Dissertations / Theses on the topic 'Protein scaffolds'
To see the other types of publications on this topic, follow the link: Protein scaffolds.
Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles
Consult the top 50 dissertations / theses for your research on the topic 'Protein scaffolds.'
Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.
You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.
Browse dissertations / theses on a wide variety of disciplines and organise your bibliography correctly.
1
Rodriguez, Marin Silvia. "Multifunctional scaffolds for selective protein-protein inhibition." Thesis, University of Leeds, 2016. http://etheses.whiterose.ac.uk/17299/.
Full textAbstract:
Protein-protein interactions (PPIs) play an important role in numerous biological processes. Consequently, modulating PPIs is fundamental for understanding and manipulating mechanisms that govern many diseases. Among the wide range of topographies that PPIs display, the α-helix is the most common secondary structure in nature and thus represents a good generic template for inhibitor design.1 Some of the most relevant approaches in this field are the proteomimetic approach, which recapitulate the key binding residues of an α-helix on a non-peptidic scaffold; and the constrained peptides, which aim to reproduce the helical structure by stabilising a helical peptide. Both approaches have generated potent inhibitors of a great diversity of α-helix mediated PPIs. However, developing a better understanding of the key features that govern the modulation of protein recognition is necessary to further advance the field and fully exploit each class of foldamer. In that context, we developed functionalised aromatic oligoamide backbones to mimic residues located on multiple faces of an -helix to target the ER/co-activator PPI. The novel scaffolds are based on bis-benzamide and N-(4-aminophenyl)terephthalamidic acid backbones functionalised with isobutyl groups to reproduce the key side chains of the co-activator α-helix. Conformational studies in combination with molecular modeling and docking analysis provide evidence that the new oligomers can adopt conformations that mimic the residues at i, i+3 and i+4 positions of the native co-activator α-helix. In addition, the rules that govern molecular recognition of protein surfaces were further investigated through the optimisation of the oligobenzamide hybrid scaffold using a structure-activity relationship (SAR) study. A library of compound analogues has been synthesised incorporating five variable sites. The modifications focused on size, polarity and stereochemistry to obtain more potent and selective proteomimetic inhibitors of the p53/hDM2 and Mcl-1/NOXA B PPIs. Finally, using existing methodologies a 3-O-alkylated proteomimetic scaffold and hydrocarbon stapling peptide strategy, have been used to design inhibitors of the Asf1/H3 interaction. The application of both approaches allowed the different inhibitor designs to be directly compared when targeting the same PPI.
2
Machado, Roque Ana Isabel. "Protein scaffolds for cell culture." Thesis, University of Newcastle Upon Tyne, 2013. http://hdl.handle.net/10443/1843.
Full textAbstract:
We report here the design, purification and structural characterization of a new protein scaffold for cell culture. Prior studies in our group revealed the structure of the bacterial protein Caf1 to be flexible protein nanofibres, up to 1.5 μm. The existing Cafl expression system was cumbersome and difficult to mutate, we have now produced a system containing the caf operon which allows for the incorporation of specific peptide motifs. The small peptide, RGDS from fibronectin was inserted into 5 different surface loops of Caf1. The Caf1 mutants were expressed and purified and a structural characterization by biophysical methods was conducted. This revealed permissive sites into which new motifs can be inserted. The characterised proteins were sterilised and used to coat 96 well plates for cell culture. In this study we used mammalian cell lines such as 3T3 fibroblasts, PC12 neuronal cells and primary osteoblasts to understand how they behave in the presence of this biomaterial, in particular the formation of focal adhesions, changes in cytoskeleton rearrangement and nuclear and cell morphology. The controlled engineering of sites within the polymer allowed us to study their implication in cell attachment, survival and proliferation. Our preliminary results have shown that cells interact poorly with the unmodified protein e.g. without any motif associated. This reveals that the polymer is inert and does not influence cell growth by itself. In contrast, the incorporation of RGDS, can invert the scenario of cell growth; promoting cell attachment, survival and proliferation. In a second stage of the project we designed a separate compatible plasmid encoding caf1 gene and used it with the previous plasmid to co-express hybrid Caf1 polymers. The long fibres can also be crosslinked with a non-toxic and non-immunogenic chemical compound – NHS-PEG. Thus a protein hydrogel composed of interchangeable folding units which can be used to incorporate different cell interacting peptide motifs. It is robust and, in the unmodified state highly protease resistant. Future studies will elucidate the versatility and potentiality for this peptide hydrogel in stem cell differentiation.
3
Badger, David B. "Design and Synthesis of Protein-Protein Interaction Inhibitor Scaffolds." Scholar Commons, 2012. http://scholarcommons.usf.edu/etd/3964.
Full textAbstract:
Many currently relevant diseases such as cancer arise from altered biological pathways that rely on protein-protein interactions. The proteins involved in these interactions contain certain functional domains that are responsible for the protein's biological activities. These domains consist of secondary structural elements such as α-helices and Β-sheets which are at the heart of the protein's biological activity. Therefore, designing drugs that inhibit protein-protein interactions by binding to these key secondary structural elements should provide an effective treatment for many diseases. Presented in this dissertation are the designs, syntheses, and biological evaluations for both novel α-helix and novel Β-sheet mimics.
The α-helix mimics were designed to inhibit the interactions between the tumor suppressor protein p53 and its inhibitor protein, MDM2. We also targeted the interactions between the Bak/Bcl-xL proteins. Using the knowledge gained from Hamilton's 1,4-terphenylene scaffold, we designed our inhibitors to be non-peptidic small molecule α-helix mimics. These molecules were designed to bind to the NH2-terminal domain of MDM2 protein thus preventing it from binding to the p53 protein thereby allowing p53 to induce apoptosis. The α-helix mimetic scaffold is designed around a central functionalized pyridazine ring while maintaining the appropriate distances between the ith, ith+4, and ith+7 positions of a natural alpha helix.
The Β-sheet mimics were designed as inhibitors for the integrin mediated extracellular matrix cell adhesion found in Multiple Myeloma. We have designed, synthesized, and incorporated novel Β-turns to induce the formation of Β-hairpins as well as to cyclize the peptides in order to increase their binding affinities and reduce proteolytic cleavage. Given that many protein-protein interactions occur through hydrophobic interactions; our primary Β-turn promoter was designed with the ability to alter the Β-hairpin's hydrophobicity depending on the sulfonyl group used in the turn. The synthesis of several different sulfonyl chlorides for use in our Β-turn promoter is included in this section. We have also provided a detailed structural analysis and characterization of these new cyclic peptides via NMR and CD spectrometry. Using standard 2D NMR methods, we have elucidated the 3D conformation of several peptides in solution. We have also studied the structure activity relationships (SAR) for these cyclic peptides and then correlated these results with those obtained from the NMR studies.
4
Haji, Ruslan Khairunnisa Nabilah. "Protein hydrogels as tissue engineering scaffolds." Thesis, University of Manchester, 2015. https://www.research.manchester.ac.uk/portal/en/theses/protein-hydrogels-as-tissue-engineering-scaffolds(45ff4e72-49ea-46df-9e7b-b9113576c096).html.
Full textAbstract:
Hydrogels aim to mimic the natural living environment by entrapping large amount of water or biological fluids in their polymeric network. There has been growing interest in the development of peptide and protein hydrogels, due to their improved biocompatibility, biodegradability and biological properties in comparison to purely synthetic polymer hydrogels. Under the appropriate conditions, biomacromolecular protein hydrogels can self-assemble into ordered meso- to macroscopic supramolecules with better resulting networks that promote tissue development. The work presented here mainly focuses on producing protein hydrogels with controlled physical properties useful for tissue regeneration process and drug delivery applications. Hen egg white lysozyme (HEWL) hydrogels were studied in the presence of water and different reducing agents forming three HEWL systems including HEWL/water, HEWL/DTT and HEWL/TCEP gels. Strong, self-supporting HEWL gels were successfully prepared in the range of pH 2 to 7, using a temperature of 85°C. At pH 2, the protein denaturation in water was relatively slow resulting in a high percentage of turn structure (~50%) that promotes HEWL gelation after 3 days of heating. No lysozyme gelation in water was observed at pH 3, 4 and 7 even after 21 days of heating. A small quantity of DTT (~20 mM) was added to encourage lysozyme unfolding and HEWL/DTT samples formed gels at higher pH including at physiological pH. The pH 2 HEWL/water gel was found to be stronger but more brittle than pH 7 HEWL/DTT gel. It was observed there were some irregularities in the distribution of pH 2 fibrils (~7µm in length) that form large pore sizes within the network. The pH 7 sample contained shorter and stiff fibrils with repetitive polygon-shaped mesh network. The use of TCEP, which is a stronger reductant than DTT, led to the formation of self-supporting HEWL gels between pH 3.5 and 5.5. The highest storage modulus was observed at pH 5, which is related to the high β-sheet content of the sample (~45%). In addition, a promising strategy has been devised to form thermoresponsive HEWL hydrogels by synthesising and incorporating a small fraction of lysozyme-PNIPAAm bioconjugates into the major protein matrix. Results show the thermoresponsive nature of PNIPAAm was conferred to HEWL protein that exhibits higher storage stability in response to changing temperature.
