Polar Amino Research Articles

Study of the retention and selectivity of cholesterol bonded phases with different linkage spacers

The chromatographic properties of four cholesterol bonded phases with different structures were studied. The columns used were packed with a stationary phase containing a cholesterol molecule attached to the silica surface using different types of linkage molecules. As a basic characteristic of the bonded phases the hydrophobicity and silanol activity (polarity) were investigated. The presence of the polar amino and carboxyl groups in the structure of the bonded ligand strongly influences the polarity of the bonded phase. Columns were compared according to methylene selectivity using a series of benzene homologues and according to their shape and size selectivity using polycyclic aromatic hydrocarbons (PAHs). The measurements were done using MeOH–water and ACN–water mobile phases. The presented results show that the coverage density of the bonded ligands and length of the linkage strongly influence the retention and selectivity of cholesterol bonded phases.

Gene cloning and enzyme structure modeling of the Aspergillus oryzae N74 fructosyltransferase

The fructooligosaccharides (FOS) represent an important source of prebiotic compounds that are widely used as an ingredient in functional foods. Recently, the strain Aspergillus oryzae N74 was reported as a potential microorganism for the industrial production of FOS, due to its high yields of FOS production. In this work, we used a PCR-cloning strategy to clone the A. oryzae N74 ftase gene as a previous step for recombinant enzyme production. Ftase showed a 1630 bp size with a 99% similarity with other A. oryzae strains and between 1 to 68% identities with other Aspergillus strains. This gene encodes for a 525 amino acids protein with 99% similarity with other A. oryzae strains and between 11 to 69% similarities with other Aspergillus strains. Finally, an A. oryzae N74 FTase tertiary structure model was predicted base on its similarity with other glycoside hydrolase 32 family members. The active site was located inside the β-propeller domain and was formed for non-charged polar and charged amino acids. In summary, these results shows the high level of sequence conservation between A. oryzae strains and represent a first step towards the development of a FOS production industrial process using recombinant microorganism carrying the ftase gene from A. oryzae N74.

A new polymorph of benzene-1,2-diamine: isomorphism with 2-aminophenol and two-dimensional isostructurality of polymorphs

A new crystalline form of benzene-1,2-diamine, C(6)H(8)N(2), crystallizing in the space group Pbca, has been identified during screening for cocrystals. The crystals are constructed from molecular bilayers parallel to (001) that have the polar amino groups directed to the inside and the aromatic groups, showing a herringbone arrangement, directed to the outside. The known monoclinic form and the new orthorhombic polymorph exhibit two-dimensional isostructurality as the crystals consist of nearly identical bilayers. In the monoclinic form, neighbouring bilayers are generated by a unit translation along the a axis, whereas in the orthorhombic form they are generated by a c-glide. Moreover, the new form of benzene-1,2-diamine is essentially isomorphous with the only known form of 2-aminophenol.

Catalytic Asymmetric Three-Component Mannich-Type Reaction of Alkenyl Trichloroacetates

A catalytic enantioselective three-component Mannich-type reaction of alkenyl trichloroacetates, ethyl glyoxalate, and aniline derivatives was achieved using an (S)-BINOL-derived chiral tin dibromide possessing a 4-trifluoromethylphenyl group at the 3- and 3'-positions as the chiral precatalyst in the presence of sodium ethoxide, sodium iodide, and ethanol. Optically active beta-amino ketones with up to 98% ee were syn-selectively obtained in high yields even from imines possessing a polar amino group under the influence of the in situ generated chiral tin bromide ethoxide.

