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1
Mayuram, Ravikumar Krishnakumar. "Region-specific role of water in collagen unwinding and assembly." Texas A&M University, 2008. http://hdl.handle.net/1969.1/85997.
Full textAbstract:
Conformational stability of the collagen triple helix affects its turnover and
determines tissue homeostasis. Although it is known that the presence of imino
acids (prolines or hydroxyprolines) confer stability to the molecule, little is known
regarding the stability of the imino-poor region lacking imino acids, which plays a
key role in collagen cleavage. In particular, there have been continuing debates about
the role of water in collagen stability. We addressed these issues using molecular
dynamics simulations on 30-residue long collagen triple helices, including a structure
that has a biologically relevant 9-residue imino-poor region from type III collagen
(Protein Data Bank ID: 1BKV). We characterized the conformational motion of the
molecule that differs between imino-rich and imino-poor regions using a torsional map
approach. At temperatures of 300 K and above, unwinding initiates at a common
cleavage site, the glycine-isoleucine bond in the imino-poor region. This provides
a linkage between previous observations that unwinding of the imino-poor region
is a requirement for collagenase cleavage, and that isolated collagen molecules are
unstable at body temperature. Unwinding of the imino-poor region is controlled by
dynamic water bridges between backbone atoms with average lifetimes on the order
of a few picoseconds, as the degree of unwinding strongly correlated with the loss
of water bridges, and unwinding could be either prevented or enhanced, respectively
by enforcing or forbidding water bridge formation. While individual water bridges
were short-lived in the imino-poor region, the hydration shell surrounding the entire
molecule was stable even at 330 K. The diameter of the hydrated collagen including the first hydration shell was about 14 Â, in good agreement with the experimentally
measured inter-collagen distances. These results elucidate the general role of water in
collagen turnover: water not only affects collagen cleavage by controlling its torsional
motion, but it also forms a larger-scale lubrication layer mediating collagen self-assembly.
2
Sun, Pei. "Ultrathin films of biomolecules with well-controlled nanostructures." Connect to this title online, 2005. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1109605487.
Full textAbstract:
Thesis (Ph. D.)--Ohio State University, 2005.Title from first page of PDF file. Document formatted into pages; contains xvi, 192 p.; also includes graphics Includes bibliographical references (p. 178-192). Available online via OhioLINK's ETD Center
3
Archer, Jared Rausch. "Synthesis, characterization, and application of thin films and mesostructured materials using self-assembled surfactant templates." The Ohio State University, 2005. http://rave.ohiolink.edu/etdc/view?acc_num=osu1111694248.
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4
Shen, Lirui, Songcheng Xu, Kun Wu, and Guoying Li. "Novel method for preparing fish collagen gels with excellent physicochemical properties via the dehydration of ethanol - 122." Verein für Gerberei-Chemie und -Technik e. V, 2019. https://slub.qucosa.de/id/qucosa%3A34167.
Full textAbstract:
Content:
Fish collagen has been considered to be an alternative for mammalian collagen, however, physicochemical properties of fish collagen-based materials such as gels are so far not adequate for actual application. In the present study, we prepared two types of fish collagen gels with sufficient elasticity: i) dehydrated fibrillogenesis collagen gels (DFCG), which were fabricated via collagen self-assembly followed by immersion in different concentrations of ethanol solutions, and ii) dehydrated cross-linking collagen gels (DCCG), which were fabricated via collagen self-assembly and simultaneous cross-linking followed by immersion in ethanol solution. Furthermore, the physicochemical properties of DFCG and DCCG were analyzed by atomic force microscopy, differential scanning calorimetry, enzymatic degradation and dynamic viscoelastic measurements. The microstructure of DFCG was consisted of characteristic Dperiodic collagen fibrils and insusceptible of ethanol concentrations (20-100% (v/v)). However, the thermal
stability, remaining weight after enzymatic degradation and mechanical properties of DFCG distinctly increased with the increase of ethanol dose, possiblely ascribing that ethanol with higher polarity might
dehydrate partial free water of DFCG and strengthen the interactions of hydrogen bond. Especially, for the gel treated by 100% (v/v) enthanol, Td increased by 32.7 °C and G′ was 55-folds than those of
undehydrated gel (43.1 °C and 239.2 Pa). In the case of DCCG, the formation of collagen fibrils was depended on the concentrations of N-hydroxysuccinimide adipic acid derivative (NHS-AA), which was
converted to [NHS-AA]/[NH2] ratios (calculated by the [active ester group] of NHS-AA and [ε-NH2] of lysine and hydroxylysine residues of collagen). As the ratio= 0.05, the characteristic D-periodic fibrils were still formed and the treatment of 60% (v/v) ethanol increased the Td (52.5 °C) and G′ (7388 Pa) values of the gel compared with those of uncross-linked gel (49 °C and 2064.32 Pa, respectively), majorly resulting from the effects of covalent cross-linking bonds and hydrogen bonds. However, when the ratio= 0.2, the collagen self-assembly was intensively inhibited and the dehydration of free water within gel structure in the absence of thick fibrils led to the shrinkage of the gel and an obvious decrease in Td (42 °C) and G′ (432 Pa). Although the [NHS-AA]/[NH2] ratio further increased to 0.8, the thermal stability and elasticity of the gel enhanced mildly suggesting that the presence of thick fibrils formed via the self-assembly was significantly crucial for reinforcing the gels.
