Browsing by Subject "Amino acids"

Now showing 1 - 12 of 12

Open Access
Analysis of free amino acid and total protein content in pollen of some allergenic taxa
(2009) Özler H.; Pehlivan, S.; Bayrak F.
This study reports the free amino acid content of pollen grains obtained from old and fresh samples belonging to Pinus nigra subsp. nigra var. caramanica (Loudon) Rehder (black pine) (Pinaceae), Juglans regia L. (walnut) (Juglandaceae), Fraxinus angustifolia Vahl. (ash) (Oleaceae) and Betula pendula L. (birch) (Betulaceae) obtained with the technique of Liquid Chromatography-Mass Spectrometry (LC/MS). Pollen samples were obtained from flowers of the above mentioned taxa in different years. Twenty one amino acids were identified. No histidine was found in F. angustifolia collected 8 years ago. Total protein content of P. nigra subsp. nigra var. caramanica pollens (25.75%) was higher than the remaining taxa; F. angustifolia (13.67%), B. pendula (7.73%) and J. regia (7.55%).© Asian Network for Scientific Information.
Open Access
Application of the Ugi reaction with multiple amino acid-derived components: Synthesis and conformational evaluation of piperazine-based minimalist peptidomimetics
(Royal Society of Chemistry, 2015) Stucchi, M.; Cairati, S.; Cetin-Atalay, R.; Christodoulou, M.S.; Grazioso G.; Pescitelli G.; Silvani, A.; Yildirim, D.C.; Lesma G.
The concurrent employment of α-amino acid-derived chiral components such as aldehydes and α-isocyanoacetates, in a sequential Ugi reaction/cyclization two-step strategy, opens the door to the synthesis of three structurally distinct piperazine-based scaffolds, characterized by the presence of l-Ala and/or l-Phe-derived side chains and bearing appropriate functionalities to be easily applied in peptide chemistry. By means of computational studies, these scaffolds have been demonstrated to act as minimalist peptidomimetics, able to mimic a well defined range of peptide secondary structures and therefore potentially useful for the synthesis of small-molecule PPI modulators. Preliminary biological evaluation of two different resistant hepatocellular carcinoma cellular lines, for which differentiation versus resistance ability seem to be strongly correlated with well defined types of PPIs, has revealed a promising antiproliferative activity for selected compounds. © The Royal Society of Chemistry 2015.
Open Access
Catalytic supramolecular self-assembled peptide nanostructures for ester hydrolysis
(Royal Society of Chemistry, 2016) Gulseren, G.; Khalily, M. A.; Tekinay, A. B.; Güler, Mustafa O.
Essential amino acids in catalytic sites of native enzymes are important in nature inspired catalyst designs. Active sites of enzymes contain the coordinated assembly of multiple amino acids, and catalytic action is generated by the dynamic interactions among multiple residues. However, catalysis studies are limited by the complex and dynamic structure of the enzyme; and it is difficult to exclusively attribute a given function to a specific residue. Minimalistic approaches involving artificial catalytic sites are promising for the investigation of the enzyme function in the absence of non-essential protein components, and self-assembling peptide nanostructures are especially advantageous in this context. Here we demonstrate the design and characterization of an enzyme-mimetic catalytic nanosystem presenting essential residues (Ser, His, Asp). The function of each residue and its combinations on the nanostructures in hydrolysis reaction was studied. The catalytic self-assembled nanostructures were used for efficient ester hydrolysis such as a model substrate (pNPA) and a natural substrate (acetylcholine) highlighting the key role of self-assembly in catalytic domain formation to test the efficiency of the de novo designed catalyst as a catalytic triad model.
Open Access
Chiral ceramic nanoparticles and peptide catalysis
(American Chemical Society, 2017) Jiang S.; Chekini, M.; Qu, Z.-B.; Wang Y.; Yeltik A.; Liu, Y.; Kotlyar, A.; Zhang, T.; Li, B.; Demir, Hilmi Volkan; Kotov, N. A.