5
Wang, Hua. "Control of protein-surface, protein-protein, and cell-matrix interactions for biomaterials as tissue engineering scaffolds /." Thesis, Connect to this title online; UW restricted, 2005. http://hdl.handle.net/1773/9894.
Full text
6
Lu, Zhengsun. "Electrospun nanofiber scaffolds and crosslinked protein membranes as scaffold materials in tissue engineering." Thesis, Queen Mary, University of London, 2015. http://qmro.qmul.ac.uk/xmlui/handle/123456789/15023.
Full textAbstract:
Scaffold materials play an essential role in tissue engineering field due to its function of accommodate and guide cell proliferation. In this study, I investigated different types of crosslinked protein membranes that can be produced in microfluidic channels and a number of various types of PLGA electrospun composite nanofiber scaffold to examine their potentials as scaffold materials in tissue engineering. A simplified fabrication technique has been developed to produce a large surface area of crosslinked protein membranes to fulfill the purpose of cell culture experiments. Bovine serum albumin is used along with two acyl chloride crosslinkers, i.e. TCL and IDCL, respectively to accomplish the cross-linking. On the other hand, PLGA is dissolved in HFIP and enhanced with silk fibroin and carbon nanotubes to make composite electrospun materials. The morphology, physicochemical properties and biocompatibility of the membranes are studied. The biocompatibility of the membranes is investigated using cell proliferation of the PC12, ADSCs and neurons cultured on the membranes. Our results show that compared to crosslinked protein membranes, the electrospun materials are easier to prepare, less toxic and more suitable for mass production. Moreover, the electrospun materials are seen to have better biocompatibility in our cell culture study. Furthermore, the composite electrospun materials with high CNTs concentrations demonstrate positive effects on the proliferation of neurons.
7
Lee, Maximillian. "Pyridazinediones : versatile scaffolds for site-selective protein modification." Thesis, University College London (University of London), 2018. http://discovery.ucl.ac.uk/10040797/.
Full textAbstract:
Disulfide bonds represent an important target for site-selective protein modification, particularly via the strategy of functional re-bridging. Reduction of interchain disulfide bonds, followed by their re-bridging allows proteins to be functionalised in a site-selective manner whilst retaining the stability and integrity offered by the original bridge. This work describes the design and development of two distinct pyridazinedione-based technologies that, through the conduit of functional disulfide re-bridging, enable the synthesis of antibody – drug conjugates with hitherto unmet levels of control and homogeneity. As proteins often contain multiple disulfide bonds that are critical to conformation and stability, reagents that allow functional disulfide re-bridging without disulfide scrambling (non-native disulfide re-bridging) in multiple disulfide containing systems are critical for the success of this method. The first presented technology is a molecule that is capable of both reducing and re-bridging disulfide bonds, enabling a rapid and efficient one-reagent protocol for the functionalisation of disulfide containing proteins, moreover, it does so in such a way that native disulfide configuration is retained via a high local concentration effect. This novel pyridazinedione scaffold has been shown to functionalise a variety of therapeutically relevant proteins, including the widely used mAb HerceptinTM, enabling the synthesis of homogenous antibody – drug conjugates from a native mAb. Shifting focus from homogeneity to control over drug loading, the second presented technology is a single pyridazinedione-based molecule that contains four cysteine reactive centres and only one bioorthogonal reactive handle, which enables the generation of antibody conjugates with a loading of two modules. A loading of two is desirable for many reasons, especially in the context of large, hydrophobic payloads, which are increasingly popular for use in antibody-drug conjugates. A loading of two drugs per antibody has been shown to provide an optimal balance between efficacy and biophysical properties in many cases. A reliable method based on a native antibody scaffold without the use of enzymes or harsh oxidative conditions has hitherto not been achieved. The use of native antibodies has several advantages in terms of cost, practicality, accessibility and time. Thus, a novel, reliable method of furnishing antibody conjugates with a loading of two modules starting from a native antibody scaffold was developed.
8
Norville, Julie Erin 1980. "Synthetic scaffolds and protein assemblies for engineering applications." Thesis, Massachusetts Institute of Technology, 2004. http://hdl.handle.net/1721.1/28737.
Full textAbstract:
Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2004.Includes bibliographical references (p. 57-63).
S-layer proteins, which naturally self-assemble on the exterior of cells, provide an interesting basis for the creation of synthetic scaffolds. In this thesis, I created a plasmid which produces a recombinant form of a well characterized S layer protein, sbpA, which has a number of properties ideal for nanotechnology applications. I also explored purification of both the native and recombinant forms of sbpA. Together these preliminary studies are the first, necessary, steps towards quantitative generation of crystallization conditions and the ultimate modifications of the protein form for a wide variety of engineering applications.
by Julie Erin Norville.
S.M.
9
Hewitt, Sarah Helen. "Multivalent scaffolds for use as protein surface mimetics." Thesis, University of Leeds, 2017. http://etheses.whiterose.ac.uk/18027/.
Full textAbstract:
The development of ligands for protein surfaces to inhibit protein-protein interactions (PPI)s is challenging, as protein surfaces often lack the clefts and pockets associated with traditionally druggable targets like enzyme active sites. One way in which protein surfaces can be targeted is by the use of protein surface mimetics, whereby a multivalent scaffold is functionalised with many binding groups on its periphery in order to achieve high affinity protein recognition. One such scaffold is a ruthenium(II) tris (bipyridine)s (Ru(II)(bpy)3). The work in this thesis aimed to further develop these Ru(II)(bpy)3 protein surface mimetics; gaining information as to how they interact with proteins, looking at new ways of achieving high affinity protein surface recognition and the development of new applications for these molecules. In Chapter 2 an indepth study of the binding of two Ru(II)(bpy)3 complexes to a model protein, cytochrome c, is presented, looking at the thermodynamic and electrostatic contributions to binding as well as using protein NMR to elucidate the binding site. In Chapter 3 the development of dynamic combinatorial chemistry (DCC) scaffolds based on Ru(II)(bpy)3 complexes and tetraphenyl porphyrins was explored as a potential avenue for new receptor design, enabling the development of biologically compatible DCC systems, prime for protein ligand discovery. Chapter 4 presents another avenue for using the Ru(II)(bpy)3 complexes; using an array approach to discriminate between different protein.
10
Sharma, Rajan. "Protein-mediated patterning of DNA scaffolds for nanoscale electronics." Thesis, University of Leeds, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.521527.
Full text
11
Wilson, Rowan Amelia. "Approaches to spiropiperidine scaffolds : targeting G-protein coupled receptors." Thesis, University of Southampton, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.484849.
Full textAbstract:
Spiropiperidines have been labelled as 'privileged structures' in regard to their ability to provide ligands for G-protein coupled receptors (GPCRs). These GPCRs are a superfamily of cell regulators implicated in the control of a vast number of disorders that range from arthritis and atherosclerosis to anxiety and depression. The work in this thesis describes the synthesis of a novel spiro [1-benzofuran-2,4'piperidine]- 3-one scaffold, aimed at providing efficient access to lead compounds within the GPCR family. Derivatisation of the spiropiperidine core has been achieved both in single chemoselective reactions, and later in the c:omposition of multi-step telescope reaction matrices. In the latter case, the compounds synthesised exhibit physical characteristics consistent with guidelines for sound drug-like properties. Synthesis of an analogous indoline-spiropiperidine was also accomplished. Taking advantage of sulfur's ability to undergo neighbouring group participation led to the optimisation of a 5-elldo-tet cyclisation to afford another privileged spiropiperidine core with the potential to serve as a novel scaffold to target GPCRs.
12
Murphy, Natasha Susan. "Design and synthesis of novel proteomimetic scaffolds for the inhibition of protein-protein interactions." Thesis, University of Leeds, 2013. http://etheses.whiterose.ac.uk/5877/.
