PubMed
Permanent URI for this collectionhttps://acikarsiv.thk.edu.tr/handle/123456789/2549
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Publication A comparison of peptide amphiphile nanofiber macromolecular assembly strategies(SPRINGER, 2019) Dana, Aykutlu; Tekinay, Ayse B.; Tekin, E. Deniz; Tekin, Emine Deniz; Stanford University; Turk Hava Kurumu University; Turkish Aeronautical Association.Supramolecular peptide nanofibers that are composed of peptide amphiphile molecules have been widely used for many purposes from biomedical applications to energy conversion. The self-assembly mechanisms of these peptide nanofibers also provide convenient models for understanding the self-assembly mechanisms of various biological supramolecular systems; however, the current theoretical models that explain these mechanisms do not sufficiently explain the experimental results. In this study, we present a new way of modeling these nanofibers that better fits with the experimental data. Molecular dynamics simulations were applied to create model fibers using two different layer models and two different tilt angles. Strikingly, the fibers which were modeled to be tilting the peptide amphiphile molecules and/or tilting the plane were found to be more stable and consistent with the experiments.Publication Alkaline Phosphatase-Mimicking Peptide Nanofibers for Osteogenic Differentiation(AMER CHEMICAL SOC, 2015) Gulseren, Gulcihan; Yasa, I. Ceren; Ustahuseyin, Oya; Tekin, E. Deniz; Tekinay, Ayse B.; Guler, Mustafa O.; Tekin, Emine Deniz; Ihsan Dogramaci Bilkent University; Turk Hava Kurumu University; Turkish Aeronautical AssociationRecognition of molecules and regulation of extracellular matrix synthesis are some of the functions of enzymes in addition to their catalytic activity. While a diverse array of enzyme-like materials have been developed, these efforts have largely been confined to the imitation of the chemical structure and catalytic activity of the enzymes, and it is unclear whether enzyme-mimetic molecules can also be used to replicate the matrix-regulatory roles ordinarily performed by natural enzymes. Self-assembled peptide nanofibers can provide multifunctional enzyme-mimetic properties, as the active sequences of the target enzymes can be directly incorporated into the peptides. Here, we report enhanced bone regeneration efficiency through peptide nanofibers carrying both catalytic and matrix-regulatory functions of alkaline phosphatase, a versatile enzyme that plays a critical role in bone formation by regulating phosphate homeostasis and calcifiable bone matrix formation. Histidine presenting peptide nanostructures were developed to function as phosphatases. These molecules are able to catalyze phosphate hydrolysis and serve as bone-like nodule inducing scaffolds. Alkaline phosphatase-like peptide nanofibers enabled osteogenesis for both osteoblast-like and mesenchymal cell lines.Publication Investigation of human β-defensins 1, 2 and 3 in human saliva by molecular dynamics(SPRINGER, 2022) Tekin, E. Deniz; Calisir, Metin; Tekin, Emine Deniz; Turkish Aeronautical Association; Turk Hava Kurumu University; Adiyaman UniversityHuman beta-defensins present in saliva have a broad spectrum of antimicrobial activities that work against infections in oral cavity. To provide a better understanding of these molecules' properties and functions at the molecular level, we have investigated and compared the important structural properties of human beta-defensin-1, -2 and -3 using molecular dynamics simulations. Our results have shown that human beta-defensin-3 has a more flexible structure in water than the other two because of its high hydrophilicity, low beta-sheet content and high repulsive forces between its charged residues. Moreover, we found that the location of the salt bridges is important in protein's stability in water.