Tesis sobre el tema "Protein chemistry"
Crea una cita precisa en los estilos APA, MLA, Chicago, Harvard y otros
Consulte los 50 mejores tesis para su investigación sobre el tema "Protein chemistry".
Junto a cada fuente en la lista de referencias hay un botón "Agregar a la bibliografía". Pulsa este botón, y generaremos automáticamente la referencia bibliográfica para la obra elegida en el estilo de cita que necesites: APA, MLA, Harvard, Vancouver, Chicago, etc.
También puede descargar el texto completo de la publicación académica en formato pdf y leer en línea su resumen siempre que esté disponible en los metadatos.
Explore tesis sobre una amplia variedad de disciplinas y organice su bibliografía correctamente.
Slavoff, Sarah Ann. "Enzyme-mediated labeling of proteins and protein-protein interactions in vitro and in living cells". Thesis, Massachusetts Institute of Technology, 2010. http://hdl.handle.net/1721.1/62060.
Texto completoVita. Cataloged from PDF version of thesis.
Includes bibliographical references.
The E. coli biotin ligase enzyme, BirA, has been previously used by the Ting research group for site-specific labeling of peptide-tagged cell surface proteins. We sought to expand the utility of biotin ligase-mediated labeling to functional group handles, including azides and alkynes, for bio-orthogonal chemistry. Since the BirA and its point mutants were unable to ligate these probes to an acceptor peptide, we screened biotin ligases from multiple species to identify more permissive enzymes. We determined that the Pyrococcus horikoshii biotin ligase utilizes an azide-bearing biotin analog and that the Saccharomyces cerevisiae biotin ligase can utilize an alkyne-functionalized biotin analog. We subsequently demonstrated that the azidefunctionalized biotin analog can be derivatized with a phosphine probe via the Staudinger ligation. We next turned to the goal of delivering quantum dots to the cytosol of living cells, which in the future may permit intracellular single-molecule imaging. We investigated viral methods of delivery, but found that our protocol caused quantum dots to be trapped in endocytic vesicles. We then validated previous reports that the pore-forming toxin streptolysin 0 be used to deliver quantum dots to the cytosol of living cells. Lipoic acid ligase, or LpIA, has been previously applied to site-specific protein labeling of peptide-tagged proteins using small molecule probes including lipoic acid and coumarin fluorophores. We utilized LpIA and its substrate, the LAP peptide, to create sensors for proteinprotein interactions. If LpIA is fused to one protein and LAP is fused to another, only when the two proteins interact do LpIA and LAP come into proximity, allowing probe ligation onto the peptide to occur as a readout of the interaction. We demonstrate that proximity-dependent coumarin ligation detects protein-protein interactions in living mammalian cells with extremely low background, a signal-to-background ratio of at least 5:1, and sufficiently fast kinetics to label interactions with a half-life of at least 1 minute. The reporter quantitatively responds to subpopulations of interacting proteins, allowing dissociation constants to be measured. Coumarin fluorescence accurately reports the subcellular localization of the interaction under study. Finally, we applied proximity-dependent coumarin ligation to imaging of the interaction of PSD-95 and neuroligin-1, two proteins involved in synaptic maturation, in neurons.
by Sarah Ann Slavoff.
Ph.D.
Bhat, Venugopal T. "Protein-directed dynamic combinatorial chemistry". Thesis, University of Edinburgh, 2011. http://hdl.handle.net/1842/8758.
Texto completoMaset, Fabio. "Protein Chemistry and Molecular Medicine". Doctoral thesis, Università degli studi di Padova, 2011. http://hdl.handle.net/11577/3422744.