Full textAbstract:
Proteins are essential parts of living organisms and protein-protein interactions (PPIs) interactions mediate many essential regulatory pathways. As such, PPIs have been implicated in a number of diseased states, however, it is currently unclear how to effectively target them due to the relatively poorly defined surface at the protein interface. When PPIs are mediated by the binding of an α-helix, key interactions usually occur on non-adjacent residues, appearing on the same face of the α-helix, resulting in close interactions. The abundance of this secondary structure in proteins and its relative rigidity provide an ideal basis for the design of synthetic mimics. In this thesis, an account of the design strategies developed to address this problem is provided, and sets the work described herein in context. Previously, the Wilson group developed 3-O-alkylated oligobenzamide (3HABA) scaffolds as potential α-helix mimetics and suitably functionalised trimers were identified as micromolar inhibitors of the p53/hDM2 interaction. To understand more how to develop potent inhibitors of this interaction, a larger library was necessary. This was achieved by generating a library of 3HABA building blocks encompassing a range of natural and unnatural functionalities. Parallel to building the monomer library, development of a general solid phase methodology for deactivated anilines was essential. The course taken was to provide a solution for this challenging technical problem, and to identify the scope of the SPS methodology. Using the developed methodology, libraries of compounds targeting the p53/hDM2 and Mcl-1/NOXA B interactions were synthesised and their biophysical properties evaluated resulting in directions for future library development. To extend the approach to helix mediated PPIs involving more than one face, bifacial scaffolds designed at target the ER/coactivator complex are also described. This works discusses how molecular modelling, initial biophysical testing and docking studies led to second generation ligands with better in silico properties.
13
Karageorgiou, Vassilis. "Bioinductive protein-based scaffolds for human mesenchymal stem cells differentiation /." Thesis, Connect to Dissertations & Theses @ Tufts University, 2004.
Find full textAbstract:
Thesis (Ph. D.)--Tufts University, 2004.Adviser: David L. Kaplan. Submitted to the Dept. of Chemical and Biological Engineering. Includes bibliographical references. Access restricted to members of the Tufts University community. Also available via the World Wide Web;
14
Cheong, Jae Eun. "DEVELOPMENT OF SPIROLIGOMER SCAFFOLDS FOR INHIBITING HIV FUSION AND POROUS ORGANIC POLYMERS." Diss., Temple University Libraries, 2016. http://cdm16002.contentdm.oclc.org/cdm/ref/collection/p245801coll10/id/406966.
Full textAbstract:
ChemistryPh.D.
This research presents a new approach to creating large, complex molecules to carry out molecular recognition and catalytic functions mimicking biological proteins. Development of new therapeutics that bind protein surfaces and disrupt protein-protein interactions was first addressed targeting the envelope transmembrane protein in HIV-1, gp41. In this work, spiroligomer inhibitors of gp41 were designed and synthesized, and then the biochemical activity was tested. Rationally designed inhibitors were developed using computational modeling with the Molecular Operating Environment software (MOE). To build the desired molecular shape according to the design, C-2 alkylation of a bis-amino acid monomer was investigated to synthesize the higher degree of bis-amino acids with various reaction conditions for access to all possible diastereomers. Based on this design and synthetic methodology, a spiroligomer targeting gp41 was built by synthesizing each monomer and then linking them together by diketopiperazine (DKP). For the biological evaluation, the gp41-5 gene was transformed into E. coli and the protein was expressed, purified, and refolded for an in vitro binding test. A direct binding, fluorescence polarization assay was used to evaluate the binding affinity of the functionalized spiroligomer to the gp41-5 protein. Its antiviral activity was assessed in collaboration with the Chaiken lab at Drexel University. In addition, investigation into how the unique structures provided by the spiroligomer backbone allow for various uses, such as functionalized struts in porous organic polymers (POPs). In the large internal space of a POP, a nucleophilic, catalytic spiroligomer was installed to increase the reaction rate for the hydrolysis of methyl paraoxon (a neurotoxin G agent stimulant). Spiroligomers were designed and synthesized with backbone DMAP moieties, and the activity of these catalysts was analyzed in collaboration with the Hupp lab at Northwestern University.
Temple University--Theses
15
Soebbing, Samantha Lynn. "Incorporation of histidine-rich metal-binding sites onto small protein scaffolds implications for imaging, therapeutics, and catalysis /." Diss., University of Iowa, 2008. http://ir.uiowa.edu/etd/37.
Full text
16
Yildirim, Eda Didem Sun Wei Guceri S. I. "Plasma and protein surface functionalization for three-dimensional polycaprolactone tissue scaffolds /." Philadelphia, Pa. : Drexel University, 2010. http://hdl.handle.net/1860/3326.
Full text
17
Hou, Zengye. "Development of Novel Protein Kinase CK2 Inhibitors with Nitrogen Heterocyclic Scaffolds." 京都大学 (Kyoto University), 2013. http://hdl.handle.net/2433/174543.
Full text
18
Pettersson, Pär L. "Alpha-class glutathione transferases as steroid isomerases and scaffolds for protein redesign." Doctoral thesis, Uppsala University, Department of Biochemistry, 2002. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-2034.
Full textAbstract:
The present work focuses on the glutathione transferase (GST) Alpha-class enzymes, their characteristics as steroid isomerases and structural plasticity as malleable scaffolds for protein design. The GSTs are a family of detoxication enzymes that appears to have a wider variety of additional functions.
Kinetic steady-state parameters for human GST A1-1 with the steroid isomerase substrate Δ5-androstene-3,17-dione (AD), an intermediate in steroid hormone biosynthesis, were determined. It was established that GST A1-1 is a highly efficient steroid isomerase with a 30-fold higher catalytic efficiency, in terms of kcat/Km, than 3β-hydroxysteroid dehydrogenase/Δ5→4-isomerase, the enzyme regarded as the mammalian Δ5→4-isomerase in steroid hormone biosynthesis. Kinetic parameters were also determined for GST A2-2, GST A4-4 and the GST A1-1 mutant Y9F. From the dependency on pH of the kinetic parameters it was established that efficient catalysis requires glutathione (GSH) in its deprotonated form and it is suggested that the GSH-thiolate acts as a base in the catalysis of the Δ5→4-3-ketosteroid isomerase reaction.
GST A2-2 is a poor catalyst of the steroid isomerase reaction while GST A3-3 is highly efficient. Their catalytic efficiencies (kcat/Km) differ 5000-fold. Stepwise point mutations were performed to GST A2-2 in order to insert the amino acid residues from the active-site of GST A3-3 that distinguishes the two isoenzymes. The result was that GST A2-2 was redesigned to a highly efficient double-bond isomerase with both the catalytic constant (kcat) and catalytic efficiency (kcat/Km) in the same order as for GST A3-3. Furthermore, this was done by only exchanging amino-acid residues with first-sphere interactions, providing empirical proof-of principle for knowledge-based enzyme design.
Kinetic studies on GST A1-1 and a T68E mutant of GST A1-1 were also performed with a GSH analog lacking the g-glutamate a-carboxylate (dGSH), and using three different electrophilic substrates (AD; 1-chloro-2,4-dinitrobenzene, CDNB; 4-nitrocinnamaldehyde). Deletion of the a-carboxylate from the GSH glutamate had a severe impact on all reaction constants and it changed the rate-limiting step for the CDNB reaction as well as changed the pKa value for the enzyme-bound GSH thiol. The loss in activity caused by dGSH could in part be compensated by the T68E mutant contributing an enzyme-bound carboxylate instead.
The C-terminus of GST A1-1 is flexible and folds over the active site when the enzyme binds a substrate. Phenylalanine residues in the C-terminal end, known to interact with active-site residues tyrosine 9 and phenylalanine 10, were mutated to abolish those interactions. Studies of viscosity dependence for CDNB and AD with regard to kcat and kcat/Km showed that the dynamic C-terminal segment influence rate-determining steps for both the larger isomerase substrate, AD, as well as for the smaller conjugation substrate, CDNB.
19
Pettersson, Pär L. "Alpha-class glutathione transferases as steroid isomerases and scaffolds for protein redesign /." Uppsala : Acta Universitatis Upsaliensis, 2002. http://publications.uu.se/theses/91-554-5327-9/.
Full text
20
Gaiotto, Tiziano. "Engineering of coiled-coil protein scaffolds as innovative tools for biosensing applications." Doctoral thesis, Università degli studi di Trieste, 2009. http://hdl.handle.net/10077/3095.
Full textAbstract:
2007/2008A new generation of protein scaffolds is becoming a valid alternative tool to recombinant antibodies of biotechnological, medical and pharmaceutical applications, where strong affinity and specificity are required. They share with antibodies important features (target affinity and specificity), but they have also some improvements (smaller size of molecule, tolerance to modification of the framework and the recognition site restricted to few residues), that can be exploited for biosensing application in nanotechnological platforms. Nanotechnology has been played an increasingly important role in the development of biosensors, improving the intrinsic features of biodevices. In this thesis work, we analyzed the coiled-coil domain, a widely spread dimerization domain shared by several protein scaffolds, and involved in protein-protein interaction in both eukaryotic and prokaryotic cells. The analysis of the coiled-coil structure allows a de novo design of new peptides, namely E and K, that can dimerize as a E/K coiled-coil system: the dimerization feature and the stability of the interaction makes this system an ideal platform to build up functional and customizable biosensors. A characterization of the E/K interaction was performed by using the protein complementation assay (PCA), a useful biological method to investigate the interaction between protein partners. With this in vivo method, we corroborate the interaction features determinate with circular dichroism, and we demonstrated that E and K coils effectively represent a protein scaffold, able to tolerate amino acid substitutions without altering its main structure. In addition, we create two libraries of K mutant coils, randomizing the peptide sequence, and with PCA we selected new K binders (Kran 5.17 and Krd F8) that showed a comparable interaction activity with the E-coil in preliminary in vitro tests. In the last part of this work, we generate a library of a new scaffold molecule (the single chain E-K) capable to bind small molecules as a single protein product containing both domains. Using the phage display selection system, we isolated scsE-K that can bind our analyte (the caffeine) with high specificity. This new molecules can be a powerful tool for analytical and biomedical applications.