The chirality of nanoparticles (NPs) and their assemblies has been investigated predominantly for noble metals and II-VI semiconductors. However, ceramic NPs represent the majority of nanoscale materials in nature. The robustness and other innate properties of ceramics offer technological opportunities in catalysis, biomedical sciences, and optics. Here we report the preparation of chiral ceramic NPs, as represented by tungsten oxide hydrate, WO3-x·H2O, dispersed in ethanol. The chirality of the metal oxide core, with an average size of ca. 1.6 nm, is imparted by proline (Pro) and aspartic acid (Asp) ligands via bio-to-nano chirality transfer. The amino acids are attached to the NP surface through C-O-W linkages formed from dissociated carboxyl groups and through amino groups weakly coordinated to the NP surface. Surprisingly, the dominant circular dichroism bands for NPs coated by Pro and Asp are different despite the similarity in the geometry of the NPs; they are positioned at 400-700 nm and 500-1100 nm for Pro- and Asp-modified NPs, respectively. The differences in the spectral positions of the main chiroptical band for the two types of NPs are associated with the molecular binding of the two amino acids to the NP surface; Asp has one additional C-O-W linkage compared to Pro, resulting in stronger distortion of the inorganic crystal lattice and greater intensity of CD bands associated with the chirality of the inorganic core. The chirality of WO3-x·H2O atomic structure is confirmed by atomistic molecular dynamics simulations. The proximity of the amino acids to the mineral surface is associated with the catalytic abilities of WO3-x·H2O NPs. We found that NPs facilitate formation of peptide bonds, leading to Asp-Asp and Asp-Pro dipeptides. The chiroptical activity, chemical reactivity, and biocompatibility of tungsten oxide create a unique combination of properties relevant to chiral optics, chemical technologies, and biomedicine.
Open Access
Controlled enzymatic stability and release characteristics of supramolecular chiral peptide amphiphile nanofiber gels
(Elsevier B.V., 2017) Zengin, A.; Cinar, G.; Güler, Mustafa O.
Supramolecular bioarchitectures formed by assembly of achiral or chiral building blocks play important roles in various biochemical processes. Stereochemistry of amino acids is important for structural organization of peptide and protein assemblies and structure-microenvironment interactions. In this study, oppositely charged peptide amphiphile (PA) molecules with L-, D- and mixture of L- and D-amino acid conformations are coassembled into supramolecular nanofibers and formed self-supporting gels at pH 7.4 in water. The enzymatic stability of the PA nanofiber gels was studied in the presence of proteinase K enzyme, which digest a broad spectrum of proteins and peptides. The structural changes on the chiral PA nanofibers were also analyzed at different time periods in the presence of enzymatic activity. Controlled release of a model cargo molecule through the chiral PA nanofiber gels was monitored. The diffusivity parameters were measured for all gel systems. Release characteristics and the enzymatic stability of the peptide nanofiber gels were modulated depending on organization of the chiral PA molecules within the supramolecular assemblies.
Open Access
Genetically encoded conductive protein nanofibers secreted by engineered cells
(Royal Society of Chemistry, 2017-06) Kalyoncu, E.; Ahan, R. E.; Olmez, T. T.; Safak Seker, U. O.
Bacterial biofilms are promising tools for functional applications as bionanomaterials. They are synthesized by well-defined machinery, readily form fiber networks covering large areas, and can be engineered for different functionalities. In this work, bacterial biofilms have been engineered for use as conductive biopolymers to interface with electrodes and connect bacterial populations to electronic gadgets. Bacterial biofilms are designed with different conductive peptide motifs, as the aromatic amino acid content of fused peptide motifs has been suggested to contribute to electronic conductivity by influencing monomer stacking behavior. To select the best candidates for constructing conductive peptide motifs, conductivity properties of aromatic amino acids are measured using two different fiber scaffolds, an amyloid-like fiber (ALF) forming peptide, and the amyloidogenic R5T peptide of CsgA protein. Three repeats of aromatic amino acids are added to fiber-forming peptide sequences to produce delocalized π clouds similar to those observed in conductive polymers. Based on the measurements, tyrosine and tryptophan residues provide the highest conductivity. Therefore, the non-conductive E. coli biofilm is switched into a conductive form by genetically inserted conductive peptide motifs containing different combinations of tyrosine and tryptophan. Finally, synthetic biofilm biogenesis is achieved with conductive peptide motifs using controlled biofilm production. Conductive biofilms on living cells are formed for bioelectronics and biosensing applications.