Preparation, Characterization, and Thermal Gelation of Amphiphilic Alkyl-poly(ethyleneimine)

Amphiphilic alkyl-poly(ethyleneimine)s (alkyl-PEI) with different degrees of polymerization have been produced by alkaline hydrolysis of alkyl-poly(2-methyl-2-oxazoline). Potentiometric titration of the alkyl-PEI shows the influence of the alkyl chain and the degree of polymerization on the titration curves and hence on the polymer conformation. Karl Fischer titration has been used to determine the water content in the polymers. Subsequent X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), and differential scanning calorimetry (DSC) measurements prove the existence of different hydration states of the PEI even under dry storage conditions. Upon cooling from hot aqueous solutions, hydrogels form. The gelation concentration decreases with increasing degree of polymerization of the PEI segment. Scanning electron microscopy (SEM and cryo-SEM) of the hydrogels reveal an alkyl-PEI fibrous network composed of fan-like units. DSC shows that the percentages of bound and free water in the hydrogels depend on the concentration of polar amino groups.

Study of Amino Functional Polysiloxane Film on Regenerated Cellulose Substrates by Atomic Force Microscopy and X-ray Photoelectron Microscopy

Film morphology, surface compositions and hydrophobic properties of N-β-aminoethyl-γ-aminopropyl polysiloxane (ASO-1) coated on regenerated cellulose (cel) substrate surface (ASO-1/cel) were investigated and studied by atomic force microscopy, X-ray photoelectron spectroscopy and other techniques. Influenced by the irregularities of cel substrate, ASO-1/cel showed a very similar microscopic morphology to the cel. In addition, the ASO-1/cel surface was hydrophobic. There were strongly hydrogen-bonded linkages at the interface between ASO-1 and cel. All the data indicate that ASO-1 molecules interact with the regenerated cellulose in such a way that the hydrophobic silicon methyl (Si-CH3) groups are oriented towards the air, while the Si—O dipole bonds as well as the polar amino groups are aligned towards the interface of the cellulose substrate.

Structure and morphology of aminopropyltriethoxysilane-modified TiO2 nano-particles derived from sol-gel processing of tetraethylorthotitanate

Amino-modified TiO2 particles were derived from precursor mixtures of tetraethylorthotitanate and aminopropyltriethoxysilane (APTES) that both were dissolved in ethanol/water solution. Size, morphology, crystalline structures, and formation mechanism of the particles were discussed in terms of the APTES amount and the pH value in the solution. The addition of APTES resulted in amorphous amino-modified TiO2 particles. The low crystallinity in the final particles was attributed to the polar amino groups.

On the codon-dependent specificity of amino acids in the junctions of biochemical and neurochemical investigations

1 Universal systematization was used for the creation of a periodical system of biological molecules. It elucidated a series of fundamental patterns in the structure and function of biological organization, particularly the existence of the 21st and 22nd genetically coded amino acids. For the first time four complementary complete molecular compositions of the genetically coded 22nd amino acid were derived (figure). The 27 codon-dependent positions of coupled interactions of polar–nonpolar amino acids (p–np) reveal the essence of the molecular mechanism of biological recognition in enzyme– substrate complexes, the matrix of ribosomal protein synthesis, and virus–cell interactions. The arrows show the reading directions of complementary codons.

A step further in the SATE mononucleotide prodrug approach

Synthesis, in vitro anti-HIV activity, stability studies as well as potential for oral absorption of some novel phenyl S-acyl-2-thioethyl (SATE) phosphotriester derivatives of AZT (zidovudine; 3'-azido-2',3'- dideoxythymidine) are reported herein. These mononucleotide prodrugs (pronucleotides) are characterized by the presence of polar (amino or hydroxyl) functions on the SATE biolabile phosphate protections. Whereas pronucleotides incorporating an amino residue in the vicinity of the thioester functionality display low chemical stability, the introduction of one or two hydroxyl groups on the SATE moiety confers high resistance of the resulting prodrugs towards esterase hydrolysis. Thus, one of these pronucleotides, derivative 2, was able to cross a Caco-2 cell monolayer mainly in intact form, probing that its further development is warranted as a possible HIV-pronucleotide candidate.