XXI Ciclo
1980
21
Luisi, Immacolata. "Identification of novel protein scaffolds for small molecules binding and for catalysis." Doctoral thesis, Università degli studi di Trieste, 2012. http://hdl.handle.net/10077/7364.
Full textAbstract:
2010/2011Protein scaffolds are stable structures capable to recognize and bind, in different conditions, small guest molecules. They are proteins with known conformation which can be used and modified for the construction of variants. The goal of this work is the identification of peptide-based artificial receptors or catalysts. To this purpose, we have considered two different protein motifs to generate new scaffolds: a synthetic E/K coiled-coil domain, and one of the binding sites of the natural protein Human serum albumin. In order to generate stable peptide hosts, we developed peptide libraries to be selected for both properties, adopting two different approaches: RANDOM mutagenesis and SITE-DIRECTED mutagenesis.
XXIV Ciclo
1985
22
Takeuchi, Tomoki. "Development of Kinesin Spindle Protein Inhibitors with Fused-indole and Diaryl Amine Scaffolds." 京都大学 (Kyoto University), 2014. http://hdl.handle.net/2433/188736.
Full text
23
Moaiyed, Baharlou Sogol. "ELECTRO-PROCESSED SOY PROTEIN-BASED SCAFFOLDS FOR SKIN TISSUE ENGINEERING AND WOUND HEALING." Diss., Temple University Libraries, 2017. http://cdm16002.contentdm.oclc.org/cdm/ref/collection/p245801coll10/id/480857.
Full textAbstract:
BioengineeringPh.D.
Wound healing is a complex, dynamic process that needs to be orchestrated in an orderly manner, involving different cell types, cytokines, and growth factors as well as extracellular matrix (ECM) interactions to avoid complications (e.g. scarring, chronic wounds, and impaired functionality). Current strategies for management of full thickness wounds are limited by material expense, limited availability of allograft tissue, autograft donor site morbidity, and even ethical problems associated with animal derived matrix components. To avoid cost, ethical, and even safety issues, there is renewed interest in using natural ingredients to construct advanced scaffolds for wound healing. At the cutting edge of the new field of regenerative medicine, demonstrated here is a scaffold based on soy protein. The second generation of soy based scaffold is constructed at the nanometer level to provide an ideal environment for cell interaction, growth, and development through a modified process termed ‘electro-processing’. The electro-processing developed here uses only water, low pressure air, and a very low current high voltage source improving not just the safety of the product, but also improving the manufacturing process. The proteins have also been indicated to release pro-healing cue to the surrounding tissue. Processing the natural soy protein to improve solubility has even enabled the new scaffolds to be generated without any harmful solvent and at rates many times faster than those previously demonstrated and at increased quality. The novel soy based electro-processed bioactive wound fabrics have been demonstrated successfully in vitro and in preliminary in vivo testing. These scaffolds have shown to be biocompatible, degradable and to improve healing quality compared to Tegaderm dressing in a rat full thickness excision model.
Temple University--Theses
24
Andersson, Linda K. "Exploring protein functionalisation : the site-selective modification of designed four-helix bundle scaffolds /." Göteborg : Göteborg university, 2001. http://catalogue.bnf.fr/ark:/12148/cb40110915c.
Full text
25
Meinel, Lorenz. "Engineering bone and cartilage like tissue using human mesenchymal stem cells and protein scaffolds /." Aachen : Shaker, 2005. http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&doc_number=013174123&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA.
Full text
26
Lee, Min. "Biomimetic architectural design of scaffolds and modulation of protein delivery for intestinal tissue engineering." Diss., Restricted to subscribing institutions, 2007. http://proquest.umi.com/pqdweb?did=1459913181&sid=1&Fmt=2&clientId=1564&RQT=309&VName=PQD.
Full text
27
Zeng, Like. "SELF-ASSEMBLY OF SILK-ELASTINLIKE PROTEIN POLYMERS INTO THREE-DIMENSIONAL SCAFFOLDS FOR BIOMEDICAL APPLICATIONS." Diss., The University of Arizona, 2014. http://hdl.handle.net/10150/325002.
Full textAbstract:
Production of brand new protein-based materials with precise control over the amino acid sequences at single residue level has been made possible by genetic engineering, through which artificial genes can be developed that encode protein-based materials with desired features. As an example, silk-elastinlike protein polymers (SELPs), composed of tandem repeats of amino acid sequence motifs from Bombyx mori (silkworm) silk and mammalian elastin, have been produced in this approach. SELPs have been studied extensively in the past two decades, however, the fundamental mechanism governing the self-assembly process to date still remains largely unresolved. Further, regardless of the unprecedented success when exploited in areas including drug delivery, gene therapy, and tissue augmentation, SELPs scaffolds as a three-dimensional cell culture model system are complicated by the inability of SELPs to provide the embedded tissue cells with appropriate biochemical stimuli essential for cell survival and function. In this dissertation, it is reported that the self-assembly of silk-elastinlike protein polymers (SELPs) into nanofibers in aqueous solutions can be modulated by tuning the curing temperature, the size of the silk blocks, and the charge of the elastin blocks. A core-sheath model was proposed for nanofiber formation, with the silk blocks in the cores and the hydrated elastin blocks in the sheaths. The folding of the silk blocks into stable cores - affected by the size of the silk blocks and the charge of the elastin blocks - plays a critical role in the assembly of silk-elastin nanofibers. The assembled nanofibers further form nanofiber clusters on the microscale, and the nanofiber clusters then coalesce into nanofiber micro-assemblies, interconnection of which eventually leads to the formation of three-dimensional scaffolds with distinct nanoscale and microscale features. SELP-Collagen hybrid scaffolds were also fabricated to enable independent control over the scaffolds' biochemical input and matrix stiffness. It is reported herein that in the hybrid scaffolds, collagen provides essential biochemical cues needed to promote cell attachment and function while SELP imparts matrix stiffness tunability. To obtain tissue-specificity in matrix stiffness that spans over several orders of magnitude covering from soft brain to stiff cartilage, the hybrid SELP-Collagen scaffolds were crosslinked by transglutaminase at physiological conditions compatible for simultaneous cell encapsulation. The effect of the increase in matrix stiffness induced by such enzymatic crosslinking on cellular viability and proliferation was also evaluated using in vitro cell assays.
28
Rashvand, Sarvenaz Nina. "SOY PROTEIN ISOLATE (SPI) “GREEN” SCAFFOLDS WITH ORIENTED MICROCHANNELS FOR APPLICATIONS IN SPINAL CORD INJURY." Master's thesis, Temple University Libraries, 2015. http://cdm16002.contentdm.oclc.org/cdm/ref/collection/p245801coll10/id/344067.
Full textAbstract:
BioengineeringM.S.
Every year, accidents, falls, sport injuries and other incidents cause thousands of people to suffer spinal cord injury (SCI). In the United States alone, it is estimated that the number of Americans that live with SCI is around 259,000, with 12,000 new cases that happen annually (1). These injuries lead to spinal cord damages expressed by massive nerve tract degeneration followed by neurological loss, paralysis and disabilities. Therapy of SCI patients with non-steroidal anti-inflammatory drugs (NSAIDs) help in diminishing secondary injury and lessen pain and swelling. However these drugs do not promote tissue repair. Therefore there is an unmet clinical need to develop technologies and therapeutic strategies that compensate loss of neuronal tissue, support and facilitate reestablishment of nerve tracks connectivity in the injured spinal cord. Recent progress in nerve regeneration indicates that a tissue engineering approach using soft tissue scaffolds, stem cells and neurotrophins, can lead to a partial therapy in animal models of SCI. Bioengineered scaffolds prepared by freeze casting technology provide an experimental tool for guidance of regenerating neuronal tracts and/or axons and therefore are useful for regeneration of injured spinal cord. In this engineering approach for scaffold preparation, temperature controlled directional solidification of an aqueous polymer(s) solution creates channels of different diameters that can direct axonal outgrowth of neurons populating the scaffold. In a previous study from our laboratory, such scaffolds promoted differentiation of neurons, a process facilitated by co-population of the scaffold’s channels with endothelial cells. “Green” plant proteins, such as soybean proteins, are becoming an attractive alternative source of natural polymers for a variety of biomedical applications including scaffold fabrication for neuronal tissue regeneration. In the present study, we developed a second generation of improved, microchanneled composite scaffolds from gelatin and soy protein isolate cross-linked with genipin (2 w/v %, 0.5 w/v %, 1 w/v %, respectively). The fabrication of these scaffolds by a controlled freeze drying technique, their mechanical properties (stiffness, ~3-4 kPa) as well as their uniform longitudinal channels of a diameter of ~30-55 µm is described. Preliminary biocompatibility experiments in 2D and 3D using the above mentioned scaffolds populated with either undifferentiated PC12 cells or nerve growth factor differentiated PC12 cells indicated partial biocompatibility of the scaffolds for neuronal growth. Improving the biocompatibility of these composite scaffolds is under investigation in our laboratory.
