Theses supervised by Doç. Dr. Mustafa Özgür Güler
10 theses · İhsan Doğramacı Bilkent University
Mekanik özellikleri ayarlanabilir biyoaktif poroz peg-peptit kompozit hidrojellerin üretimi
Mimicking the instructive cues of native extracellular matrix (ECM) is fundamental to understand and control the processes regulating cell function and cell fate. Extensive research on the structure and biological complexity of ECM has shown that three types of critical information from the ECM have influence on cellular behaviour: (1) biophysical properties (elasticity, stiffness), (2) biochemical properties (bioactive peptide epitopes of ECM molecules), and (3) nanoarchitecture (nanofibrillar structure, porosity) of ECM. Recent efforts have therefore focused on the construction of ECM mimetic materials to modulate tissue specific cell functions. Advances in biomaterial platforms include artificial ECM mimics of peptide conjugated synthetic polymer hydrogels presenting bioactive ligands produced with covalent chemistry. These materials have already found application in tissue engineering, however, these biomaterial platforms represent oversimplified mimics of cellular microenvironment and lack the complexity and multifunctional aspects of native ECM. In this work, we developed a novel polyethylene glycol (PEG)-peptide nanofiber composite hydrogel system with independently tunable biochemical, mechanical and physical cues that does not require any chemical modification of polymer backbone to create synthetic ECM analogues. This approach allows non-interacting modification of multifactorial niche properties (i.e. bioactive ligands, stiffness, porosity), since no covalent conjugation method was used to modify PEG monomers for the incorporation of bioactivity and porosity. Combining the self-assembled peptide nanofibers with crosslinked polymer network simply by facile mixing followed by photo-polymerization resulted in the formation of porous hydrogel systems. Resulting porous network can be functionalized with desired bioactive signalling epitopes by simply altering the amino acid sequence of peptide amphiphile molecules. In addition, the mechanical properties of the composite system can be precisely controlled by changing the PEG concentration. Ultimately, multifunctional PEG-peptide composite scaffolds reported in this work, can fill a critical gap in the available biomaterials as versatile synthetic mimics of ECM with independently tunable properties. Such a system could provide a useful tool allowing the investigation of how complex niche cues interplay to influence cellular behaviour and tissue formation both in 2D and 3D platforms.
Kendiliğinden düzenlenen peptit nanoyapıların nanomalzeme üretiminde çok yönlü kullanılması
Several peptides such as amyloid like peptides (ALPs) and peptide amphiphiles (PAs) were synthesized by solid phase peptide synthesis technique. These peptides were utilized in fabrication of nanostructured materials. ALPs with amino (Ac-KFFAAK-Am) and carboxylate (Ac-EFFAAE-Am) functional groups were used in growth of titanium dioxide (titania) in solution. On the other hand, PA with amino group (lauryl-VVAGK-Am) was used in growth of titania by atomic layer deposition method. Obtained nanostructured titania in each case was used in construction of dye-sensitized solar cells. Peptide amphiphile with phytochelatin mimetic sequence and adamantyl functionality (ADAc-6-Ahx-GECECECG-Am) was used in noncovalent functionalization of electrospun hydroxypropyl-β-cyclodextrin (HPβCD) mesh; HPβCD mesh functionalized with peptide was further used in metal ion scavenging. PA with sequence lauryl-VVAGH-Am was used in noncovalent encapsulation of zinc phthalocyanine derivative. New photophysical properties of encapsulated chromophore were studied and ultrafast energy transfer was observed. L and D peptide amphiphiles (L/D-pyrenebutyryl-6-Ahx-VVAGH-Am and L/D-lauryl-VVAGH-Am) were used to induce chiral organization of achiral chromophore (pyrene) in self-assembled nanofibers of PAs. Two strategies were involved to induce chiral organization: first strategy envisioned conjugation of pyrene to peptide sequence, whereas second strategy involved direct encapsulation of the chromophore. Achiral pyrene molecules organized in supramolecular chiral manner were observed to demonstrate circular dichroism.