Texto completoLa proteomica riguarda lo studio sistematico delle proteine al fine di fornire una visione completa della funzione, della struttura e della regolazione dei sistemi biologici. I progressi avvenuti negli ultimi decenni, sia per quanto riguarda la strumentazione sia le metodologie utilizzate, hanno permesso di ampliare il campo di studi biologici passando dall’analisi di proteine purificate all’analisi di miscele complesse. La proteomica sta rapidamente diventando una componente essenziale della ricerca biologica ed associato ai progressi della bioinformatica, questo approccio alla descrizione dei sistemi biologici avrà indubbiamente un impatto notevole sulla nostra comprensione dei fenotipi sia delle cellule normali e malate. Inizialmente la proteomica era focalizzata principalmente sulla generazione di mappe proteiche bidimensionali utilizzando elettroforesi su gel di poliacrilammide. La verifica dell’espressione o la misurazione quantitativa dei livelli globali di proteine può ancora essere fatta sulla base dei gel bidimensionali, tuttavia oramai questi compiti sono affidati alla spettrometria di massa la quale può contare su di un’elevata sensibilità e specificità. La spettrometria di massa applicata alle proteine offre molti vantaggi: oltre a calcolare il peso molecolare con elevata precisione, questa tecnica permette di analizzare e caratterizzare la sequenza aminoacidica. Può anche essere utilizzata nello studio delle modificazioni post-traduzionali e per monitorare la formazione di complessi in soluzione. Infine può essere applicata con differenti scopi, quali l'analisi conformazionale, l'analisi della cinetica di ripiegamento e di studi sulle attività catalitiche delle proteine. Durante il dottorato di ricerca la mia attenzione è stata focalizzata soprattutto sull’utilizzo di tale tecnica abbinata a metodologie di chimica delle proteine quali ad esempio l’elettroforesi mono e bidimensionali, differenti cromatografie in fase liquida, la sintesi peptidica in fase solida e l’utilizzo di proteasi enzimatiche. In particolare in questa Tesi di Dottorato gli argomenti di studio sono stati trattati singolarmente, distinguendo i principali progetti in cui sono stato coinvolto in capitoli indipendenti. Brevemente, nel capitolo 2 è proposto lo studio di protease nexin-1 (PN-1), il principale inibitore della trombina a livello cerebrale, volto a chiarire la funzione della porzione glucidica sulla conformazione, stabilità e funzione della proteina mediante lo studio della proteina ricombinante prodotta in E. coli. Nel capitolo 3 è riportato il lavoro concernente la purificazione e la caratterizzazione chimica, in particolare dell’identificazione de novo della sequenza amminoacidica, di un analogo dell’inibitore della fosfolipasi A2 estratto dal siero di Python sebae, il quale ha dimostrato di possedere un effetto citotossico pro-apoptotico e che potrebbe essere sfruttato per lo sviluppo di nuove strategie antitumorali. Nel capitolo 4 l’attenzione è stata concentrata a chiarire le dinamiche molecolari che portano allo sviluppo di iperossaluria primaria di tipo I mediante lo studio del mutante G41R dell’enzima alanina:gliossilato amminotransferasi (AGT) analizzando in particolar modo i meccanismi che portano G41R ad essere maggiormente soggetto a degradazione e aggregazione rispetto alla proteina WT. Infine, il capitolo 5 tratta dell’effetto dello stress ossidativo sul metabolismo del fattore di von Willebrand (VWF). Il fattore di von Willebrand è una glicoproteina plasmatica estremamente complessa le cui dimensioni contribuiscono a regolare l’equilibrio emostatico. Nello specifico, è stato osservato come l’ossidazione di un residuo di metionina situato nel dominio A2 della glicoproteina impedisca il taglio proteolitico da parte di ADAMTS-13, mentre non vada ad influenzare o in alcuni casi addirittura favorisca la proteolisi di VWF da parte di proteasi leucocitarie liberate dai polimorfonucleati in seguito a stati infiammatori.
Laos, Roberto y Steven A. Benner. "Linking chemistry and biology: protein sequences". Revista de Química, 2016. http://repositorio.pucp.edu.pe/index/handle/123456789/99314.
Texto completoIn the last twenty years, the number of complete genomes that have been sequenced and deposited in data banks has grown dramatically. This abundance in sequence information has supported the creation of the discipline known as paleogenetics. In this article, without going into complex algorithms, we present some key concepts for understanding how proteins have evolved in time. We then illustrate how paleogenetic analysis can be used in biotechnology. These examples highlight the connection between chemistry and biology, two disciplines that twenty years ago seemed to be more different than what they seem to be today.
Fernández, Suárez Marta. "New reporters of protein trafficking and protein-protein interactions in live cells". Thesis, Massachusetts Institute of Technology, 2008. http://hdl.handle.net/1721.1/44678.
Texto completoVita.
Includes bibliographical references.