화학 개질된 실크세리신 필름의 특성

Polar amino groups of the waste SS(silk-sericin) were modified by two isocyanate compounds of MOI(2-(methacryloyloxy)ethyl isocyanate) and AOI (2-(acryloyloxy)ethyl isocyanate). When the MOISS (MOI-modified silk sericin) or AOISS(AOI-modified silk sericin) was pressed hot, vinyl groups in the MOI or AOI were polymerized and then the flexible and transparent films were obtained. Tensile moduli and strengths of the MOISS films were significantly improved as the MOI contents increased. By the addition of the isocyanate compounds, silk sericin films exhibited lower solubility to the distilled water(80℃ ) and also lower swell ratio to the distilled water(room temperature). In the effect of tensile properties and restraining the water swelling, MOI was better than AOI. BOD(biochemical oxygen demand)/TOD(theoretical oxygen demand) of the pure sericin film was almost 100% perfect level after 10 days immersion into the activated sludge. With increasing isocyanate content reacted with polar amino groups, BOD/TOD decreased. When more than 50 mol% of polar amino groups remained unreacted, sericin films could retain more biodegradability. Comparing with MOI from the viewpoint of biodegradability, AOI was more effective.

CvP-bias as an Index to Predict the Life Style of Last Common Ancestor

CvP-bias (difference between proportions of charged and polar non-charged amino acids) has been recognized as an efficient criterion to distinguish hyperthermophiles from mesothermophiles. By analyzing the CvP-biases of seven barophiles's proteomes, we reveal that this criterion still works for barophiles. As a result, CvP-bias criterion is applicable to disclosing some secrets in the lifestyles of the last common ancestor (LCA), no matter the LCA lived in deep sea or not, which is helpful to building a self-consistent model for the LCA.

Prediction of Peptide Retention in RP-LC

The retention of small peptides can be predicted by summing the hydrophobic contribution to retention of each amino acid of peptides. But the retention time of peptides larger than 10–15 residues are less than that predicted by summing the retention coefficients of each constitutive residue. A new prediction model, considering the effects of the peptide length and contact area of each amino acid with the stationary phase for larger peptides was proposed. The model was validated by 136 peptides identified by nano-flow 2-D-LC-ESI-MS-MS platform and other retention data observed from literature. The high degree of correlation between the observed and predicted retention time by using the new model is not only good evidence for the accuracy of our predictive method, but supports the supposition that the peptide length and contact area of each amino acid with stationary phase are important factors affecting peptide retention time for larger peptide. In addition it is found that the range of peptide length is wider, the accuracy of prediction is better. The ratio coefficient of surface area of non-polar, polar and charged amino residues contacting with the stationary phase were all calculated to be less than one.

Biocompatible Polysaccharide‐Based Electrorheological Suspensions

In the polysaccharide family and its modified forms, chitosan, cellulose phosphate, and potato starch phosphate have been adopted as anhydrous electrorheological (ER) fluids to improve the shortcomings of the corresponding pristine hydrous polysaccharides of cellulose and potato starch, including temperature limitation and density difference between dispersed particles and the oil medium. The biocompatible polysaccharides with polar organic modifications containing electronic donor groups show polarizability due to the branched polar amino and hydroxyl groups. These polysaccharide‐based systems in silicone oil were observed to demonstrate Bingham flow response under imposed electric fields. The ER properties were also characterized via dielectric relaxation mismatch as well as static yield stress.

Complexation behavior of cucurbit[6]uril with short polypeptides

The binding properties of cucurbit[6]uril towards various peptides have been investigated in acidic aqueous solution. Stability constants and thermodynamic values of the complex formation between following peptides: glycyl- l-alanine, l-leucyl- l-valine, glycyl- l-asparagine, l-leucyl- l-phenylalanine, l-leucyl- l-tryptophan, glycyl- l-histidine, l-glutathione reduced (γ- l-glutamyl- l-cysteinyl-glycine, GSH), and dl-leucyl-glycyl- dl-phenylalanine) with cucurbit[6]uril in aqueous formic acid (50%, v/v) have been calculated from calorimetric titrations. From these results it can be seen that the peptides form exclusion complexes with cucurbit[6]uril. Due to the polar peptide bond they are not included within the hydrophobic cavity of cucurbit[6]uril. The complex formation is favoured by entropic contributions. The release of water molecules from the polar amino groups of the peptides and the carbonyl groups of cucurbituril are responsible.