Peptit nanoyapı şablonuyla enerji depolama uygulamaları için demir fosfat nanoyapıların geliştirilmesi
The use of primary cells has been replaced with rechargeable batteries due to environmental concerns. Li-ion batteries are examples of the rechargeable batteries that have replaced other types of rechargeable batteries from market due to high capacity, high electrochemical potential, superior energy density, durability, as well as the flexibility in design. Compared to other cathode materials used in Li-ion batteries, the iron oxide (FePO4) is less toxic, environmentally friendly, and less expensive. Inorganic materials can be fabricated by template-directed mineralization to enable control over size and morphology. One-Dimensional (1-D) nanostructures can be used for template directed mineralization method. The nanostructures are particularly interesting as electrode materials due to their high surface area, large surface-to-volume ratio, and favorable structural stability. They provide fast ion/electron transfer by sufficient contact between the active materials and electrolyte. In this thesis, 1-D nanostructures of FePO4 materials with high surface area were synthesized to enhance the efficiency of Li-ion batteries. The synthesis of iron phosphate nanostructures was performed by using peptide amphiphile nanostructures. Iron (III) chloride (FeCl3) was used to trigger the self-assembly of the peptide amphiphile molecules forming nanostructures, which can nucleate FePO4 formation. The electrochemical performance of these nanostructures for Li-ion battery was analyzed. In conclusion, the template directed electrode materials revealed fast ion/electron transfer and sufficient contact between materials and electrolyte. They also exhibited enhanced flexibility leading to higher capacity than the electrode material synthesized without the template.
Kendiliğinden düzenlenen supramoleküler kiral peptit nanoyapılar
Self-assembly process is an easy and convenient bottom-up technique for designing novel functional materials. Self-assembled peptide amphiphile (PA) molecules are remarkable building blocks for a wide-range of applications due to their easy synthesis, biocompatibility, biodegradabability and dynamic nature in aqueous conditions. Controlling self-assembly behavior still remains complex, since it can be affected by multiple factors. Chirality is an important parameter for designing and controlling self-assembled supramolecular nanomaterials. In this thesis, self-assembly mechanism of chiral peptide molecules was studied with different driving forces in order to develop new methods for producing self-assembled nanomaterials. In addition to self-assembly mechanism, different morphologies and chiral behaviors of the self-assembled supramolecular chiral peptide amphiphile nanostructures were monitored with various characterization methods. pH is a significant contributor for the self-assembly process and this effect was studied in detail to elucidate pH dependency of supramolecular conformation. According to morphological characterizations, histidine containing PA molecules form nanosheet like structures under acidic pH. At the isoelectric point of imidazole, they have a tendency to form twisted fiber or ribbon structures. At high pH conditions, pH 10, they form nanotubes due to the neutralization of imidazole groups and π-π interactions at the side chain of histidine moiety. When another aromatic ring is included in the sequence, in this case phenylalanine residue, different nanostructures were observed. In addition to histidine PA, lysine and glutamic acid containing peptide building blocks were also studied to understand the effect of electrostatic interactions. Phenylalanine containing PAs and valine containing PAs were compared in terms of their chiral self-assembly behaviors. As a result of self-assembly of the positively charged and negatively charged peptides, well defined nanostructures were obtained. While valine containing PA molecules form straight nanofibers, phenyl alanine containing PAs form well ordered rigid twisted fibers and twisted ribbon structures.