Here, we describe our attempts to harness the exquisite specificity of natural protein and RNA enzymes to develop improved methods to study protein localization and protein-protein interactions in live cells. We first attempted to detect endogenous protein-protein interactions (PPIs) in live cells by means of a ribozyme complementation assay, but we found that the strategy was limited by the interaction affinity constraints and by low ribozyme activity in cells. We then sought to still detect interactions among endogenous proteins but in fixed cells. We devised an improved immunofluorescence (IF) technique, in which the antibodies are conjugated to an enzyme-substrate pair. We chose E. coli biotin ligase (BirA), which catalyzes the covalent ligation of biotin to a 15amino acid recognition sequence (AP). Only upon PPI would BirA be in close enough proximity to biotinylate the AP. Although the use of proximity biotinylation within the IF scheme proved challenging because of the geometric rigidity of the antibody conjugates, we later successfully applied the concept to the study of recombinant proteins in live cells, where BirA and AP were each genetically fused to the proteins of interest. We demonstrated that this method offers a combination of high spatial and temporal resolution with a low rate of false positives. We engineered the BirA/AP affinity to reduce background and eliminate false positives, while still allowing robust detection of relatively transient PPIs (half-life > 1 minute). We demonstrated that the methodology exhibits high specificity for the detection of PPIs in living mammalian cells, with a fold induction in the detected signal upon PPI of - 5-25. Using FRB-FKBP12 system as a model, the BirA/AP(-3) pair was also able to quantitatively predict interaction KIds.
(cont.) Importantly, we showed that proximity biotinylation can detect the subcellular localization of the PPI under study. We also developed a new method for site-specific labeling of proteins in live cells. Through rational design, we re-directed E. coli lipoic acid ligase (LplA) to specifically ligate an unnatural alkyl azide substrate to an engineered 22-amino acid LplA acceptor peptide (LAP) tag. The alkyl azide can then be selectively derivatized with a cyclooctyne conjugated to any probe of interest. We first demonstrated that LplA can be used to label LAP-tagged proteins with Cy3, AlexaFluor568, and biotin at the surface of living mammalian cells, and we then applied the methodology to one- and two-color cellsurface receptor labeling. Finally, we also showed that LplA can site-specifically label intracellular proteins, although the signal/background ratio still needs to be improved.
by Marta Fernández Suárez.
Ph.D.
Keiser, Michael James. "Relating protein pharmacology by ligand chemistry". Diss., Search in ProQuest Dissertations & Theses. UC Only, 2009. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3378494.
Texto completoRyan, C. P. "Advances in organometallic and protein chemistry". Thesis, University College London (University of London), 2010. http://discovery.ucl.ac.uk/20307/.
Texto completoLiu, Xingquan 1959. "Import of proteins into mitochondria : biogenesis of the uncoupling protein and identification of a mitochondrial signal peptide binding protein". Thesis, McGill University, 1989. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=74310.
Texto completoAn integral mitochondrial membrane protein (p30) that binds a mitochondrial signal peptide in intact mitochondria in vitro has been purified by an affinity approach. The protein has been identified as a member of the ADP/ATP carrier (AAC) family based on both immunoblotting and peptide mapping. The irreversible association of the signal peptide with AAC in intact mitochondria has been correlated with inhibition of protein import into the organelle.
Ju, Yue. "MASS SPECTROMETRIC STUDY OF PROTEIN AND PROTEIN LIGAND COMPLEXES". The Ohio State University, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=osu1449219266.
Texto completoBennett, Matthew Stuart. "Crystallography of biomolecular complexes, revealing protein-nucleoside, protein-protein acid-drug interactions". Thesis, King's College London (University of London), 2002. https://kclpure.kcl.ac.uk/portal/en/theses/crystallography-of-biomolecular-complexes-revealing-proteinnucleoside-proteinprotein-aciddrug-interactions(4a85b5cd-8a9a-4969-bee3-95fbe46e4257).html.
Texto completoAlmonacid, Coronado Daniel Eduardo. "The chemistry and evolution of protein catalysis". Thesis, University of Cambridge, 2008. https://www.repository.cam.ac.uk/handle/1810/252074.
Texto completoMatsuzaki, Hideki. "Protein and Enzyme Chemistry of Cathepsin A". Kyoto University, 1998. http://hdl.handle.net/2433/182423.
