DL‐phenylalanine with the appropriate aliphatic acid anhydrides followed by hydrolysis and reaction with potassium cyanate or potassium thiocyanate. Compounds 3a‐d were alkylated with ethoxymethyl chloride to give the alkylated imidazoles 5a‐d which were considered analogues of Emivirine with deletion of carbonyl group at the 4‐position. Alkylation of 7a‐d afforded the corresponding S‐alkylated derivatives 8a‐p which in a similar way were considered analogues of S‐DABO. However all the imidazole derivatives were devoid of activity against HIV.     

The Behaviour of Reduced, Alkylated and Native Proteins in a pH-Gradient LC System

Two dimensional (2D) liquid chromatography (LC) separations of proteins can be obtained faster and more automated than traditional 2D gel electrophoresis. Previously we have described a 2D LC method for separation of native proteins with separation according to pI by pH-gradient strong anion exchange (SAX) chromatography in the first dimension, and according to hydrophobicity by reversed phase chromatography in the second dimension. Since there are few literature reports on the combination of reduced/alkylated proteins and modern LC, a basic study of the chromatographic properties of a few reduced /alkylated proteins was undertaken with a pH-gradient SAX chromatographic system. Proteins where the disulfide groups were reduced, but not alkylated, were also included. The conditions that separated native proteins according to pI could not be used for neither reduced nor reduced/alkylated proteins. High concentrations of urea (4–8 M) were needed in the mobile phase in order to obtain good peak shapes. Addition of urea had an undesired impact on both the retention of the proteins and the pH gradient profile, with the effect that little correlation between reported pI values and elution pH was found. The conclusion was that proteins should be separated in the native state if good pI–pH correlations are important, and in the alkylated state with urea if other considerations are more important.     

Phosphorylation of polyethyleneimine in the solutions of calyx[4]resorcinolarene and its mixture with the surfactant

Phosphorylation of alkylated polyethyleneimine in chloroform in the presence of alkylated calyx[4]-resorcinolarenes with 2-hydroxyethoxy- and phosphorus-containing substituents and cetyl(3-hydroxypropyl)-dimethylammonium bromide was studied by means of the UV spectrophotometry. It was found that the character and the degree of the effect of calyxarene and its mixture with the surfactant depend on the hydrophobicity of macroring and the ratio of concentrations of components in the solution. The increase in the content of calyxarene and decrease in the concentration of polymer leads to the transformation of the catalytic action into the inhibiting one.     

Reaction of alkoxyuridines with ammonia

2-Alkoxy- and 4-alkoxyuridines were converted into isocytidine and cytidine by reaction with ammonia at room temperature. Reaction with hydrogen sulfide produced 2-thio- and 4-thiouridine but the reaction was incomplete. The reaction may be helpful in the identification of alkylated pyrimidine nucleosides in DNA.