Kendiliğinden bir araya gelen peptit nanofiberlerden oluşan jellerin enzimatik degredasyonu
The self-assembled peptide nanofiber gels have received enormous attention because of their inherent biocompatible, biodegradable and functional properties. They provide a smart platform for a range of applications such as tissue engineering, drug delivery and wound healing. These gels are formed through noncovalent interactions such as hydrogen bonding, hydrophobic interactions and electrostatic interactions among the peptideamphiphile molecules at physiological conditions. In order to understand thestability of these gels in the presence of proteases in natural conditions, we studied degradation behavior of the gels with proteinase K, which is anonspecificprotease cleaving the peptide bonds. Degradation process was studied by measuring weight measurement and TEM imaging. In addition, sustained releaseof Rhodamine B from these gels was also studied in the presence of proteases.The results clearly demonstrated that presence of D- amino acids in the peptide release profile of the encapsulated molecules in the gels. These findings are interesting for biomedical applications of these materials dueto their tunable degradation and controlled release behavior
Peptit nanoyapıların biyomedikal uygulamaları
Nature as an important inspirational source for scientists presents complex and elegant examples for adaptive and intelligent systems created by self-assembly. There has been a great endeavour for understanding these sophisticated systems and self assembly gives us an opportunity to emulate these systems by customized molecular designs. In this thesis, next-generation biomaterials were developed by integrating peptide amphiphile molecules into sugar, lipid or inorganic based materials through covalent or noncovalent interactions and their biomedical applications were investigated. Peptide amphiphiles can form morphologically different supramolecular nanostructures based on the amino acid sequence they bear. Also, a bioactive amino acid sequence can be inserted into the peptide backbone not only to enhance the biocompatibility of the material but also to direct cellular responses. On the other hand, amphiphilic character of peptide amphiphiles enables to interact with other amphiphilic molecules or hydrophobic surfaces via hydrophobic interactions. In the scope of the present thesis, peptide based systems were utilized in three different biomedical applications: drug delivery, bioimaging and regenerative medicine. In the first chapter, the self-assembly as one of the bottom-up approaches, peptide self-assembly, the forces and factors triggering the peptide assembly, the importance of peptide amphiphile design in the resulting nanostructure and the biomedical applications of peptide amphiphiles are shortly introduced. In the second chapter, a new drug delivery system is devised by incorporating peptide amphiphile molecules, which are synthesized using arginine residues that are known to enhance cell penetration, into the liposomal system. Beside the investigation of model dye and anticancer drug encapsulation capacities of the prepared formulation, cellular uptake profiles and therapeutic effects of liposomal systems are also examined. In the third chapter, mesoporous silica nanoparticles, which are anticipated to be used in drug delivery and theranostic applications, are individually functionalized with two distinct peptide amphiphile molecules with different overall charges and their biocompatibilities and cellular uptake profiles are examined. In the fourth chapter, superparamagnetic iron oxide nanoparticles that have also potential to be utilized in clinical applications are shown to be applicable as negative contrast agents in magnetic resonance imaging after coating with peptide amphiphiles. The last chapter covers the development of glycopeptides nanofibers that can mimic natural hyaluronic acid abundantly found in native cartilage tissue and its effect on the cartilage regeneration.
Bioinspired organic-inorganic composite materials
Nature has been an inspiration and information source for scientists over centuries, for developing new materials. A great effort has been spent in order to understand biological materials. The biomineralization process is observed in the nature and it creates perfectly hierarchical structures, which give the living organisms extraordinary properties. It is also a fact that along with the nature; living creatures such as nacre and bacteria employ biomineralization in order to produce minerals for protection and navigation purposes. In addition, bone is a composite material which protects the internal organs and provides mechanical support and is a result of biomineralization process. In this thesis, the biomineralization processes of living organisms and bone is mimicked by employing peptide amphiphile nanofibers as templates for inorganic materials production. Glutamic acid residue is used in order the mimic the negatively charged domains for proteins, which play crucial roles in biomineralization process in some organisms and bone. In order to mimic the structure of sea shell, which is composed of calcium carbonate, and bone, which consists of calcium phosphate, relevant mineral solutions were used. In conclusion, when organic and inorganic components are used together, they demonstrate superior mechanical properties, when compared to organic molecules alone.