Open Access
Hierarchical self-assembly of histidine-functionalized peptide amphiphiles into supramolecular chiral nanostructures
(American Chemical Society, 2017) Koc, M. H.; Ciftci, G. C.; Baday, S.; Castelletto, V.; Hamley, I. W.; Güler, Mustafa O.
Controlling the hierarchical organization of self-assembling peptide amphiphiles into supramolecular nanostructures opens up the possibility of developing biocompatible functional supramolecular materials for various applications. In this study, we show that the hierarchical self-assembly of histidine- (His-) functionalized PAs containing d- or l-amino acids can be controlled by both solution pH and molecular chirality of the building blocks. An increase in solution pH resulted in the structural transition of the His-functionalized chiral PA assemblies from nanosheets to completely closed nanotubes through an enhanced hydrogen-bonding capacity and π-π stacking of imidazole ring. The effects of the stereochemistry and amino acid sequence of the PA backbone on the supramolecular organization were also analyzed by CD, TEM, SAXS, and molecular dynamics simulations. In addition, an investigation of chiral mixtures revealed the differences between the hydrogen-bonding capacities and noncovalent interactions of PAs with d- and l-amino acids.
Open Access
A novel model-based method for feature extraction from protein sequences for classification
(IEEE, 2006) Saraç, Ö. S.; Atalay, V.; Çetin-Atalay, Rengül
Representation of amino-acid sequences constitutes the key point in classification of proteins into functional or structural classes. The representation should contain the biologically meaningful information hidden in the primary sequence of the protein. Conserved or similar subsequences are strong indicators of functional and structural similarity. In this study we present a feature mapping that takes into account the models of the subsequences of protein sequences. An expectation-maximization algorithm along with an HMM mixture model is used to cluster and learn the models of subsequences of a given set of proteins.
Open Access
Prediction of protein subcellular localization based on primary sequence data
(IEEE, 2004) Özarar, M.; Atalay, V.; Çetin-Atalay, Rengül
Subcellular localization is crucial for determining the functions of proteins. A system called prediction of protein subcellular localization (P2SL) that predicts the subcellular localization of proteins in eukaryotic organisms based on the amino acid content of primary sequences using amino acid order is designed. The approach for prediction is to find the most frequent motifs for each protein in a given class based on clustering via self organizing maps and then to use these most frequent motifs as features for classification by the help of multi layer perceptrons. This approach allows a classification independent of the length of the sequence. In addition to these, the use of a new encoding scheme is described for the amino acids that conserves biological function based on point of accepted mutations (PAM) substitution matrix. The statistical test results of the system is presented on a four class problem. P2SL achieves slightly higher prediction accuracy than the similar studies.
Open Access
Profiling turkish honeys to determine authenticity using physical and chemical characteristics
(2009) Senyuva H.Z.; Gilbert J.; Silici, S.; Charlton, A.; Dal, C.; Gürel, N.; Cimen, D.
Seventy authentic honey samples of 9 different floral types (rhododendron, chestnut, honeydew, Anzer (thymus spp.), eucalyptus, gossypium, citrus, sunflower, and multifloral) from 15 different geographical regions of Turkey were analyzed for their chemical composition and for indicators of botanical and geographical origin. The profiles of free amino acids, oligosaccharides, and volatile components together with water activity were determined to characterize chemical composition. The microscopic analysis of honey sediment (mellissopalynology) was carried out to identify and count the pollen to provide qualitative indicators to confirm botanical origin. Statistical analysis was undertaken using a bespoke toolbox for Matlab called Metabolab. Discriminant analysis was undertaken using partial least-squares (PLS) regression followed by linear discriminant analysis (LDA). Four data models were constructed and validated. Model 1 used 51 variables to predict the floral origin of the honey samples. This model was also used to identify the top 5 variable important of projection (VIP) scores, selecting those variables that most significantly affected the PLS-LDA calculation. These data related to the phthalic acid, 2-methylheptanoic acid, raffinose, maltose, and sucrose. Data from these compounds were remodeled using PLS-LDA. Model 2 used only the volatiles data, model 3 the sugars data, and model 4 the amino acids data. The combined data set allowed the floral origin of Turkish honey to be accurately predicted and thus provides a useful tool for authentication purposes. However, using variable selection techniques a smaller subset of analytes have been identified that have the capability of classifying Turkish honey according to floral type with a similar level of accuracy. © 2009 American Chemical Society.