Temple University--Theses
29
Yan, Hongji. "New insights into principles of scaffolds design for bone application." Doctoral thesis, Uppsala universitet, Polymerkemi, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-308318.
Full textAbstract:
This thesis presents deeper insights into bone applicable biomaterials’ design. Poor affinity of BMP-2 towards scaffolds required supra-physiological dose administration. Though molecules containing sulfate could sustain BMP-2 release, side effects occurred due to BMP-2 supra-dose, or these sulfate-containing biomolecules. Improved affinity between BMP-2 and scaffolds was first witnessed by using an acidic carrier (paper I). Hyaluronic acid (HA) hydrazone derived hydrogels having a pH of 4.5-loaded BMP-2 showed sustained release of bioactive BMP-2 in vitro and enhanced bone formation in vivo, while pH 7 HA hydrogels showed Fickian behavior and less bone formation in vivo. Computational evaluation revealed stronger electrostatic interactions between BMP-2, and HA were predominant at pH 4.5, whereas, weaker Van der Waals interactions played a key role at pH 7. During the pre-bone formation phase, endogenous cell responses to pH 4.5 and 7 with or without BMP-2 were investigated. HA hydrogels exhibited extraordinary biocompatibility and recruitment of neutrophils, monocytes, macrophages and stromal cells regardless of hydrogels’ pH and BMP-2 presence. The different inflammatory responses to HA hydrogels were observed (Appendix). Thiol derivatives can cleave the disulfide bond of BMP-2 to generate inactive monomeric BMP-2. In paper II, thiol-acrylate chemistry-based HA hydrogels (HA-SH) were compared to hydrazone-based HA hydrogels as BMP-2 carriers. Thiol modified HA disrupted BMP-2 integrity and bioactivity. HA-SH hydrogels with BMP-2 exhibited less bioactive BMP-2 release in vitro and induced less bone formation in vivo. Accumulated evidence has shown great osteogenic potential of lithium ions (Li). In paper III, we coordinated Li onto HA-PVA hydrazone hydrogels (Li-gel); Li-gel enhanced 3D cultured hMSCs osteogenic differentiation and induced higher bone formation in CAM defect model. Instead of BMP-2 protein, delivery of BMP-2-coding-plasmid can produce BMP-2 over a long term at a closer physiological level. Yet, efficient gene delivery reagents are needed. In paper IV, two novel gene delivery nanoplexes were developed by post coating DNA-nanoplexes with chondroitin sulfate (CS). To ensure the stability, aldehyde-modified CS (CS-CHO) reacted with free amines of pDNA/PEI complexes. We provided first evidence that CS-CHO coated nanoplexes controlled the release from endosomes, which is essential for higher transfection efficiency.
30
Li, Jingxuan. "EVALUATION OF BONE MORPHOGENETIC PROTEIN-2 RELEASE FROM KERATIN SCAFFOLDS IN VITRO AND IN VIVO." Miami University / OhioLINK, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=miami1462919774.
Full text
31
Hulsart, Billström Gry. "Bone Regeneration with Cell-free Injectable Scaffolds." Doctoral thesis, Uppsala universitet, Ortopedi, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-234846.
Full textAbstract:
Bone is a remarkable multifunctional tissue with the ability to regenerate and remodel without generating any scar tissue. However, bone loss due to injury or diseases can be a great challenge and affect the patient significantly. Transplanting bone graft from one site in the patient to the site of fracture or bone void, i.e. autologous bone grafting is commonly used throughout the world. The transplanted bone not only fills voids, but is also bone inductive, housing the particular cells that are needed for bone regeneration. Nevertheless, a regenerative complement to autograft is of great interest and importance because the benefits from an off-the-shelf product with as good of healing capacity as autograft will circumvent most of the drawbacks with autograft. With a regenerative-medicine approach, the use of biomaterials loaded with bioactive molecules can avoid donor site morbidity and the problem of limited volume of material. Two such regenerative products that utilize bone morphogenetic protein 7 and 2 have been used for more than a decade in the clinic. However, some severe side effects have been reported, such as severe swelling due to inflammation and ectopic bone formation. Additionally, the products require open surgery, use of supra physiological doses of the BMPs due to poor localization and retention of the growth factors. The purpose of this thesis was to harness the strong inductive capability of the BMP-2 by optimizing the carrier of this bioactive protein, thereby minimizing the side effects that are associated with the clinical products and facilitating safe and localized bone regeneration at the desired site. We focused on an injectable hyaluronan-based carrier. The strategy was to use the body’s own regenerative pathway to stimulate and enhance bone healing in a manner similar to the natural bone-healing process. The hyaluronan-based carrier has a similar composition to the natural extracellular matrix and is degraded by resident hyaluronidase enzymes. Earlier studies have shown a more controlled release and improved mechanical properties when adding a weight of 25 percent of hydroxyapatite, a calcium phosphate that constitutes the inorganic part of the bone matrix. In Paper I, the aim was to improve the carrier by adding other forms of calcium phosphate. The results indicated that the bone formation was enhanced when using nano-sized hydroxyapatite. We wished to further develop the carrier system but were lacking an animal model with high output and easy access. We also wanted to provide paired data and were committed to the 3 Rs of refinement, reduction and replacement. To meet these challenges, we developed and refined an animal model, and this is described in Paper II. In Paper III, we characterized and optimized the handling properties of the carrier. In Paper IV, we discovered the importance of crushing the material, thus enhancing permeability and enlarging the surface area. In Paper V, we sought to further optimize biomaterial properties of the hydrogel through covalently bonding of bisphosphonates to the hyaluronan hydrogel. The results demonstrated exceptional retention of the growth factor BMP-2. In Paper VI, the in vivo response related to the release of the growth factor was examined by combining a SPECT/PET/µCT imaging method to visualize both the retention of the drug, and the in-vivo response in terms of mineralization.
32
Hulsart, Billström Gry. "Bone Regeneration with Cell-free Injectable Scaffolds." Doctoral thesis, Uppsala universitet, Ortopedi, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-310312.
Full textAbstract:
Bone is a remarkable multifunctional tissue with the ability to regenerate and remodel without generating any scar tissue. However, bone loss due to injury or diseases can be a great challenge and affect the patient significantly. Autologous bone grafting is commonly used throughout the world. Autograft both fills the void and is bone inductive, housing the particular cells that are needed for bone regeneration. However, a regenerative complement to autograft is of great interest as the use of biomaterials loaded with bioactive molecules can avoid donor site morbidity and the problem of a limited volume of material. Two such regenerative products that utilise bone morphogenetic protein (BMP)-7 and -2 have been used for more than a decade clinically. Unfortunately, several side effects have been reported, such as severe swelling due to inflammation and ectopic bone formation. Additionally, the products require open surgery and use of supra physiological doses of the BMPs due to poor localisation and retention of the growth factor. The purpose of this thesis was to harness the strong inductive capacity of the BMP-2 by optimising the carrier of this bioactive protein, thereby minimising the side effects that are associated with the clinical products and facilitating safe and localised bone regeneration. We focused on an injectable hyaluronan-based carrier developed through polymer chemistry at the University of Uppsala. The strategy was to use the body’s own regenerative pathway to stimulate and enhance bone healing in a manner similar to the natural bone-healing process. The hyaluronan-based carrier has a similar composition to the natural extracellular matrix and is degraded by resident enzymes. Earlier studies have shown improved properties when adding hydroxyapatite, a calcium phosphate that constitutes the inorganic part of the bone matrix. In Paper I, the aim was to improve the carrier by adding other forms of calcium phosphate. The results indicated that bone formation was enhanced when using nano-sized hydroxyapatite. In Paper II, we discovered the importance of crushing the material, thus enhancing permeability and enlarging the surface area. We wished to further develop the carrier system, but were lacking an animal model with relatively high throughput, facilitated access, paired data, and we were also committed to the 3Rs of refinement, reduction, and replacement. To meet these challenges, we developed and refined an animal model, and this is described in Paper III. In Paper IV, we sought to further optimise the biomaterial properties of the hydrogel through covalent bonding of bisphosphonates to the hyaluronan hydrogel. This resulted in exceptional retention of the growth factor BMP-2. In Paper V, SPECT/PET/µCT was combined as a tri-modal imaging method to allow visualisation of the biomaterial’s in situ action, in terms of drug retention, osteoblast activity and mineralisation. Finally, in Paper VI the correlation between existing in vitro results with in vivo outcomes was observed for an array of biomaterials. The study identified a surprisingly poor correlation between in vitro and in vivo assessment of biomaterials for osteogenesis.