Take-Away:
The fish collagen gels with excellent elasticity were prepared via the treatment of ethanol.
The physicochemical properties of the dehydrated gels were depended on the concentrations of ethanol.
The presence of characteristic D-periodic fibrils was significantly crucial for reinforcing the gels.
5
Voldánová, Michaela. "Studium kinetiky samouspořádávacího procesu kolagenu I." Master's thesis, Vysoké učení technické v Brně. Fakulta chemická, 2016. http://www.nusl.cz/ntk/nusl-240522.
Full textAbstract:
Collagen, the most abundant protein of connective tissues, in various forms has a wide applications due to their diverse biological and chemical properties. One of the forms are collagen hydrogels, which are considered very suitable material for applications in tissue engineering, because they are able to provide biodegradable scaffolds that its properties correspond with living tissues. These systems are used for example as scaffold for targeted drug delivery with controlled release, in combination with cells can be used for the regeneration and reconstruction of tissues and organs. Heating the aqueous solution of collagen leads to spontaneous self-assembly process to variously distributed fibrillar structures, which are at a later stage of fibrillogenesis prerequisite for creating a three-dimensional supporting network, which is the basic building block of the gel. The resulting properties of the hydrogel depend not only on its structure, but also on the conditions which cause self-assembly process. Hydrogels were performed at 37 ° C and physiological pH. Studied structural variable was the concentration of collagen. So far, for the research of self-assembly were used spectrometric methods, which only provide information about kinetics of morphogenesis. In this work to study the kinetics of collagen I self-assembly were used rheological methods, which additionally give information about viscoelastic properties of the resulting material. The obtained experimental data confirmed two-step process of collagen I fibrillogenesis consisting of nucleation and growth process. Rheological hydrogels collagen behaved as a nonlinear yield-pseudoplastic. An attempt was made to molecular interpretation of the results. Using two-parametric Avrami equation was determined the rate of self-assembly for each concentration of collagen and the value of Avrami exponent determining the shape of produced units. The prepared hydrogels were subjected to increasing shear stresses (strain amplitude, shear rate). Larger amplitudes leads to collapse of the hydrogel structure, which is able to again partially regenerated.
6
Kopuletá, Ema. "Struktura a vlastnosti nanokompozitních sítí kolagen/HAP." Doctoral thesis, Vysoké učení technické v Brně. Fakulta chemická, 2014. http://www.nusl.cz/ntk/nusl-233390.
Full textAbstract:
Polymerní biomateriály jsou jedním ze současných populárních témat vzhledem k možnosti potenciální aplikace v tkáňovém inženýrství a řízeného dávkování léčiv v organismech. Kolagen je jako jeden z nejčastěji se vyskytujících proteinů zvláště zajímavý díky svým rozmanitým vlastnostem bez imunoreakce organismu příjemce. Tato práce je zaměřena na samouspořádávací procesy, kinetiku, obecné zákonitosti řídící proces samouspořádání a mechanické vlastnosti kolagenních roztoků. Dále je zkoumán efekt hydroxyapatitových nanočástic na samouspořádávání kolagenu a mechanické vlastnosti výsledných nanokompozitních hydrogelů. Jsou objasněny možné mechanismy interakcí mezi kolagenem I a hydroxyapatitem spolu s popisem vývoje struktury a vlastností na různých úrovních struktury. Byly měřeny a molekulárně interpretovány závislosti viskoelastických veličin na smykové rychlosti spolu s viskoelastickým chováním. Dále byla studována struktura kolagenních scaffoldů a určen vliv HAP a síťování. Závěrem byly diskutovány výsledky v souvislosti s jejich aplikovatelností v tkáňovém inženýrství chrupavek tvrdých tkání a v regenerativní medicíně.
7
Zubal, Lukáš. "Zpracování, gelace a charakterizace atelokolagenu." Doctoral thesis, Vysoké učení technické v Brně. CEITEC VUT, 2018. http://www.nusl.cz/ntk/nusl-385280.
Full textAbstract:
Předkládaná disertační práce se zabývá charakterizací, zpracováním a gelací rozpustného kolagenu. Literární rešerše shrnuje postavení kolagenu na trhu s transplantáty, jeho aplikace a jednotlivé typy kolagenu. Detailně jsou rozebrány jednotlivé metody charakterizace rozpustného kolagenu a způsoby jeho gelace. Experimentální část je rozdělena na dvě podkapitoly. První podkapitola experimentální části se zabývá rozpouštěním a gelací rozpustného kolagenu v natlakované CO2 atmosféře. Proti jiným podobným metodám, metoda pracuje na poměrně nízkém tlaku (do 0.9MPa) a je bezpečná z pohledu denaturace kolagenu neboť funguje za nízké teploty blízké 0°C. Tímto způsobem mohou být průhledné gely, obsahující velmi tenká vlákna kolagenu, vytvořeny mnohem rychleji než za použití konvenčních metod. Rychlost gelace a transparentnost dává konceptu potenciál v oblasti oftalmologie a měla by přinést podstatné výhody pro injektovatelné produkty, vytváření mikro kuliček a 3D tisk. Druhá část popisuje unikátní charakterizaci rozpustného kolagenu v nativním stavu pomocí metody průtokové frakcionace s víceúhlovým rozptylem světla (AF4-MALS). Získaná molekulová hmotnost (při nejvyšší detekované koncentraci) odpovídá předpovězené hmotnosti a nativní i denaturovaný kolagen lze snadno rozeznat v konformačním grafu. Tato nová metoda poskytuje konzistentní a stabilní výsledky ve srovnání s ostatními zavedenými metodami. Metoda může být použita pro optimalizaci kvality výtěžků během výroby rozpustného kolagenu, nebo pro citlivou detekci denaturace během zpracování kolagenu.