A novel substrate for in situ synthesis of oligonucleotide: plasma-treated polypropylene microporous membrane

Polypropylene microporous membrane was treated with plasma in a mixture of nitrogen and hydrogen (1:2 in volume). Attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR), X-ray photoelectron spectroscopy (XPS) and ultra-violet (UV) spectra demonstrated the success of amino functional groups grafting. The density of polar amino groups on the membrane surface is approximately 0.5 μmol/cm 2, which is much higher than that of amino functional groups on modified glass slides. The as-treated membranes were successively applied to the in situ synthesis of oligonucleotides and an average coupling yield of more than 98% was achieved. These modified microporous membranes open novel prospects for the in situ synthesis of DNA microarrays.

High Resolution Crystal Structures of Piscine Transthyretin Reveal Different Binding Modes for Triiodothyronine and Thyroxine

Transthyretin (TTR) is an extracellular transport protein involved in the distribution of thyroid hormones and vitamin A. So far, TTR has only been found in vertebrates, of which piscine TTR displays the lowest sequence identity with human TTR (47%). Human and piscine TTR bind both thyroid hormones 3,5,3'-triiodo-l-thyronine (T(3)) and 3,5,3',5'-tetraiodo-l-thyronine (thyroxine, T(4)). Human TTR has higher affinity for T(4) than T(3), whereas the reverse holds for piscine TTR. X-ray structures of Sparus aurata (sea bream) TTR have been determined as the apo-protein at 1.75 A resolution and bound to ligands T(3) and T(4), both at 1.9 A resolution. The apo structure is similar to human TTR with structural changes only at beta-strand D. This strand forms an extended loop conformation similar to the one in chicken TTR. The piscine TTR.T(4) complex shows the T(4)-binding site to be similar but not identical to human TTR, whereas the TTR.T(3) complex shows the I3' halogen situated at the site normally occupied by the hydroxyl group of T(4). The significantly wider entrance of the hormone-binding channel in sea bream TTR, in combination with its narrower cavity, provides a structural explanation for the different binding affinities of human and piscine TTR to T(3) and T(4).

936. Phage-Selected Motifs Internalize Via Multiple Endocytic Pathways and Facilitate Gene Delivery

Top of pageAbstract The ability to direct internalization of macromolecules into cells or across endothelial barriers efficiently has tremendous therapeutic implications. Several internalization motifs (IM) that exist in nature have been defined and exploited, including the third -helix of the Drosophila Antennapedia homeodomain and the HIV TAT protein. To investigate the general properties required for protein-based macromolecule internalization we constructed and performed peptide phage display (PPD) with T7 bacteriophage random 7-mer peptide libraries. Functional biopanning with the T7 libraries was performed on microvascular endothelial cells (EC) to select peptide motifs that could internalize phage. The titer of internalized phage increased through sequential rounds of biopanning and resulted in selection of phage expressing IM with a finite shared sequence relationship between charged, polar, and hydrophobic amino acids. Selected IM were synthesized as rhodamine-labeled free peptides and their internalization properties were investigated in EC. Internalization of IM was inhibited at 4 degrees, suggesting an energy dependent mechanism of internalization. Confocal data showed that the IM was internalized via at least two different endocytic pathways: clathrin-coated pits and lipid rafts. Treatment with inhibitors of clathrin-mediated and lipid raft endocytosis inhibited uptake of IM, consistent with the result from confocal study. Further, in vitro and in vivo studies indicated that precomplexing of adenovirus with the IM facilitated the degree of viral transduction into endothelial cells and across endothelial barriers. These data suggest that relatively short peptide motifs are capable of directing macromolecules to diverse internalization pathways. It may be possible to exploit these characteristics for targeted delivery of therapeutic macromolecules to cells and tissues, and potentially to develop more efficient methods of gene transfer.

