Browsing by Subject "Biopolymers"
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Item 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.Item Open Access Nanoengineering hybrid supramolecular multilayered biomaterials using polysaccharides and self-assembling peptide amphiphiles(Wiley-VCH Verlag, 2017) Borges, J.; Sousa, M. P.; Cinar, G.; Caridade, S. G.; Güler, Mustafa O.; Mano, J. F.Developing complex supramolecular biomaterials through highly dynamic and reversible noncovalent interactions has attracted great attention from the scientific community aiming key biomedical and biotechnological applications, including tissue engineering, regenerative medicine, or drug delivery. In this study, the authors report the fabrication of hybrid supramolecular multilayered biomaterials, comprising high-molecular-weight biopolymers and oppositely charged low-molecular-weight peptide amphiphiles (PAs), through combination of self-assembly and electrostatically driven layer-by-layer (LbL) assembly approach. Alginate, an anionic polysaccharide, is used to trigger the self-assembling capability of positively charged PA and formation of 1D nanofiber networks. The LbL technology is further used to fabricate supramolecular multilayered biomaterials by repeating the alternate deposition of both molecules. The fabrication process is monitored by quartz crystal microbalance, revealing that both materials can be successfully combined to conceive stable supramolecular systems. The morphological properties of the systems are studied by advanced microscopy techniques, revealing the nanostructured dimensions and 1D nanofibrous network of the assembly formed by the two molecules. Enhanced C2C12 cell adhesion, proliferation, and differentiation are observed on nanostructures having PA as outermost layer. Such supramolecular biomaterials demonstrate to be innovative matrices for cell culture and hold great potential to be used in the near future as promising biomimetic supramolecular nanoplatforms for practical applications.Item Open Access An ontology for collaborative construction and analysis of cellular pathways(Oxford University Press, 2004-02-12) Demir, Emek; Babur, Özgün; Doğrusöz, Uğur; Gürsoy, Atilla; Ayaz, Aslı; Güleşır, Gürcan; Nişancı, Gürkan; Çetin Atalay, RengülMotivation: As the scientific curiosity in genome studies shifts toward identification of functions of the genomes in large scale, data produced about cellular processes at molecular level has been accumulating with an accelerating rate. In this regard, it is essential to be able to store, integrate, access and analyze this data effectively with the help of software tools. Clearly this requires a strong ontology that is intuitive, comprehensive and uncomplicated. Results: We define an ontology for an intuitive, comprehensive and uncomplicated representation of cellular events. The ontology presented here enables integration of fragmented or incomplete pathway information via collaboration, and supports manipulation of the stored data. In addition, it facilitates concurrent modifications to the data while maintaining its validity and consistency. Furthermore, novel structures for representation of multiple levels of abstraction for pathways and homologies is provided. Lastly, our ontology supports efficient querying of large amounts of data. We have also developed a software tool named pathway analysis tool for integration and knowledge acquisition (PATIKA) providing an integrated, multi-user environment for visualizing and manipulating network of cellular events. PATIKA implements the basics of our ontology. © Oxford University Press 2004; All rights reserved.Item Open Access Oxygen plasma modification of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) film surfaces for tissue engineering purposes(John Wiley & Sons, Inc., 2003) Hasirci, V.; Tezcaner, A.; Hasirci, N.; Süzer, Ş.Plasma glow-discharge application is known as a technique to coat or modify the surfaces of various materials. In this study, the influence of oxygen rf-plasma treatment on surface and bulk properties of a biological polyester, poly(3-hydroxybutyrate-co-3-hydroxyvalerate), were studied by determining water content and water contact angle, and by using X-ray photoelectron spectroscopy (XPS) and scanning electron microscopy (SEM). The plasma-treated films absorbed more water than the untreated film, and the absorbance increased with the total power applied. The water contact angles decreased and O/C atomic ratio increased on treatment, indicating that the material became more hydrophilic due to increases in the oxygen-containing functional groups on the surface of the polymer. A direct relation could be observed when the O/C ratio was plotted against the total power applied (treatment duration x treatment power). SEM revealed a visual record of surface modification, the extent of which increased with increased total power. It was thus possible to alter the surface chemistry and relevant properties of the polymer film using oxygen plasma as a tool.Item 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.Item Open Access Unifying the efforts of medicine, chemistry, and engineering in biosensing technologies to tackle the challenges of the COVID-19 pandemic(American Chemical Society, 2022-01-11) Erdem, Özgecan; Eş, İsmail; Saylan, Y.; İnci, Fatih