Browsing by Subject "Molecular model"
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Item Open Access Antibacterial electrospun zein nanofibrous web encapsulating thymol/cyclodextrin-inclusion complex for food packaging(Elsevier, 2017-10) Aytac Z.; Ipek, S.; Durgun, Engin; Tekinay, T.; Uyar, TamerThymol (THY)/γ-Cyclodextrin(γ-CD) inclusion complex (IC) encapsulated electrospun zein nanofibrous webs (zein-THY/γ-CD-IC-NF) were fabricated as a food packaging material. The formation of THY/γ-CD-IC (1:1 and 2:1) was proved by experimental (X-ray diffraction (XRD), thermal gravimetric analysis (TGA), 1H NMR) and computational techniques. THY/γ-CD-IC (2:1) exhibited higher preservation rate and stability than THY/γ-CD-IC (1:1). It is worth mentioning that zein-THY/γ-CD-IC-NF (2:1) preserved much more THY as observed in TGA and stability of THY/γ-CD-IC (2:1) was higher, as shown by a modelling study. Therefore, much more THY was released from zein-THY/γ-CD-IC-NF (2:1) than zein-THY-NF and zein-THY/γ-CD-IC-NF (1:1). Similarly, antibacterial activity of zein-THY/γ-CD-IC-NF (2:1) was higher than zein-THY-NF and zein-THY/γ-CD-IC-NF (1:1). It was demonstrated that zein-THY/γ-CD-IC-NF (2:1) was most effective in inhibiting the growth of bacteria on meat samples. These webs show potential application as an antibacterial food packaging material.Item Open Access Determining the origin of synchronous multifocal bladder cancer by exome sequencing(BioMed Central Ltd., 2015) Acar, Ö.; Özkurt, E.; Demir, G.; Saraç, H.; Alkan C.; Esen, T.; Somel, M.; Lack, N. A.Background: Synchronous multifocal tumours are commonly observed in urothelial carcinomas of the bladder. The origin of these physically independent tumours has been proposed to occur by either intraluminal migration (clonal) or spontaneous transformation of multiple cells by carcinogens (field effect). It is unclear which model is correct, with several studies supporting both hypotheses. A potential cause of this uncertainty may be the small number of genetic mutations previously used to quantify the relationship between these tumours. Methods: To better understand the genetic lineage of these tumours we conducted exome sequencing of synchronous multifocal pTa urothelial bladder cancers at a high depth, using multiple samples from three patients. Results: Phylogenetic analysis of high confidence single nucleotide variants (SNV) demonstrated that the sequenced multifocal bladder cancers arose from a clonal origin in all three patients (bootstrap value 100 %). Interestingly, in two patients the most common type of tumour-associated SNVs were cytosine mutations of TpC*dinucleotides (Fisher's exact test p < 10-41), likely caused by APOBEC-mediated deamination. Incorporating these results into our clonal model, we found that TpC*type mutations occurred 2-5× more often among SNVs on the ancestral branches than in the more recent private branches (p < 10-4) suggesting that TpC*mutations largely occurred early in the development of the tumour. Conclusions: These results demonstrate that synchronous multifocal bladder cancers frequently arise from a clonal origin. Our data also suggests that APOBEC-mediated mutations occur early in the development of the tumour and may be a driver of tumourigenesis in non-muscle invasive urothelial bladder cancer.Item Open Access Molecular entrapment of volatile organic compounds (VOCs) by electrospun cyclodextrin nanofibers(Elsevier, 2016-02) Celebioglu A.; Sen, H. S.; Durgun, Engin; Uyar, TamerIn this paper, we reported the molecular entrapment performance of hydroxypropyl-beta-cyclodextrin (HPβCD) and hydroxypropyl-gamma-cyclodextrin (HPγCD) electrospun nanofibers (NF) for two common volatile organic compounds (VOCs); aniline and benzene. The encapsulation efficiency of CD samples were investigated depending on the various factors such as; CD form (NF and powder), electrospinning solvent (DMF and water), CD (HPβCD and HPγCD) and VOCs (aniline and benzene) types. BET analysis indicated that, electrospun CD NF have higher surface area compared to their powder form. In addition DMA measurement provided information about the mechanical properties of CD NF. The encapsulation capability of CD NF and CD powder was investigated by 1H-NMR and HPLC techniques. The observed results suggested that, CD NF can entrap higher amount of VOCs from surroundings compared to their powder forms. Besides, molecular entrapment efficiency of CD NF also depends on CD, solvent and VOCs types. The inclusion complexation between CD and VOCs was determined by using TGA technique, from the higher decomposition temperature of VOCs. Finally, our results were fortified by the modeling studies which indicated the complexation efficiency variations between CD and VOC types. Here, the inclusion complexation ability of CD molecules was combined with very high surface