Is use of the hydrophobic moment a sound basis for predicting the structure-function relationships of membrane interactive alpha-helices?

Amphiphilic alpha-helices play a fundamental role in protein membrane association and show a segregation of polar and apolar amino acid residues. Based on correlations between amphiphilic properties and biological function, a number of theoretical approaches have been developed, which quantify alpha-helix amphiphilicity and then attempt to assign function. The most commonly used measure of amphiphilicity is the hydrophobic moment, < microH >, which, when used in conjunction with an alpha-helix's mean hydrophobicity, < H >, has been used to classify membrane interactive amphiphilic alpha-helices as either surface active or transmembrane. Here, the predictive efficacy of plot methodology is reviewed by examining published data, which compare the function of known membrane interactive amphiphilic alpha-helices to that assigned by this methodology. The results of this review are discussed in relation to the reliability of < microH > as a quantifier of alpha-helical amphiphilicity, and the ability of < microH > and < H > to describe alpha-helical structure / function relationships. It is concluded that hydrophobic moment plot methodology is not a generally reliable predictor of alpha-helical structure / function relationships. It appears that the inefficacy of plot methodology is primarily due to the inability of the plot diagram to accommodate the heterogeneity of the alpha-helical classes it attempts to define. However, the predictive efficacy of the methodology appears to be improved if other alpha-helical parameters are also considered when assigning alpha-helical function. It is suggested that the conventional methodology should be seen only as an indicator for the assignation of structure / function relationships, providing a guide to future experimental investigations.

Alteration in Catalytic Properties of Human CYP2D6 Caused by Substitution of Glycine-42 with Arginine, Lysine and Glutamic Acid

The effects of the substitution of glycine at position 42 with various other amino acid residues on the functions of CYP2D6 were studied using debrisoquine (DB) and bunitrolol (BTL) 4-hydroxylations as indices of drug-metabolizing enzymes. The substitution with hydrophobic amino acid residues such as valine and phenylalanine did not affect the enzymatic properties such as reduced CO-difference spectra, microsomal CYP contents and oxidation activities towards DB and BTL. The substitution of glycine-42 with a polar but noncharged amino acid residue (serine) exhibited a similar reduced CO-different spectrum, but the substitution with a charged basic (lysine and arginine) or acidic (glutamic acid) amino acid residue commonly produced a peak at 420 nm in addition to a Soret peak at 450 nm. Cytochrome P450 contents and microsomal contents of G42S, G42K, G42R and G42E estimated spectrophotometrically and estimated by Western blot analysis, respectively, were lower than those of the wild-type. Kinetic analysis revealed that the substitution of glycine-42 with charged amino acid residues such as lysine, arginine and glutamic acid markedly increased the apparent K(m) values for DB and BTL oxidations without remarkable changes in the V(max) values. The subsitution with noncharged amino acid residues such as serine, valine and phenylalanine did not cause such a marked change in the K(m) values. Efficiencies (V(max)/K(m)) as DB and BTL 4-hydroxylases of CYP2D6 mutant proteins having charged amino acid residues were found to be decreased mainly by increasing their K(m) values. These results indicate that the properties of amino acid residues at position 42 affect the behavior of CYP2D6 proteins such as anchoring into ER membranes, conversion of P450 to P420 and incorporation of heme into apoproteins.

Spectral study and global analysis of fluorescence decays of the inclusion complexes of 2-amino-4,6-dimethyl pyrimidine with α- and γ-cyclodextrins

The steady state and time-resolved fluorescence study of 2-amino-4,6-dimethyl pyrimidine (ADMP) have been studied in aqueous solution of α- and γ-cyclodextrins (CDs). In the presence of CDs, the fluorescence spectra of ADMP point out an enhancement of the emission without significant shift. The experimental data show the presence of only one kind of complex for ADMP in α- and γ-CDs. Although, ADMP partially included within the interior CD cavities, it encapsulated inside the γ-CD cavity more deeply, compared with the α-CD. The results also revealed that the polar amino group along with the endocyclic nitrogen remains located near the aqueous environment.