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Publication Characterizations of self-assembly of peptides and self-assembled peptide nanonetworks(AMER CHEMICAL SOC, 2014) Cinar, Goksu; Tekin, Emine Deniz; Guler, Mustafa Ozgur; Tekin, Emine Deniz; Ihsan Dogramaci Bilkent University; Turk Hava Kurumu University; Turkish Aeronautical AssociationPublication Odd-even effect in the potential energy of the self-assembled peptide amphiphiles(ELSEVIER, 2014) Tekin, E. Deniz; Tekin, Emine Deniz; Turkish Aeronautical Association; Turk Hava Kurumu UniversityWe report on an example of odd even effect in self-assembled peptide amphiphiles (PAs) forming a cylindrical nanofiber. Minimum energy of the nanofiber depends on whether there are odd or even number of layers and whether each layer has odd or even number of PAs. More specifically, minimum energy for a nanofiber built of odd number of layers is achieved if each layer has even number of PAs uniformly, and radially aligned with alkyl chains in the center. On the other hand if the number of layers is even, energy is minimized if each layer has an odd number of PAs. (C) 2014 Elsevier B.V. All rights reserved.Publication Molecular dynamics simulations of self-assembled peptide amphiphile based cylindrical nanofibers(ROYAL SOC CHEMISTRY, 2015) Tekin, E. Deniz; Tekin, Emine Deniz; Turk Hava Kurumu University; Turkish Aeronautical AssociationWe carried out united-atom molecular dynamics simulations to understand the structural properties of peptide amphiphile (PA)-based cylindrical nanofibers and the factors that play a role in the Self-Assembly process on some specific nanofibers. In our simulations, we start from various cylindrical nanofiber structures with a different number of layers and a different number of PAs in each layer, based on previous experimental and theoretical results. We find that the 19-layered nanofiber, with 12 PAs at each layer, distributed radially and uniformly with alkyl chains in the center, is the most stable configuration with a diameter of 8.4 nm which is consistent with experimental results. The most dominant secondary structures formed in the fibers are random coils and beta-sheets, respectively. We also find that hydrophobic interactions between the VVAG-VVAG moiety of the PA molecules and electrostatic interactions between D-Na+ and between E-R are responsible for the fiber's self-assembly properties. During the aggregation process, first dimers, then trimers are formed.Publication Force and time-dependent self-assembly, disruption and recovery of supramolecular peptide amphiphile nanofibers(IOP PUBLISHING LTD, 2018) Dikecoglu, F. Begum; Topal, Ahmet E.; Ozkan, Alper D.; Tekin, E. Deniz; Tekinay, Ayse B.; Guler, Mustafa O.; Dana, Aykutlu; Tekin, Emine Deniz; Ihsan Dogramaci Bilkent University; Ihsan Dogramaci Bilkent University; Johannes Kepler University Linz; Turkish Aeronautical Association; Turk Hava Kurumu University; University of Chicago; Stanford UniversityBiological feedback mechanisms exert precise control over the initiation and termination of molecular self-assembly in response to environmental stimuli, while minimizing the formation and propagation of defects through self-repair processes. Peptide amphiphile (PA) molecules can self-assemble at physiological conditions to form supramolecular nanostructures that structurally and functionally resemble the nanofibrous proteins of the extracellular matrix, and their ability to reconfigure themselves in response to external stimuli is crucial for the design of intelligent biomaterials systems. Here, we investigated real-time self-assembly, deformation, and recovery of PA nanofibers in aqueous solution by using a force-stabilizing double-pass scanning atomic force microscopy imaging method to disrupt the self-assembled peptide nanofibers in a force-dependent manner. We demonstrate that nanofiber damage occurs at tip-sample interaction forces exceeding 1 nN, and the damaged fibers subsequently recover when the tip pressure is reduced. Nanofiber ends occasionally fail to reconnect following breakage and continue to grow as two individual nanofibers. Energy minimization calculations of nanofibers with increasing cross-sectional ellipticity (corresponding to varying levels of tip-induced fiber deformation) support our observations, with high-ellipticity nanofibers exhibiting lower stability compared to their non-deformed counterparts. Consequently, tip-mediated mechanical forces can provide an effective means of altering nanofiber integrity and visualizing the self-recovery of PA assemblies.Publication Molecular dynamics simulations of self-assembled peptide amphiphiles(AMER CHEMICAL SOC, 2014) Tekin, Emine D.; Tekin, Emine Deniz; Turk Hava Kurumu University; Turkish Aeronautical AssociationPublication 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 Amyloid Inspired Self-Assembled Peptide Nanofibers(AMER CHEMICAL SOC, 2012) Cinar, Goksu; Ceylan, Hakan; Urel, Mustafa; Erkal, Turan S.; Tekin, E. Deniz; Tekinay, Ayse B.; Dana, Aykutlu; Guler, Mustafa O.; Tekin, Emine Deniz; Turk Hava Kurumu University; Turkish Aeronautical Association; Ihsan Dogramaci Bilkent UniversityAmyloid peptides are important components in many degenerative diseases as well as in maintaining cellular metabolism. Their unique stable structure provides new insights in developing new materials. Designing bioinspired self-assembling peptides is essential to generate new forms of hierarchical nanostructures. Here we present oppositely charged amyloid inspired peptides (AIPs), which rapidly self-assemble into nanofibers at pH 7 upon mixing in water caused by noncovalent interactions. Mechanical properties of the gels formed by self-assembled AIP nanofibers were analyzed with oscillatory rheology. AIP gels exhibited strong mechanical characteristics superior to gels formed by self-assembly of previously reported synthetic short peptides. Rheological studies of gels composed of oppositely charged mixed AIP molecules (AIP-1 + 2) revealed superior mechanical stability compared to individual peptide networks (AIP-1 and AIP-2) formed by neutralization of net charges through pH change. Adhesion and elasticity properties of AIP mixed nanofibers and charge neutralized AIP-1, AIP-2 nanofibers were analyzed by high resolution force distance mapping using atomic force microscopy (AFM). Nanomechanical characterization of self-assembled AIP-1 + 2, AIP-1, and AIP-2 nanofibers also confirmed macroscopic rheology results, and mechanical stability of AIP mixed nanofibers was higher compared to individual AIP-1 and AIP-2 nanofibers self-assembled at acidic and basic pH, respectively. Experimental results were supported with molecular dynamics simulations by considering potential noncovalent interactions between the amino acid residues and possible aggregate forms. In addition, HUVEC cells were cultured on AIP mixed nanofibers at pH 7 and biocompatibility and collagen mimetic scaffold properties of the nanofibrous system were observed. Encapsulation of a zwitterionic dye (rhodamine B) within AIP nanofiber network was accomplished at physiological conditions to demonstrate that this network can be utilized for inclusion of soluble factors as a scaffold for cell culture studies.