33
Vahdati, Leïla. "Synthesis of peptidomimetics containing bifunctional diketoopiperazine scaffolds and their evaluation as modulators of amyloid-B peptide oligomerization." Thesis, Paris 11, 2015. http://www.theses.fr/2015PA114811/document.
Full textAbstract:
La formation des agrégats des peptides et des protéines par l'interaction de feuillets β a de plus en plus attiré l'attention car elle se produit dans de nombreuses maladies humaines généralisées, telles que la sclérose latérale amyotrophique (SLA), la maladie d'Alzheimer (AD), la maladie de Parkinson (PD), les maladies à prions et la maladie de Huntington (HD). La maladie d'Alzheimer est la forme la plus courante de démence qui provoque la perte de la mémoire chez les personnes âgées. En 2013, il y avait 35 millions de personnes souffrant de AD à travers le monde, un chiffre qui devrait doubler d'ici 2050. Etiologiquement ces maladies se manifestent par des dépôts anormaux de protéines, y compris les plaques neuritiques séniles (PNS) et les dégénérescences neurofibrillaires (DNF). L'accumulation extracellulaire d'agrégats insolubles de la protéine β-amyloide (A) conduit à la formation de plaques séniles, tandis que DNF se produisent à l’intérieur des neurones et sont composés par des filaments hélicoidaux appariés de la protéine tau hyperphosphorylée. Les peptides A sont produits en tant que monomères solubles et subissent l'oligomérisation et la formation de fibrilles amyloides par un processus qui n’a pas été complètement clarifié. Il est suggéré que les peptides Aß solubles jouent un rôle important dans la croissance neuronale, la survie et la modulation synaptique, tandis que les oligomères et fibrilles ont des propriétés toxiques. Une nouvelle stratégie thérapeutique vers la prévention ou le traitement de maladies associées à des structures -feuillet et, en particulier, AD, est représentée par la synthèse de mimes de -brins qui peuvent antagoniser la formation ou la reconnaissance de feuillet ß. En fait, dans la maladie d’Alzheimer, le processus d'agrégation des protéines implique une transition de la structure secondaire non ordonnée/α-hélice à une conformation riche en feuillet β, conduisant à la formation de feuillet croisés. Sur la base des quelques données publiées récemment sur des mimes d’épingles et en particulier des structures macrocycliques de Nowick, comme inhibiteurs de l'agrégation des protéines, nous avons supposé qu’une pré-structuration des molécules peptidomimétiques pourrait augmenter leur affinité pour les peptides A et donc augmenter leur activité inhibitrice de l'agrégation. Notre conception vers un mime d’épingle stable, qui pourrait interagir et éventuellement agir en tant que ligand de feuillets β et inhibiteur de l'agrégation, implique l’assemblage d’une dicétopipérazine bifonctionnelle en tant que scaffold , d’un brin peptidomimétique pour stabiliser la formation de feuillets β et enfin d’une séquence peptidique convenable pour la liaison à la protéine. Ces molécules ont montré une interaction avec le peptide Aβ1-42 ainsi qu’une modulation de la cinétique d’agrégationThe formation of peptide and protein aggregates through the interaction of β-sheets has increasingly drawn attention since it occurs in many widespread human diseases, such as amyotrophic lateral sclerosis (ALS), Alzheimer’s disease (AD), Parkinson's disease (PD), prion diseases, and Huntington's disease (HD). Alzheimer’s disease is the most common form of dementia that causes memory loss in the elderly. In 2013, 35 million people were afflicted with AD worldwide, a number expected to double by 2050. Etiologically, the most common findings are abnormal protein deposits, including senile neuritic plaques (SNPs) and neurofibrillary tangles (NFTs). The extracellular accumulation of insoluble aggregates of β-amyloid protein (Aβ) leads to the formation of senile plaques, whereas NFTs occur intracellulary and are composed of paired helical filaments of hyperphosphorylated tau protein. Aβ peptides are produced as soluble monomers and undergo oligomerization and amyloid fibril formation via an unclear process. It is suggested that soluble A peptides play an important role in neuronal growth, survival, and synaptic modulation, while the oligomers and fibrils have toxic properties. Mimicking -strands to antagonize -sheet formation or recognition represent a new therapeutic strategy toward the prevention or treatment of diseases associated with -sheet structures such as AD. In this pathology, protein aggregation process involves a secondary structure transition from unordered/α-helix to a β-sheet rich conformation, leading to cross β-sheet structure formation. Based on the few recent published data on β-hairpin mimics, in particular on the macrocyclic structures of Nowick, as inhibitors of protein aggregation, we hypothesized that pre-structuring the peptidomimetic molecules might increase their affinity for Aβ peptides and thus increase their aggregation inhibitory activity. Our design towards a stable β-hairpin mimic (Figure 1), which could interact and eventually act as a β-sheet binder and aggregation inhibitor, involved assembling of a bifunctional diketopiperazine scaffold , a peptidomimetic strand to stabilize the formation of β-sheets and finally a suitable peptide sequence for binding to the aggregating protein. These molecules were shown to interact with the native Aβ1-42 peptide and modulate the kinetics of aggregation
34
Meinel, Lorenz [Verfasser]. "Engineering Bone and Cartilage-Like Tissue Using Human Mesenchymal Stem Cells and Protein Scaffolds / Lorenz Meinel." Aachen : Shaker, 2005. http://d-nb.info/1181620252/34.
Full text
35
Schäfer, Gesa [Verfasser]. "Development of helix-mimetic scaffolds as potential disruptors of the interaction between protein kinase A and A kinase anchoring proteins / Gesa Schäfer." Berlin : Freie Universität Berlin, 2012. http://d-nb.info/1029937028/34.
Full text
36
Kutikov, Artem B. "Amphiphilic Degradable Polymer/Hydroxyapatite Composites as Smart Bone Tissue Engineering Scaffolds: A Dissertation." eScholarship@UMMS, 2014. https://escholarship.umassmed.edu/gsbs_diss/755.
Full textAbstract:
Over 600,000 bone-grafting operations are performed each year in the United States. The majority of the bone used for these surgeries comes from autografts that are limited in quantity or allografts with high failure rates. Current synthetic bone grafting materials have poor mechanical properties, handling characteristics, and bioactivity. The goal of this dissertation was to develop a clinically translatable bone tissue engineering scaffold with improved handling characteristics, bioactivity, and smart delivery modalities. We hypothesized that this could be achieved through the rational selection of Food and Drug Administration (FDA) approved materials that blend favorably with hydroxyapatite (HA), the principle mineral component in bone. This dissertation describes the development of smart bone tissue engineering scaffolds composed of the biodegradable amphiphilic polymer poly(D,L-lactic acid-co-ethylene glycol-co- D,L-lactic acid) (PELA) and HA. Electrospun nanofibrous HA-PELA scaffolds exhibited improved handling characteristics and bioactivity over conventional HApoly( D,L-lactic acid) composites. Electrospun HA-PELA was hydrophilic, elastic, stiffened upon hydration, and supported the attachment and osteogenic differentiation of rat bone marrow stromal cells (MSCs). These in vitro properties translated into robust bone formation in vivo using a critical-size femoral defect model in rats. Spiral-wrapped HA-PELA scaffolds, loaded with MSCs or a lowdose of recombinant human bone morphogenetic protein-2, templated bone formation along the defect. As an alternate approach, PELA and HA-PELA were viii rapid prototyped into three-dimensional (3-D) macroporous scaffolds using a consumer-grade 3-D printer. These 3-D scaffolds have differential cell adhesion characteristics, swell and stiffen upon hydration, and exhibit hydration-induced self-fixation in a simulated confined defect. HA-PELA also exhibits thermal shape memory behavior, enabling the minimally invasive delivery and rapid (>3 sec) shape recovery of 3-D scaffolds at physiologically safe temperatures (~ 50ºC). Overall, this dissertation demonstrates how the rational selection of FDA approved materials with synergistic interactions results in smart biomaterials with high potential for clinical translation.
37
Kutikov, Artem B. "Amphiphilic Degradable Polymer/Hydroxyapatite Composites as Smart Bone Tissue Engineering Scaffolds: A Dissertation." eScholarship@UMMS, 2011. http://escholarship.umassmed.edu/gsbs_diss/755.