area and versatile features of CD NF. So these findings revealed that, electrospun CD NF can serve as useful filtering material for air filtration purposes due to their molecular entrapment capability of VOCs.Item Open Access Polymer-free nanofibers from vanillin/cyclodextrin inclusion complexes: high thermal stability, enhanced solubility and antioxidant property(Royal Society of Chemistry, 2016) Celebioglu A.; Kayaci-Senirmak, F.; Ipek, S.; Durgun, Engin; Uyar, TamerVanillin/cyclodextrin inclusion complex nanofibers (vanillin/CD-IC NFs) were successfully obtained from three modified CD types (HPβCD, HPγCD and MβCD) in three different solvent systems (water, DMF and DMAc) via an electrospinning technique without using a carrier polymeric matrix. Vanillin/CD-IC NFs with uniform and bead-free fiber morphology were successfully produced and their free-standing nanofibrous webs were obtained. The polymer-free CD/vanillin-IC-NFs allow us to accomplish a much higher vanillin loading (∼12%, w/w) when compared to electrospun polymeric nanofibers containing CD/vanillin-IC (∼5%, w/w). Vanillin has a volatile nature yet, after electrospinning, a significant amount of vanillin was preserved due to complex formation depending on the CD types. Maximum preservation of vanillin was observed for vanillin/MβCD-IC NFs which is up to ∼85% w/w, besides, a considerable amount of vanillin (∼75% w/w) was also preserved for vanillin/HPβCD-IC NFs and vanillin/HPγCD-IC NFs. Phase solubility studies suggested a 1:1 molar complexation tendency between guest vanillin and host CD molecules. Molecular modelling studies and experimental findings revealed that vanillin:CD complexation was strongest for MβCD when compared to HPβCD and HPγCD in vanillin/CD-IC NFs. For vanillin/CD-IC NFs, water solubility and the antioxidant property of vanillin was improved significantly owing to inclusion complexation. In brief, polymer-free vanillin/CD-IC NFs are capable of incorporating a much higher loading of vanillin and effectively preserve volatile vanillin. Hence, encapsulation of volatile active agents such as flavor, fragrance and essential oils in electrospun polymer-free CD-IC NFs may have potential for food related applications by integrating the particularly large surface area of NFs with the non-toxic nature of CD and inclusion complexation benefits, such as high temperature stability, improved water solubility and an enhanced antioxidant property, etc.Item Open Access Protein folding, misfolding and aggregation: the importance of two-electron stabilizing interactions(Public Library of Science, 2017) Cieplak, A. S.Proteins associated with neurodegenerative diseases are highly pleiomorphic and may adopt an all-α-helical fold in one environment, assemble into all-β-sheet or collapse into a coil in another, and rapidly polymerize in yet another one via divergent aggregation pathways that yield broad diversity of aggregates’ morphology. A thorough understanding of this behaviour may be necessary to develop a treatment for Alzheimer’s and related disorders. Unfortunately, our present comprehension of folding and misfolding is limited for want of a physicochemical theory of protein secondary and tertiary structure. Here we demonstrate that electronic configuration and hyperconjugation of the peptide amide bonds ought to be taken into account to advance such a theory. To capture the effect of polarization of peptide linkages on conformational and H-bonding propensity of the polypeptide backbone, we introduce a function of shielding tensors of the Cα atoms. Carrying no information about side chain-side chain interactions, this function nonetheless identifies basic features of the secondary and tertiary structure, establishes sequence correlates of the metamorphic and pH-driven equilibria, relates binding affinities and folding rate constants to secondary structure preferences, and manifests common patterns of backbone density distribution in amyloidogenic regions of Alzheimer’s amyloid β and tau, Parkinson’s α-synuclein and prions. Based on those findings, a split-intein like mechanism of molecular recognition is proposed to underlie dimerization of Aβ, tau, αS and PrPC, and divergent pathways for subsequent association of dimers are outlined; a related mechanism is proposed to underlie formation of PrPSc fibrils. The model does account for: (i) structural features of paranuclei, off-pathway oligomers, non-fibrillar aggregates and fibrils; (ii) effects of incubation conditions, point mutations, isoform lengths, small-molecule assembly modulators and chirality of solid-liquid interface on the rate and morphology of aggregation; (iii) fibril-surface catalysis of secondary nucleation; and (iv) self-propagation of infectious strains of mammalian prions. © 2017 Andrzej Stanisław Cieplak. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.