8
Mermoz, Sebastien. "Auto-assemblage assisté par capillarité et collage direct." Thesis, Université Grenoble Alpes (ComUE), 2015. http://www.theses.fr/2015GREAI114/document.
Full textAbstract:
Parmi les différentes techniques permettant d'assembler à la fois mécaniquement et électriquement les puces empilées, le collage direct de surfaces mixtes Cu-SiO2 représente l'option la plus prometteuse à ce jour. En effet, cette méthode permet d'atteindre la densité d'interconnexions de 10^6/cm² visée par l'industrie, tout en offrant une faible résistivité de contact et une excellente fiabilité. Les méthodes d’assemblages actuelles reposent sur l’utilisation d’outils de Pick&place par l’intermédiaire desquels les puces sont positionnées mécaniquement. Cette technique rencontre néanmoins de plus en plus de difficultés à concilier précision d’alignement et cadence d’assemblage. Cette thèse propose d’adresser cette problématique au travers de la mise au point d’un procédé d’auto-assemblage assisté par capillarité et collage direct. Grâce à l’utilisation des forces de capillarités, il est possible de réaliser l’alignement des puces de façon spontanée : on parle alors d’auto-assemblage. La première partie de ce manuscrit présente une analyse synthétique des méthodes d’assemblages et d’interconnexions existantes et statue sur l’état de maturité de chaque procédé. Cette partie permet par la même occasion d’introduire les mécanismes de collages SiO2-SiO2 sur lesquels repose la méthode d’assemblage développée dans ce manuscrit. Un design de puce permettant la mise en œuvre du procédé d’auto-assemblage est ensuite établit dans la seconde partie. La capacité de la puce à confiner le film de liquide apparait comme l’élément moteur du processus d’auto-alignement. Des auto-assemblages présentant des valeurs d’alignement inférieur au micromètre sont ainsi obtenus, tout en conservant un procédé répétable. La mise en place de simulations numériques permettant de modéliser l’effet d’auto-alignement est présenté dans la troisième partie. Ce modèle a ensuite été généralisé a des puces de formes polygonales. Enfin la dernière partie présente le transfert du procédé d’auto-assemblage a des puces présentant des surfaces de cuivre et d’oxyde de silicium. L’utilisation de ce type de puce a notamment permis de valider la viabilité électrique du processus d’auto-assemblageAmong the various techniques allowing to assemble both mechanically and electrically stacked chips, the direct bonding of Cu-SiO2 mixed surfaces is the most promising option to date. Thanks to this method, the interconnection density of 106/cm² aimed by the industry is achievable, while providing a low contact resistivity and excellent reliability.Current assemblies’ processes are based on Pick&place tools thanks to which the dies are mechanically placed.Nevertheless, these tools have difficulties to council high throughput and high alignment accuracy. This thesis proposes to address this issue through the development of a process of self-assembly assisted by capillary forces and direct bonding.Through the use of capillaries forces, it is possible to achieve spontaneously chips alignment: it is called self-assembly. The first part of this manuscript presents a synthetic analysis of the different assemblies and interconnections technics and decides on the maturity of each process.As the same time, this section allows to introduce the SiO2 -SiO2 bonding mechanisms underlying the assembly method developed in this manuscript.A specific chip design is then established in a second part allowing deploying self-assemblies with SiO2 full sheet chips.The ability of the chip to confine the liquid film appears as the driving element of the self- alignment process. Self- assemblies with alignment values lower than one micrometer are obtained while maintaining a repeatable process. The introduction of numerical simulations to model the self-alignment effect is presented in the third part. This model was then generalized has polygonal shaped chips. Finally the last part presents the transfer of the self- assembly process on SiO2-Cu patterned chips.The use of this kind of chip has enabled to validate the electrical viability of the self-assembly process
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Spitzner, Eike-Christian. "Subsurface and MUSIC-Mode Atomic Force Microscopy." Doctoral thesis, Universitätsbibliothek Chemnitz, 2012. http://nbn-resolving.de/urn:nbn:de:bsz:ch1-qucosa-94864.