Open Access
Protein folding rates correlate with heterogeneity of folding mechanism
(American Physical Society, 2004) Öztop, B.; Ejtehadi, M. R.; Plotkin, S. S.
The folding rates of protein were shown to correlate with the degree of heterogeneity in the formation of native contacts. It was shown that both experimental rates and simulated free energy barriers for 2-state proteins depend on the degree of heterogeneity present in the folding process. Heterogeneity due to variance in the distribution of native loop lengths, and variance in the distribution of φ values, were observed to increase folding rates and reduce folding barriers. The observed effect due to φ variance was found to be the most statistically significant, because φ variance captures both heterogeneity arising from native topology and that arising from energetics.
Open Access
Single-site mutation and secondary structure stability: an isodesmic reaction approach. The case of unnatural amino acid mutagenesis Ala→Lac
(American Chemical Society, 2004) Cieplak, A. S.; Sürmeli, N. B.
A method is described to evaluate backbone interactions in proteins via computational unnatural amino acid mutagenesis. Several N-acetyl polyalanyl amides (AcA nNH 2) were optimized in the representative helical (3 10-, 4 13-, and a "hybrid" κ-helix, n = 7, 9, 10, 14) and hairpin (two- and three-stranded antiparallel β-sheets with type I turns βααε, n =6, 9, 10) conformations, and extended conformers of N-acetyl polyalanyl methylamides (n = 2, 3) were used to derive multistranded β-sheet fragments. Subsequently, each residue of every model structure was substituted, one at a time, with L-lactic acid. The resulting mutant structures were again optimized, and group-transfer energies ΔE GT were obtained as heats of the isodesmic reactions: AcA nNHR + AcOMe → AcA xLacA yNHR + AcNHMe (R = H, C H 3). These group-transfer energies correlate with the degree of charge polarization of the substituted peptide linkages as measured by the difference Δe in H and O Mulliken populations in HN-C=O and with the H-bond distances in the "wild-type" structures. A good correlation obtains for the HF/3-21G and B3LYP/6-31G* group-transfer energies. The destabilization effects are interpreted in terms of loss of interstrand and intrastrand H-bonds, decrease in Lewis basicity of the C-O group, and O⋯O repulsion. On the basis of several comparisons of Ala → Lac ΔE GT's with heats of the NH → CH 2 substitutions, the latter contribution is estimated (B3LYP/6-31G*) to range between 1.5 and 2.4 kcal mol -1, a figure close to the recent experimental ΔδG° value of 2.6 kcal mol -1 (McComas, C. C.; Crowley, B. M.; Boger, D. L. J. Am. Chem. Soc. 2003, 125, 9314). The partitioning yields the following maximum values of the electronic association energy of H-bonds in the examined sample of model structures (B3LYP/6-31G* estimates): 3 10-helix D e = -1.7 kcal mol -1, α-helix D e = -3.8 kcal mol -1 β-sheet D e = -6.1 kcal mol -1. The premise of experimental evaluations of the backbone-backbone H-bonding that Ala → Lac substitution in proteins is isosteric (e.g., Koh, J. T.; Cornish, V. W.; Schultz, P. G. Biochemistry 1997, 36, 11314) is often but not always corroborated. Examination of the integrity of H-bonding pattern and ψ i, ψ i distribution identified several mutants with significant distortions of the "wild-type" structure resulting inter alia from the transitions between i, i + 3 and i, i + 4 H-bonding in helices, observed previously in the crystallographic studies of depsipeptides, (Ohyama, T.; Oku, H.; Hiroki, A.; Maekawa, Y.; Yoshida, M.; Katakai, R. Biopolymers 2000, 54, 875; Karle, I. L.; Das, C.; Balaram, P. Biopolymers 2001, 59, 276). Thus, the isodesmic reaction approach provides a simple way to gauge how conformation of the polypeptide chain and dimensions of the H-bonding network affect the strength of backbone-backbone C=O⋯HN bonds. The results indicate that the stabilization provided by such interactions increases on going from 3 10-helix to α-helix to β-sheet.