Moleküler kontrollü bir araya gelme yöntemiyle oluşturulan peptit bazlı biyomalzemelerin ilaç taşınımı ve rejeneratif tıp alanlarında uygulamaları
Self-assembly is a nature inspired novel engineering tool to build functional new generation of adaptable and complex biomaterials with variety of chemical and physical properties based on recent discoveries at the interface of chemistry, biology and materials science. Within self-assembling building blocks, peptides consisting natural amino acids and possibilities to integrate other molecules via synthetic approaches are intriguing biomacromolecules to obtain dynamic architectures at both nano and bulk scales for biomedical applications. In this thesis, the development of novel biomaterials through molecular self-assembly of the biomimetic peptides, bioactive peptide amphiphiles and their composite architectures with polymeric system for biomedical applications were presented. In the first chapter, the concept of self-assembly, design principles of the self-assembling peptide based building blocks and advanced characterization techniques for these materials were discussed to provide general perspective on the field. The applications of peptide based biomaterials with an emphasis on the drug delivery and regenerative medicine purposes were also highlighted in this part. In the second chapter, amyloid inspired self-assembling peptides and their supramolecular assemblies were presented in the context of developing nature-inspired biocompatible and mechanically stable supramolecular peptide based biomaterials. In the third chapter, supramolecular PA nanofiber gels which can form supramolecular nanofibrous networks at physiological conditions and encapsulate chemotherapeutics with high efficacy were examined as controlled local drug delivery system at both in vitro and in vivo conditions. In the fourth chapter, the facile fabrication strategy to create a novel self-assembled peptide amphiphile (PA) nanofibers and PEG composite hydrogel system as synthetic ECM analogues was discussed. It was showed that the synergistic combination of different classes of materials provide us new opportunities to develop biomaterials with independently tunable biochemical, mechanical and physical properties.
Kendıliğinden düzenlenen peptit nanolif kalıplar ve atomik katman kaplama yöntemiyle fonksiyonel nanomalzeme üretimi
There are mainly two basic approaches in nanostructured materials synthesis. The first one is the top-down approach and requires material removal from a bulk substrate material by chemical, physical, mechanical or thermal means; acid etching, focused ion milling, and laser ablation are among these top-down synthesis techniques. It is a straightforward – albeit poor in material architecture control – method that has established its niche in today's high-volume CMOS transistor fabrication technology which already produces single-digit nanometer-scale device features. On the other hand, bottom-up approach exploits fine-tuned materials assembly. Bottom-up approach is realized via direct self-assembly of target nanostructures or material growth on synthetic or natural nanotemplates. Bottom-up nanostructured materials synthesis offers considerably wider spectrum of achievable material architectures and structural hierarchies. Synthesis of nanostructured materials on self-assembled soft nanotemplates is of significant importance because many biological systems utilize this very similar approach to construct complex biomolecule-templated materials. Peptide amphiphile (PA) molecules with their intrinsic property to self-assemble into nanostructures such as fibers, present a versatile tool in inorganic material templating. PAs were used as soft templates in several studies for fabrication of nanoscale inorganic materials. Most of these studies are focused on in-solution material deposition on the surface of a template. Even though this approach allows successful material deposition, precise control over material thickness, uniformity, and high conformality is difficult to achieve in a repeatable manner. In order to circumvent this challenge, in this thesis, atomic layer deposition (ALD) technique was deployed for conformal coating of PA nanonetwork templates. ALD involves low-temperature iterative vapor-phase material deposition in a self-limiting fashion. In each deposition half-cycle, Ti- or Zn- containing volatile metalorganic complexes form a self-limiting uniform monolayer that consequently reacts with water vapor (H2O) as an oxygen precursor in the subsequent process half-cycle. As each half-cycle is separated with purge cycles, no gas-phase reactions occurs and material growth proceeds only with surface chemical ligand-exchange reactions. ALD approach allowed obtaining TiO2 or ZnO nanonetworks with tunable wall thickness and ultimate conformality. Obtained metal oxide-peptide hybrid materials were further treated differently. In the case of TiO2, organic template was removed upon calcination at 450 °C, a temperature at which amorphous titania transforms to anatase form. ZnO-peptide hybrid materials on the other hand, did not undergo any thermal processing, as ZnO already grows in wurtzite crystalline form during ALD process. In principle, nanostructured anatase TiO2 and wurtzite ZnO are wide bandgap semiconductors which can be used as photoanode materials. Nanostructured anodic materials still attract a great interest as the matter at nanoscale regimes can provide considerable enhancement in charge carrier separation, charge carrier transport, and active surface area. Here we demonstrate the fabrication of nanostructured TiO2 and ZnO on self-assembled soft templates. As a proof of principle, we utilized semiconducting TiO2 and ZnO in assembly of dye sensitized solar cells and studied material thickness effect on device performance parameters such as open circuit voltage (Voc), short circuit current (Jsc), and fill factor. Three sets of nanostructured photoanodes with different TiO2 deposition cycles (100, 150, and 200) and ZnO deposition cycles (100, 125 and 150) were fabricated. TiO2 and ZnO nanonetworks in photoanodes form a system of interconnected nanotubes, which can facilitate electron transfer. Moreover, these networks are porous high-surface area materials and they can drastically increase number of sensitizer molecules attached to the semiconductor material surface.