Full textAbstract:
Ziel dieser Arbeit war die Entwicklung neuer Methoden in der Rasterkraftmikroskopie, um die Qualität und Interpretierbarkeit von Oberflächenabbildungen auf der Nanometerskala, vor allem jener sehr weicher Proben, entscheidend zu verbessern. Der für polymere und biologische Materialien standardmäßig verwendete intermittierende Kontaktmodus führt auf weichen Oberflächen zu verfälschten Abbildungen der Topographie und der mechanischen Eigenschaften. In dieser Arbeit wurden Techniken entwickelt, die einerseits zerstörungsfreie, tiefenaufgelöste Rasterkraftmikroskopie und andererseits Einzelmessungen mit variabler Dämpfung im intermittierenden Kontaktmodus ermöglichen. Die laterale Auflösung beider Methoden liegt dabei im Rahmen herkömmlicher Techniken (< 10 nm). Die Tiefenauflösung konnte im Vergleich zu anderen Methoden um eine Größenordnung auf unter 1 nm verbessert werden. Die neuen Methoden wurden auf einer breiten Palette polymerer Materialien angewandt. Die räumliche Struktur oberflächennaher Bereiche eines Blockcopolymerfilms konnte im Vergleich zu herkömmlichen Methoden deutlich genauer abgebildet werden. Gleiches wurde auf elastomerem Polypropylen erreicht. Es konnten weiche, amorphe Deckschichten auf teilkristallinen Polymeren nachgewiesen und vermessen werden, was in der organischen Elektronik eine wichtige Rolle spielen kann. Die innere Struktur selbstangeordneter Nanodrähte aus Oligothiophen-Aggregaten konnte aufgelöst werden und es wurde die Selbstanordnung von Kollagenfibrillen im gequollenen Zustand beobachtet.
10
Su, Pao-chuan, and 蘇堡銓. "Light-controlled self-assembly of collagen." Thesis, 2014. http://ndltd.ncl.edu.tw/handle/zgu9n8.
Full textAbstract:
碩士國立中央大學
生物物理研究所
103
Collagen represents the major structural protein of the extracellular matrix. Elucidating the mechanism of its assembly is important for understanding many cell biological and medical processes as well as for tissue engineering and biotechnological approaches. In this work, conditions for the self-assembly of collagen type I molecules on a supporting surface were characterized. By applying deposition dynamics deposition of collagen on a substrate at room temperature using an appropriate solvent, collagen assembled into ultrathin ( 4nm) highly anisotropic ribbon-like structures coating the entire support. We use stimulated Raman scattering system enables absorption of specific functional groups to allow local resonance absorption, causing local heating of the material, and applying a ponderomotive force to the collagen fibers, in order to achieve a stable directional control.
11
"Design, self-assembly and applications of heterotrimeric collagen mimics." Thesis, 2009. http://hdl.handle.net/1911/61872.
Full textAbstract:
Collagen, a fibrous protein, is an essential structural component of all connective tissues, including cartilage, skin, tendon, ligaments and bone. Type I collagen is an AAB heterotrimer assembled from two identical alpha1 and one alpha2 chain. Missense mutations in either the alpha1 or alpha2 chains of type I collagen, which lead to the substitution of Gly in the ubiquitous X-Y-Gly repeat by bulky amino acids lead to Osteogenesis imperfecta (OI) of varying severity. However, the majority of studies on the effects of amino acid substitutions on triple helix stability have been performed on collagen-like peptides homotrimers. We report the design, synthesis, self-assembly and characterization of a series of peptides that self-assemble to form collagen-like heterotrimers directed through electrostatic interactions. First, we utilize a series of peptides with net charge ranging from -10 to +10 to show the assembly of various AAB and ABC heterotrimers. We then analyze the ability of various charge pairs based upon naturally occurring amino acids, for instance E--R, E--K, D--R and D--K charge pairs, to stabilize a collagen triple helix. We report the synthesis of a surprisingly stable ABC heterotrimer, composed of (DOG)10, (PKG)10 and (POG) 10 chains (O = hydroxyproline), with a stability comparable to (POG) 10 homotrimer. This high stability heterotrimer is then used to develop a peptide model for OI, a hereditary disorder observed in type I collagen. We report the design of a novel peptide model that can mimic glycine mutations in either of the alpha1 or alpha2 chains of type I collagen. This design utilizes an electrostatic recognition motif in three chains that can force the interaction of any three peptides, including AAA (all same) homotrimers, AAB (two same, one different) heterotrimers and ABC (all different) heterotrimers. The component peptides can be designed in such a way that the mutations are present in none, one, two or all three chains. We successfully report collagen mutants, for the first time, with the structure relevant to the native forms of OI. Furthermore, we are able to differentiate between four triple helices that differ from each other in the frequency of glycine mutations at a particular position. Thus, the ease of preparation of heterotrimers, coupled with our ability to separate single mutations, provides us with a tool to understand mutations in natural collagens that lead to various connective tissue disorders in general and OI in particular. We also introduce another peptide model based upon the ABC heterotrimer to understand the effect of proline hydroxylation and fluorination to the stability of a collagen triple helix, in a chain dependent manner.
12
Anderson, Darren. "Collagen self-assembly : a complementary experimental and theoretical perspective /." 2006. http://link.library.utoronto.ca/eir/EIRdetail.cfm?Resources__ID=442418&T=F.
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Cheng, Calvin Chia-Hung. "Investigating Type I Collagen Self-assembly Processes and End Products." Thesis, 2012. http://hdl.handle.net/1807/32568.