Full textAbstract:
Over 600,000 bone-grafting operations are performed each year in the United States. The majority of the bone used for these surgeries comes from autografts that are limited in quantity or allografts with high failure rates. Current synthetic bone grafting materials have poor mechanical properties, handling characteristics, and bioactivity. The goal of this dissertation was to develop a clinically translatable bone tissue engineering scaffold with improved handling characteristics, bioactivity, and smart delivery modalities. We hypothesized that this could be achieved through the rational selection of Food and Drug Administration (FDA) approved materials that blend favorably with hydroxyapatite (HA), the principle mineral component in bone. This dissertation describes the development of smart bone tissue engineering scaffolds composed of the biodegradable amphiphilic polymer poly(D,L-lactic acid-co-ethylene glycol-co- D,L-lactic acid) (PELA) and HA. Electrospun nanofibrous HA-PELA scaffolds exhibited improved handling characteristics and bioactivity over conventional HApoly( D,L-lactic acid) composites. Electrospun HA-PELA was hydrophilic, elastic, stiffened upon hydration, and supported the attachment and osteogenic differentiation of rat bone marrow stromal cells (MSCs). These in vitro properties translated into robust bone formation in vivo using a critical-size femoral defect model in rats. Spiral-wrapped HA-PELA scaffolds, loaded with MSCs or a lowdose of recombinant human bone morphogenetic protein-2, templated bone formation along the defect. As an alternate approach, PELA and HA-PELA were viii rapid prototyped into three-dimensional (3-D) macroporous scaffolds using a consumer-grade 3-D printer. These 3-D scaffolds have differential cell adhesion characteristics, swell and stiffen upon hydration, and exhibit hydration-induced self-fixation in a simulated confined defect. HA-PELA also exhibits thermal shape memory behavior, enabling the minimally invasive delivery and rapid (>3 sec) shape recovery of 3-D scaffolds at physiologically safe temperatures (~ 50ºC). Overall, this dissertation demonstrates how the rational selection of FDA approved materials with synergistic interactions results in smart biomaterials with high potential for clinical translation.
38
De, Raffele Daria. "Computational studies of the Retro-Aldol reaction catalyzed by different protein scaffolds. Towards the redesign of an improved enzyme." Doctoral thesis, Universitat Jaume I, 2022. http://dx.doi.org/10.6035/14122.2022.709183.
Full textAbstract:
The main objective of this dissertation was to investigate the structure-function relationship in different designed Retro-Aldolases, to understand not only their catalytic efficiency but to provide information to design a new more efficient enzyme. In particular, the first step of the project was to investigate and analyze the reaction mechanism of two previously published de novo Retro-Aldolases (RA95.5-5 and RA95.5-8F) and one catalytic antibody (33F12). The free-energy landscape of the whole chemical process was explored through statistical methods with multiscale quantum mechanics / molecular mechanics (QM/MM) potentials, in terms of the PMF. The agreement between the theoretical predictions and the experimental data allowed to carry out deeper analysis, exploring the structural function and the interaction with the residues. The comparative analysis of the data generated from the computational simulations on the three protein scaffolds allowed to suggest a new variant of de novo Retro-Aldolase with a predicted higher catalytic efficiency.Programa de Doctorat en Química Teòrica i Modelització Computacional
39
Takahashi, Yoshitake. "MATERIAL DESIGN OF BIODEGRADABLE CELL SCAFFOLDS FOR CONTROLLED RELEASE OF BONE MORPHOGENETIC PROTEIN-2 AND THE BONE REGENERATION POTENTIAL." Doctoral thesis, 京都大学 (Kyoto University), 2007. http://hdl.handle.net/2433/44145.
Full textAbstract:
学位授与年月日: 2007-07-23 ; 学位の種類: 新制・論文博士 ; 学位記番号: 論工博第3968号GENERAL INTRODUCTION: Bone reconstruction is a clinically important procedure to treat bone defects and has been widely tried by different methods. Basically, bone has the inherent ability to spontaneously repair itself for the bone fracture of small size. However, such a self-repairing cannot always be expected for large-size defects that are caused by trauma, tumor resection, spinal arthodesis, and congenital abnormalities. This situation often happens clinically and the therapeutic demand has been being increased recently [1]. Autograft, which is considered to be a gold standard as bone substitutes, is applied to the defect site because it provides a suitable environment for cell attachment, proliferation, and differentiation for bone regeneration [2]. However, it has several disadvantages, such as the limited donor supply, potential complications with chronic pain at the donor sites [3, 4]. On the other hand, allograft is being performed clinically [2], but the rate of graft integration into the surrounding natural bone is lower than that of autograft. In addition, it is necessary for the allograft to consider a risk of disease transmission and postoperative complications due to the tissue rejection [4, 5]. Therefore, under these circumstances, as the substitute for the bone grafts, the biomaterials of metals and ceramics have been investigated and developed. Although the above problems may be cleared, they have other disadvantages, such as the lack of biodegradability under physiological conditions and the limited processability [6]. Especially, metals show poor integration property to the bone tissue at the implantation site compared with the autograft and allograft although they provide mechanical support [7]. Different from artificial biomaterials, one of the important advantages for the bone graft is to positively accelerate osteoconduction and osteoinduction. As one trial to tackle and improve the points to be resolved, bone tissue engineering has been attracted much attention as a new therapeutic technology [8-11]. The basic idea is to provide key cells the local environment suitable to promote their proliferation and differentiation for the induction of tissue regeneration. (...) In summary, this thesis describes the feasibility of gelatin-based scaffolds in the controlled release carrier of BMP-2 and the three-dimensional matrix of MSC for osteogenic differentiation. It is concluded that this material design of scaffold is promising to effectively induce bone regeneration based on tissue engineering.
京都大学
0048
新制・論文博士
博士(工学)
乙第12103号
論工博第3968号
新制||工||1418(附属図書館)
UT51-2007-M983
(主査)教授 田畑 泰彦, 教授 岩田 博夫, 教授 木村 俊作
学位規則第4条第2項該当
Doctor of Engineering
Kyoto University
DFAM
40
Sheremet, Andriy. "Bioinspired polyethersulfone-based hollow fiber membranes as the scaffolds in renal assist device for protein-bound toxins removal from blood." Master's thesis, Faculdade de Ciências e Tecnologia, 2014. http://hdl.handle.net/10362/13308.
Full textAbstract:
Dissertation for obtaining the Master degree in Membrane EngineeringErasmus Mundus Master in Membrane Engineering
Using bioartificial kidney is the promising approach for removal of non-dializable, proteinbound uremic toxins, which are responsible for high mortality and morbidity in treating kidney failure related conditions. Additionaly, bioartificial kidney device could perform the physiological roles of the kidney such as metabolic replacement, endocrine function and immunomodulation. In the current work two commercial polyethersulfone-based membranes, Gambro HCO 1100 and Membrana MicroPES TF10 used in haemofiltration and plasma separation applications respectively were investigated. To provide adequate cytocompatibility of the membrane biomimetic, biomimetic double layer coating was developed. First, the membranes were coated with musselinspired synthetic polydopamine film, following with the coating of Collagen Type IV. Transport properties of the coated and native membranes were investigated. Increase in pure water permeability of the coated HCO 1100 membranes was observed. Membrane surface hydrophilization was assumed as the major factor responsible for the effect. Membrane permeabilities for bovine serum albumin and immunoglobulin G solutions were studied. Significant increase in protein rejection was observed for double coated HCO 1100 membranes with small or no effect of the double coated MicroPES TF10 membranes. Next, formation of confluent monolayers of the renal epithelial cells on the membrane scaffolds was studied. Cell seeding strategy was developed and two seeding conditions were tested. Specifically, the cells were allowed to adhere to the biomimetic membranes passively, and the negative pressure was applied to facilitate cell adhesion. After cultivation in semi-batch conditions the monolayer formation was examined. Confluent monolayers were observed for the conditions with passive cell adherence for the both membranes. Cell contacts formation and cell polarization were confirmed with the staining for ZO-1 protein. Applying the pressure to facilitate cell adhesion, on the contrary, resulted in the loss of cell ability to form functional monolayers.
EM3E Master is an Education Programme supported by the European Commission, the European Membrane Society (EMS), the European Membrane House (EMH), and a large international network of industrial companies, research centres and universities
41
Caves, Jeffrey Morris. "Architecturally defined scaffolds from synthetic collagen and elastin analogues for the fabrication of bioengineered tissues." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2008. http://hdl.handle.net/1853/31731.
Full textAbstract:
Thesis (Ph.D)--Biomedical Engineering, Georgia Institute of Technology, 2009.Committee Chair: Elliot L. Chaikof; Committee Member: Ajit Yoganathan; Committee Member: Larry McIntire; Committee Member: Marc Levenston; Committee Member: Mark Allen. Part of the SMARTech Electronic Thesis and Dissertation Collection.