Kendiliğinden düzenlenen peptit kalıplar yardımıyla inorganik tek-boyutlu nanoyapıların sentezi ve uygulama alanları
Engineering at the nano scale has been an active area of science and technology over the last decade. Inspired by nature, synthesis of functional inorganic materials using synthetic organic templates constitutes the theme of this thesis. Developing organic template directed synthesis approach for inorganic nanomaterial synthesis was aimed. For this purpose, an amyloid like peptide sequence which is capable of self-assembling into nanofibers in convenient conditions was designed and decorated with functional groups showing relatively high affinity to special inorganic ions, which are presented at the periphery of the one-dimensional peptide nanofiber. These chemical groups facilitated the deposition of targeted inorganic monomers onto the nanofibers yielding one-dimensional organic-inorganic core-shell nanostructuresThe physical and chemical properties of the synthesized peptide nanofibers and inorganic nanostructures were characterized using both qualitative and quantitative methods.First, silica nanotubes were obtained by silica mineralization around these peptide nanofiber templates for the construction of sensors for explosives. The fluorescence dye was used to coat the silica nanotubes to detect explosive vapor. The surface of the silica nanotubes were porous enough to adsorb more dye compared to the silica nanoparticles and silica film, and causes faster fluorescence quenching in the presence of explosives like trinitrotoluene and dinitrotoluene. The silica nanotubes which synthesized with this peptide nanofiber templates can be used in catalysis and sensors in which high surface area is advantageous. In the second part of the thesis,titanium dioxide nanotubes were obtained from titania mineralization. They are wellknown with their fascinating properties as a result of the one-dimensionalnanostructure, such as more efficient electron transfer and less electron-hole recombination. The sufficient photoactivity of titanium dioxide makes them suitable materials for Dye-Sensitized Solar-Cell construction. It is demonstrated that the peptide nanofiber templated titanium dioxide nanotubes have more than two times more efficiency compared to template-free synthesized titanium dioxide particles.Finally, designed peptide sequence was conducted to a multi-step seeding mediated growth method for gold mineralization around peptide nanofibers. The gold-peptide hybrid nanostructures with different packing characteristics and sizes were synthesized and fully characterized. Further, it was demonstrated that the dry film of these nanostructures showed a resistive switching dominant conductivity, due to thenanogaps in between gold nanoparticles as a result of particle alignment driven by the peptide nanofiber. The results obtained in this thesis encourage use of a new ?bottom-up? synthesis approach. Specially designed peptides with desired properties and functional groups were synthesized and peptide nanofibers formed were further used as templates for inorganic mineralization. Not only it is possible to synthesis high amount of nanostructure with this approach, but also formed one-dimensional nanostructures show advance functionalities used in several applications as a part of the thesis scope. This methodology is suitable for many metals and metal oxide basedapplications.Keywords: Biomimetic mineralization, Nanomaterials, Peptide, Self-assembly, One-Dimensional Nanostructures, Template Directed Synthesis