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Segmental long spacing (SLS) collagen self-assembly was studied by analyzing aggregates formed from different nucleoside triphosphates at various protonation stages. Triple-negatively charged triphosphate groups were determined to be critical for SLS assembly, electrostatically bridging basic residues between collagen monomers. In the second part of this thesis, the nominal elastic modulus for each of the three forms of Type I collagen aggregate was measured and compared. Fibrous long spacing collagen, often associated with diseased tissues, exhibited lower stiffness in comparison to the other forms, native and SLS, suggesting decreased structural stability in diseased tissues. In the last section, a unidirectional pattern of native fibrils was assembled using mica as a template; the ability to customize and change the surface morphology was also demonstrated. For the first time, collagen monomers deposited on the mica were demonstrated to gain lateral mobility.
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Cheng, Wan-Jung, and 鄭琬蓉. "Self-Assembly of Collagen-Related Peptides by Metal-Histidine Coordination." Thesis, 2013. http://ndltd.ncl.edu.tw/handle/54342054588784043334.
Full textAbstract:
碩士國立清華大學
化學系
101
Collagen is a biodegradable and biocompatible material, and has been applied in medical uses for decades. However, animal-derived collagens have several drawbacks, such as low thermal stability, nonspecific cell adhesion, and antigenicity. To solve these problems, preparing collagen-related biomaterial from short mimetic collagen peptides has received many attentions and become an emerging research topic. Our previous studies have shown that His-metal coordination can induce unstable short mimetic collagen peptides to assemble into a higher order structure. In this work, we prepared three collagen related peptides (CRPs): HG(POG)9GH, HG(POG)4PHG(POG)4GH, and GG(POG)9GG, of which two peptides contain His residues, to study their assembled structures. The size and topology of results show that His-metal coordination can promote mimetic collagen peptides to form macro-scale structures, and the topologies depend on metals and the time of adding metal ions into peptide solutions. Circular dichroism spectroscopy was used to examine the structure and the thermal stability of collagen mimetic peptides. Dynamic light scattering (DLS), SEM, and TEM were used to assess the size and the topology of the assembled structures. The CRPs in this work can form microstructures without the assistance of metal ions. Thus, pH dependent assembly of these CRPs was also examined. Although we are not able to clarify the process of self-assembly at the present stage, we did find the impact of the rate of self-assembly, His-metal coordination, and the His-His interaction on the assembly of CRPs. Our results may be useful and helpful for the future development of collagen-related materials.
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Huang, Pei-Shiou, and 黃培修. "Using Second Harmonic Generation Microscopy to Monitor Collagen Self-Assembly Process." Thesis, 2009. http://ndltd.ncl.edu.tw/handle/10467538111633009023.
Full textAbstract:
碩士國立臺灣大學
物理研究所
97
Second harmonic generation (SHG) microscopy has already established as a viable and useful technics in imaging collagen scaffold; it is also holds promise as a noninvasive, less photodamage imaging technics for characterizing collagen structure. Since collagen, especially type-I collagen, is one of the most abundant protein in human body, its assembly into functioning units is an important process in maintaining homeostasis of many tissue types. However, the kinetic details of collagen self-assembly process remains unclear. Therefore, in this study, we used SHG microscopy based on a pulsed laser scanning system to monitor the collagen self-assembly process in real-time. Using SHG microscopy to monitor collagen self-assembly process can provide structural informationsI that is important for understanding the fibrillogenesis process. We used self-assembly in collagen hydrogel as our model as this system has already been investigated extensively using other many different techniqus. Electron microscopy, reflected confocal microscopy, and spectrophotometry had been widely used to investigate the process of collagen self-assembly. However, only the non-centrosymmetric requirement of SHG allows the assembly into collagen fibrils to be studied unequivocably and without additional specimen processing. Moreover, the informations of forwad and backward SHG ratio provide information of the fibril diameter. Our results demonstrate that the collagen self assembly process can be studied by SHG microscopy in vitro, with additional development; our approach can be extended to in vivo investigations of the fibrillogenesis process.
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(8992049), Vallabh Suresh. "The Metal Triggered Self Assembly of Cell-Adhesive and Fluorinated Collagen Mimetic Peptides." Thesis, 2020.
Find full textAbstract:
Collagen I, a natural protein found in animal tissues, can self-assemble into fibrous matrices
that support cell and tissue growth. Peptide mimics of collagen are able to recapitulate this selfassembly process towards the development of biomaterials for tissue engineering. In recent years,
the metal mediated self-assembly of collagen mimetic peptides (CMPs) has allowed access to
various particle morphologies. Herein, two studies are presented. In the first, NCOH-FOGER, a
cell adhesive CMP capable of metal-triggered self-assembly, was utilized to develop a model
system to mimic natural collagen’s interactions with endothelial cells. Notably, a cobalt(III)-
NCoH-FOGER assembly was able to induce endothelial cells to form network-like structures. In
the second, a CMP was modified to include an unnatural amino acid, L-4-trans-fluoroproline,
which increased the thermostability of its folded state. The effect of this substitution on the
morphology of self-assembled particles was evaluated.