42
Ruiz-Gómez, Gloria, John C. Hawkins, Jenny Philipp, Georg Künze, Robert Wodtke, Reik Löser, Karim Fahmy, and M. Teresa Pisabarro. "Rational Structure-Based Rescaffolding Approach to De Novo Design of Interleukin 10 (IL-10) Receptor-1 Mimetics." Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2017. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-215877.
Full textAbstract:
Tackling protein interfaces with small molecules capable of modulating protein-protein interactions remains a challenge in structure-based ligand design. Particularly arduous are cases in which the epitopes involved in molecular recognition have a non-structured and discontinuous nature. Here, the basic strategy of translating continuous binding epitopes into mimetic scaffolds cannot be applied, and other innovative approaches are therefore required. We present a structure-based rational approach involving the use of a regular expression syntax inspired in the well established PROSITE to define minimal descriptors of geometric and functional constraints signifying relevant functionalities for recognition in protein interfaces of non-continuous and unstructured nature. These descriptors feed a search engine that explores the currently available three-dimensional chemical space of the Protein Data Bank (PDB) in order to identify in a straightforward manner regular architectures containing the desired functionalities, which could be used as templates to guide the rational design of small natural-like scaffolds mimicking the targeted recognition site. The application of this rescaffolding strategy to the discovery of natural scaffolds incorporating a selection of functionalities of interleukin-10 receptor-1 (IL-10R1), which are relevant for its interaction with interleukin-10 (IL-10) has resulted in the de novo design of a new class of potent IL-10 peptidomimetic ligands.
43
Ruiz-Gómez, Gloria, John C. Hawkins, Jenny Philipp, Georg Künze, Robert Wodtke, Reik Löser, Karim Fahmy, and M. Teresa Pisabarro. "Rational Structure-Based Rescaffolding Approach to De Novo Design of Interleukin 10 (IL-10) Receptor-1 Mimetics." Public Library of Science, 2016. https://tud.qucosa.de/id/qucosa%3A30052.
Full textAbstract:
Tackling protein interfaces with small molecules capable of modulating protein-protein interactions remains a challenge in structure-based ligand design. Particularly arduous are cases in which the epitopes involved in molecular recognition have a non-structured and discontinuous nature. Here, the basic strategy of translating continuous binding epitopes into mimetic scaffolds cannot be applied, and other innovative approaches are therefore required. We present a structure-based rational approach involving the use of a regular expression syntax inspired in the well established PROSITE to define minimal descriptors of geometric and functional constraints signifying relevant functionalities for recognition in protein interfaces of non-continuous and unstructured nature. These descriptors feed a search engine that explores the currently available three-dimensional chemical space of the Protein Data Bank (PDB) in order to identify in a straightforward manner regular architectures containing the desired functionalities, which could be used as templates to guide the rational design of small natural-like scaffolds mimicking the targeted recognition site. The application of this rescaffolding strategy to the discovery of natural scaffolds incorporating a selection of functionalities of interleukin-10 receptor-1 (IL-10R1), which are relevant for its interaction with interleukin-10 (IL-10) has resulted in the de novo design of a new class of potent IL-10 peptidomimetic ligands.
44
Kwan, Ann H. Y. "Protein design based on a PHD scaffold." Connect to full text, 2004. http://setis.library.usyd.edu.au/adt/public_html/adt-NU/public/adt-NU20041202.102526/index.html.
Full textAbstract:
Thesis (Ph. D.)--School of Molecular and Microbial Biosciences, Faculty of Science, University of Sydney, 2004.Chapter headings on separately inserted unnumbered cream coloured leaves. Bibliography: leaves 122-135.
45
Ham, Trevor Richard. "Covalent Growth Factor Tethering to Guide Neural Stem Cell Behavior." University of Akron / OhioLINK, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=akron1555347467862553.
Full text
46
Feng, Wei. "Structural studies of supramolecular complex assembly by neuronal scaffold proteins /." View abstract or full-text, 2005. http://library.ust.hk/cgi/db/thesis.pl?BICH%202005%20FENG.
Full text
47
Matskova, Liudmila V. "EBV membrane protein LMP2A interactions with ubiquitin ligases and signaling scaffold /." Stockholm, 2004. http://diss.kib.ki.se/2004/91-7140-068-0/.
Full text
48
Knave, Axel. "Production and characterization of alternative scaffold proteins for medical applications." Thesis, KTH, Skolan för kemi, bioteknologi och hälsa (CBH), 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-278838.
Full textAbstract:
Antibodies, as forerunners in the field of biological drugs, are originally an organism’s answer to the invasion of different pathogens. Today, antibodies are a common treatment for many chronic diseases such as the immune-mediated inflammatory diseases rheumatoid arthritis or psoriasis. It is suspected that the cytokines interleukin 17a (IL17a) and interleukin 17c (IL17c) are involved in those diseases and are commonly treated with antibodies that inhibit the cytokines. Even though antibodies have been a huge success as biological drugs they also have downsides when it comes to their production, size and stability. In quest of finding alternatives to antibodies in diagnostics and therapy, a novel class of biologics has been developed. So-called alternative scaffold proteins are small polypeptide chains that can be engineered to show affinity towards different biomarkers. ABD-Derived Affinity ProTeins or ADAPTs are one example of these alternative scaffolds that can be modified to bind a biomarker as target and keep their affinity to Human Serum Albumin (HSA) at the same time, making them bispecific. In this project, twenty-four previously selected ADAPT binder candidates that have shown good prospects towards IL17a and IL17c in previous experiments were cloned, produced, purified and characterized to determine if they show potential as tools in diagnostics or therapy of autoimmune diseases. The proteins were produced in E. coli, purified by affinity chromatography and characterized using Surface Plasmon Resonance (SPR), Circular Dichroism (CD) and Size Exclusion Chromatography (SEC). All candidates were successfully cloned into E. coli and out of these, 10 could be produced and 5 showed affinity towards their target using SPR. Examination by SEC and CD showed that the protein variants did not seem to be structurally stable and hints of impurities in the samples could be detected. This and a low yield could be further confirmed via SDS-PAGE. In conclusion, binders were produced that could theoretically be promising candidates as tools in diagnostics or therapy of chronic diseases were IL17a and/or IL17c are important. Nevertheless, in order to support these claims further investigations and developments are necessary.Antikroppar, som föregångare inom området biologiska läkemedel, är ursprungligen en organisms svar på invasionen av olika patogen. Idag är antikroppar en vanlig behandling för många kroniska sjukdomar, såsom de immunmedierade inflammatoriska sjukdomarna reumatoid artrit eller psoriasis. Cytokinerna interleukin 17a (IL17a) och interleukin 17c (IL17c) tros vara involverade i dessa sjukdomar och behandlas vanligtvis med antikroppar som hämmar cytokinerna. Trots att antikroppar har varit en stor framgång som biologiska läkemedel har de också nackdelar när det gäller deras produktion, storlek och stabilitet. För att hitta alternativ till antikroppar inom diagnostik och terapi har en ny klass av biologiska läkemedel utvecklats. Så kallade alternative scaffold proteins är små polypeptidkedjor som kan manipuleras för att visa affinitet gentemot olika biomarkörer. ABD-Derived Affinity ProTeins eller ADAPTs är ett exempel på dessa alternative scaffolds som kan modifieras för att binda en biomarkör som mål utan att påverka affiniteten till Humant Serum Albumin (HSA), vilket gör dem bispecifika. I detta projekt klonades, producerades, renades och karakteriserades tjugofyra tidigare utvalda ADAPT-bindarkandidater som har visat goda förutsättningar gentemot IL17a och IL17c i tidigare experiment. Proteinerna producerades i E. coli, renades genom affinitetskromatografi och karakteriserades med användning av Surface Plasmon Resonance (SPR), Circular Dichroism (CD) och Size Exclusion Chromatography (SEC). Alla kandidater klonades framgångsrikt i E. coli och av dessa kunde 10 produceras. Fem bindare visade affinitet till deras mål med SPR. Undersökning med SEC och CD visade dock att proteinvarianterna inte var strukturellt stabila och antydan till föroreningar kunde detekteras i proverna. Detta och ett lågt utbyte kunde ytterligare bekräftas via SDS-PAGE. Sammanfattningsvis kunde bindare producerades och dessa kan teoretiskt vara lovande kandidater till diagnostik eller terapi av kroniska sjukdomar där IL17a och/eller IL17c är viktiga. För att stödja dessa påståenden krävs dock ytterligare experiment och utveckling av bindarna.
49
Kouvatsos, Nikolaos. "Characterisation of rabbit ileal lipid binding protein and design of new β-scaffold proteins." Thesis, University of Nottingham, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.442293.
Full text
50
Kantamneni, Sriharsha. "Identification and characterisation of proteins interacting with novel GABAβ receptor interacting scaffold protein (GISP)." Thesis, University of Bristol, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.412275.
Full text