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Zhu, Jieling. "Characterizing and controlling structural and mechanical properties of type I collagen self-assembly." Thesis, 2015. https://doi.org/10.7916/D8J67G83.
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Type I collagen matrices are used across a variety of applications in bioengineering and biophysical studies; however, a fuller understanding of the collagen self-assembly process is required to optimize control of the matrix structural and mechanical properties in these applications. The work in this thesis sought to 1) characterize collagen self-assembly using simultaneous imaging, spectroscopy, and rheological methods, 2) use collagen gels as three-dimensional microenvironments to study glioma invasion, and 3) develop a model using experimental research data to teach data analysis tools to undergraduate students. Chapter 1 provides a brief overview of collagen in the body, its applications, structural details about the collagen monomer, and descriptions of in vivo and in vitro fibrillogenesis. Advantages and disadvantages of methodologies used to study collagen self-assembly are discussed for in vitro fibrillogenesis. The materials and methods used in this thesis are described in Chapter 2. Chapters 3 and 4 describe insights into collagen self-assembly using multiple modalities. In Chapter 3, turbidity and confocal reflectance microscopy were simultaneously employed to track collagen fibrillogenesis and reconcile the information reported by the two techniques, with confocal fluorescence microscopy used to supplement information about early events in fibrillogenesis. Chapter 4 describes the novel use of simultaneous rheology and confocal microscopy to study the development of mechanical and structural properties of collagen gels. In Chapter 5, glioma migratory and invasive behaviors are observed and perturbed in the context of well-controlled in vitro two- and three-dimensional environments, including implanting multicellular tumor spheroids in collagen gels across several concentrations to test the effects of pore size on glioma invasion. This chapter serves as a preliminary investigation into how glioma behavior changes depending on environment dimensionality and lays out further studies to fully investigate the mechanisms underlying glioma invasion. Finally, Chapter 6 describes the development, evaluation, and redesign of a Microsoft Excel-based activity where data analysis from contemporary research (published in Chapter 3) was adapted into a training exercise for students taking an introductory General Chemistry Laboratory course. This activity humanized the research enterprise for the undergraduate students and can serve as a model for future collaborations between research and instructional laboratories.
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Huang, Pei Wen, and 黃佩雯. "The effects of glycosylated (2S,4R)-hydroxyproline on collagen stability and self-assembly." Thesis, 2015. http://ndltd.ncl.edu.tw/handle/96473822142759878273.
Full textAbstract:
碩士國立清華大學
化學系
103
Collagen, the most abundant protein in mammalian tissues, has been widely used in biomedical materials. Many researchers have been performing various modifications on collagen to increase its applicability. Different non-covalent interactions were also applied to promote the self-assembly of collagen into higher order structure. Collagen is a right-handed triple helix, and each helix is a left-handed polyproline type II structure containing many (X-Y-Gly)n repeats. On the other hand, carbohydrates are a necessity to organism and play an important role in biological functions. In this work, we modified (2S,4R)-hydroxyproline with 1.2,3,4,6-penta-O-acetyl-β-D-galactopyranoside and synthesized a series of collagen-related peptides containing this modified amino acid to study the consequences of glycosylation on collagen stability and self-assembly. CD measurements indicate that glycosylation will destabilize the collagen triple helices. However, TEM shows that the modification promotes the self-assembly of collagen-related peptides into higher-order structures, suggesting that glycosylation could enhance the interactions between collagen-related peptides to speed their assembly.
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Lin, Chun Ta, and 林駿達. "The Effects of High Self-Assembled Oligopeptides on the Folding and Self-Assembly of Collagen Mimetic Peptides." Thesis, 2015. http://ndltd.ncl.edu.tw/handle/17541057117200441616.
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碩士國立清華大學
化學系
103
Collagen, the most abundant protein in mammals, has been widely used in biomedical materials. In order to increase the structural stability of collagen, we designed and synthesized the collagen mimetic peptides (CMPs) in which an oligopeptide with a high self-assembly propensity was attached. By this design, we expected that the oligopeptide could stabilize the collagen triple helix and assist their self-assembly into higher order structures. Since some of the CMPs containing Ab(16-22) sequence showed the ability to inhibit the aggregation of A protein in our previous studies, in the first part of this study, we further investigated their cytotoxicity by MTT assay. The results indicate that these CMPs are actually toxic to a Neuro cell N2a. Therefore, in the second part, we chose another oligopeptide CILFWG as an attachment to CMPs. From this design, we synthesized a series of CMPs : CILFWG(POG)7 , (POG)7CILFWG, and OG(POG)4CILFWG. The collagen peptide (POG)7 and CILFWG peptide were also synthesized for comparison. We used UV-VIS spectroscopy, TEM, and CD to characterize these peptides. The results showed that the oligopeptide could stabilize the collagen triple helices and assist their self-assembly into higher order structures. In particular, this oligopeptide has a more pronounced effect on CILFWG(POG)7 than any other peptide studied. Thus, this oligopeptide could be potentially useful in designing stable collagen assemblies and related biomaterials.
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Hsu, Wei, and 徐維. "Self-Assembly of Mimetic Collagen Peptides via Histidine-Metal Coordination and Cation-π Interactions." Thesis, 2011. http://ndltd.ncl.edu.tw/handle/26551639616482318229.
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碩士國立清華大學
化學系
99
Collagen, the most abundant protein in mammals, has been widely used in biomedical materials. Searching for an effective way to assemble short mimetic collagen peptides into a higher order structure has been an emerging topic for the preparation of collagen-related biomaterials. In this work, we have incorporated histidine residue into two mimetic collagen peptides to promote the self-assembly of short collagen triple helices into supermolecular structure via His-metal coordination. Our results indicate that His-metal coordination can serve as an effective force to assemble mimetic collagen peptides into large scale structures and their topology depends on metal ions and His-metal coordination sites. Furthermore, the process of self-assembly can be reversed upon adding the cation chelator, EDTA, in solution. In addition, we have introduced a cationic residue into the N-terminus and an aromatic residue into the C-terminus of a collagen-related peptide which can generate favorable cation-π interactions between the termini of collagen triple helices. The experimental results demonstrate that cation-π interactions can promote the self-assembly of collagen triple helices into higher-order fibril structures in a head-to-tail manner. The work shows that cation-π interactions can serve as an effective force in preparing collagen-related biomaterials.
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Chen, Chia-Ching, and 陳佳青. "Study of Cation-π interactions in the stability and self-assembly of collagen triple helix." Thesis, 2010. http://ndltd.ncl.edu.tw/handle/50835071376218003030.
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Ting, Yi Han, and 丁翊涵. "Metal-Induced Self-Assembly of Collagen-Mimetic Peptides and Their Catalytic Activity for Ester Hydrolysis." Thesis, 2016. http://ndltd.ncl.edu.tw/handle/86145626161298119800.
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碩士國立清華大學
化學系
104
Collagen is the most abundant protein in mammals and has been widely used in biomedical materials. Searching for an effective way to assemble short collagen mimetic peptides (CMPs) into a high order structure has received many attentions and been an emerging research topic for increasing biomaterial applicability. In the first part of this thesis, we have incorporated histidine (His) into CMPs to promote their self-assembly into supramolecular structures via His-metal coordination. In this study, we used (POG)9 as the parent peptide to design a series of CMPs with His residues incorporated into different positions. Our aim was to investigate the effects of the number and location of His residues on the self-assembly of CMPs. The results showed that incorporting His residues into the ends of a CMP could speed the self-assembly process but the assemblies were less ordered. In contrast, the CMPs without His residues at their ends could assemble into a more ordered and microflorettes like structures though the assembly process was very slow. Although we were not able to clarify the self-assembly process of collagen, we did find the impact of the location of His replacement on the rate of self-assembly and the morphology of assemblies. Our results may be useful and helpful for the future development of collagen-related materials. In the second part of the experiment, we mimicked the active site of zinc metalloenzymes to design metal-CMPs assemblies as catalysts for ester hydrolysis. We used the His residues at both ends of the triple helix as the ligands to coordinate with metal ions and serve as the catalytic active site for ester hydrolysis. It is analogous to the active site of the zinc metalloenzyme carbonic anhydrase (CA). Our results indicated that the catalytic efficiency of the designed peptides was not good at neutral pH, but increased significantly at higher pH values, reflecting the deprotonation of a His side chain. In addition, at pH 9.75 and without the addition of metal, HG(POG)4(PHG)(POG)4GH peptide exhibited an excellent catalytic efficiency, which is three times greater than the previous reported three strained coiled-coils. And these results may be helpful for the development of catalysts for the ester hydrolysis with the collagen triple helix as the based peptide.
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Fallas, Valverde Jorge. "Design and Structural Characterization of Self-Assembling Triple Helical Heterotrimers." Thesis, 2012. http://hdl.handle.net/1911/71303.
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Design of self-assembling ABC-type collagen triple helical heterotrimers is challenging due to the number of competing species that can be formed in ternary mixture of peptides with a high propensity to fold into triple helices and the fact that well understood rules for pair-wise amino acid stabilization of the canonical collagen triple helix have remained elusive. Given the required one amino acid stagger between adjacent peptide strands in this fold, a ternary mixture of peptides can form as many as 27 triple helices with unique composition or register. Previously we have demonstrated that electrostatic interactions can be used to bias the helix population towards a desired target but the presence of competing states in mixtures has remained an outstanding problem. In this work we use high-resolution structural biology techniques to do a detailed study of stabilizing pair-wise interactions between positively and negatively charged amino acids in triple helices. Two types of contacts with distinct sequence requirements depending on the relative stagger of the interacting chains are observed: axial and lateral. Such register-specific interactions are crucial for the understanding of the registration process of collagens and the overall stability of proteins in this family. Using this knowledge we developed distinct design strategies to improve the specificity of our designed systems towards the desired ABC heterotrimeric target state. We validate our strategies through the synthesis and characterization of the designed sequences and show that they self-assemble into a highly stable ABC triple helices with control over composition in the case of the rational approach and with control over both composition and register in the case of the computational approach.
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Köster, Sarah Friederike. "Biological Matter in Microfluidic Environment - from Single Molecules to Self-Assembly." Doctoral thesis, 2006. http://hdl.handle.net/11858/00-1735-0000-0006-B59C-F.
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Xing, Yong-Nian, and 邢永年. "Control of cell phenotype by collagen fibril islands fabricated by substrate-guided self-assembly of collagen molecules and micro-patterning using masked UV exposure and trypsin etching." Thesis, 2019. http://ndltd.ncl.edu.tw/handle/amdmne.
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碩士國立中央大學
物理學系
107
It has been known that the microscale and nanoscale substrate topography of cell-culturing substrate can regulate cell adhesion, migration, proliferation, and differentiation. It is also known that extracellular matrix is made of most importantly collagen fibrils, which possess specific molecular identity and structural characteristics that may be crucial for controlling cell behaviors such as cell phenotype. In this work, we combined the techniques of self-assembly of collagen molecules and lithographic micropatterning to produce collagen fibril islands. The collagen fibril island substrates were used to culture human mesenchymal stem cells (MSC) to control their shape. We also added PLL-g-PEG on the substrate and observed the cell type to know PLL-g-PEG contribution. In future, We will observe MSC differentiation rate by various collagen fibril islands.We will use DNA, F-actin to observe cell internal transform by collagen fibril islands.
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Mayuram, Ravikumar Krishnakumar. "A Computational Study of the Role of Hydration in the Assembly of Collagen and Other Bio laments." Thesis, 2011. http://hdl.handle.net/1969.1/ETD-TAMU-2011-08-9908.
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Hydration is known to be crucial in biomolecular interactions including ligand binding and self-assembly. In our earlier studies we have shown the key role of water in stabilizing the specific parts of the collagen triple helix depending on the imino acid content. We further showed that the primary hydration shell around collagen could act as a lubricating layer aiding in collagen assembly. But key details on the structure and dynamics of water near protein surfaces and its role in protein-protein interactions remain unclear. In the current study we have developed a novel method to analyze hydration maps around peptides at 1-A resolution around three self-assembling lament systems with known structures, that respectively have hydrated (collagen), dry non-polar and dry polar (amyloid) interfaces. Using computer simulations, we calculate local hydration maps and hydration forces. We find that the primary hydration shells are formed all over the surface, regardless of the types of the underlying amino acids. The weakly oscillating hydration force arises from coalescence and depletion of hydration shells as two laments approach, whereas local water diffusion, orientation, or hydrogen bonding events have no direct effect. Hydration forces between hydrated, polar, and non-polar interfaces differ in the amplitude and phase of the oscillation relative to the equilibrium surface separation. Therefore, water-mediated interactions between these protein surfaces ranging in character from ‘hydrophobic’ to ‘hydrophilic,’ have a common molecular origin based on the robustly formed hydration shells, which is likely applicable to a broad range of biomolecular assemblies whose interfacial geometry is similar in length scale to those of the present study.
In a related study through simulations we show that the rate of tissue optical clearing by chemical agents correlated with the preferential formation of hydrogen bond bridges between agent and collagen. Hydrogen bond bridge formation disrupts the collagen hydration layer and facilitates replacement by a chemical agent to destabilize the tertiary structure of collagens thereby reducing light scattering. This study suggests that the clearing ability of an alcohol not only depends on its molecular size, but also on the position of hydroxyl groups on its backbone.
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"Multi-Hierarchical Self-Assembly of Collagen Mimetic Peptides into AAB Type Heterotrimers, Nanofibers and Hydrogels Driven by Charged Pair Interactions." Thesis, 2012. http://hdl.handle.net/1911/70377.
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Replicating the multi-hierarchical self-assembly of collagen (peptide chain to triple helix to nanofiber and, finally, to a hydrogel) has long attracted scientists, both from the fundamental science perspective of supramolecular chemistry and for the potential biomedical applications perceived in tissue engineering. In terms of triple helical formation, collagen is the most abundant protein in the human body with at least 28 types, yet research involving collagen mimetic systems has only recently began to consider the innate ability of collagen to control helix composition and register. Collagen triple helices can be homotrimeric or heterotrimeric and while some types of natural collagen form only one specific composition of helix, others can form multiple. It is critical to fully understand and, if possible, reproduce the control that native collagen has on helix composition and register. In terms of nanofiber formation, many approaches to drive the self-assembly of synthetic systems through the same steps as natural collagen have been partially successful, but none have simultaneously demonstrated all levels of structural assembly. In this work, advancements in the ability to control helix composition and replicate the multi-hierarchical assembly of collagen are described. Both positive and negative design for the assembly of AAB type collagen heterotrimers were utilized by promoting heterotrimer formation though the use of charged amino acids to form intra-helix electrostatic interactions, while simultaneously discouraging homotrimers, resulting in the identification of multiple peptide systems with full control over the composition of the resulting triple helix. Similar salt-bridged hydrogen bonds between charged residues were incorporated into nanofiber forming peptides, one of which successfully assembled into sticky-ended triple helices, nanofibers with characteristic triple helical packing visible in the solution state, and strong hydrogels that are degraded by collagenase at a similar rate to natural collagen. Together, these results provide a better understanding of the self-assembly of collagenous sequences as well as a novel design scheme for synthetic extracellular matrix mimetics with potential applications in regenerative medicine and drug delivery.