Texto completo0048
新制・課程博士
博士(農学)
甲第7562号
農博第1023号
新制||農||772(附属図書館)
学位論文||H10||N3212(農学部図書室)
UT51-99-A248
京都大学大学院農学研究科農芸化学専攻
(主査)教授 林 力丸, 教授 天知 輝夫, 教授 清水 昌
学位規則第4条第1項該当
Lauffer, Benjamin E. L. "Protein interactions mediating endocytic recycling of G protein-coupled receptors". Diss., Search in ProQuest Dissertations & Theses. UC Only, 2008. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3339215.
Texto completoBayro, Marvin J. "Protein MAS NMR methodology and structural analysis of protein assemblies". Thesis, Massachusetts Institute of Technology, 2010. http://hdl.handle.net/1721.1/57800.
Texto completoVita. Cataloged from PDF version of thesis.
Includes bibliographical references.
Methodological developments and applications of solid-state magic-angle spinning nuclear magnetic resonance (MAS NMR) spectroscopy, with particular emphasis on the analysis of protein structure, are described in this thesis. MAS NMR studies of biomolecules ranging from model peptides and proteins in crystalline form to amyloid fibrils and whole bacterial organelles are reported. The methods presented include novel pulse sequences and optimized pulse sequence elements, experimental approaches designed for multiple-spin systems, a protocol for efficient sequential resonance assignment of proteins in the solid state, and techniques to determine the inter-molecular organization of amyloid fibrils formed by moderately sized proteins. Notably, an efficient dipolar recoupling technique, bandselective radio frequency-driven recoupling (BASE RFDR), is introduced and combined with alternating 13C-12C labeling to yield highly sensitive 13C-13C correlation spectra between distant nuclei in proteins. Various applications of the BASE RFDR scheme are presented, including protein resonance assignment, determination of tertiary structure of amyloid fibrils, and variable-temperature studies of protein dynamics. The main biological systems analyzed are amyloid fibrils formed by the SH3 domain of P13 kinase (P13-SH3) and intact gas vesicles from anabaena flos-aquae, for which atomic-level structural information was previously unavailable. P13-SH3 (86 residues) is a system thoroughly studied as a model of protein misfolding and amyloid formation by a natively globular protein. Gas vesicles are bacterial buoyancy organelles, with walls composed almost entirely by a single protein (GvpA, 70 residues), whose formation and structure constitute a highly intriguing biophysical problem. Nearly complete 13C and 'IN resonance assignments and the molecular conformations of the polypeptide backbones of both P13-SH3 and GvpA have been obtained via MAS NMR spectroscopy, enabling the proposal of models for the structure of these two protein assembly systems. In addition, the tertiary structure of P13-SH3 amyloid fibrils has been elucidated by the application of novel methodology introduced in this thesis. Finally, investigations regarding the effects of temperature and protein dynamics on MAS NMR experiments and biomolecular dynamic nuclear polarization studies are presented.
by Marvin J. Bayro.
Ph.D.
Measey, Thomas J. Schweitzer-Stenner Reinhard. "Unfolded, misfolded, and self-organized short alanine-rich peptides : implications for fundamental science, human disease, and biotechnology /". Philadelphia, Pa. : Drexel University, 2010. http://hdl.handle.net/1860/3317.
Texto completoLian, Wenlong. "DEVELOPMENT AND OPTIMIZATION OF PROTEIN-PROTEIN INTERACTION INHIBITORS BY COMBINATORIAL AND MEDICINAL CHEMISTRY". The Ohio State University, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=osu1449161031.
Texto completoSpatara, Michelle L. "Protein folding and aggregation in vitro and in vivo". Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file, 162 p, 2009. http://proquest.umi.com/pqdweb?did=1892027491&sid=2&Fmt=2&clientId=8331&RQT=309&VName=PQD.
Texto completoLee, Joongoo. "A semisynthetic protein nanoreactor for single-molecule chemistry". Thesis, University of Oxford, 2015. http://ora.ox.ac.uk/objects/uuid:b0c61278-5483-44b7-a662-f079c0f2c23f.
Texto completoApgar, James R. (James Reasoner). "Modeling the flexibility of alpha helices in protein interfaces : structure based design and prediction of helix-mediated protein-protein interactions". Thesis, Massachusetts Institute of Technology, 2008. http://hdl.handle.net/1721.1/43778.
Texto completoVita.
Includes bibliographical references.
Protein-protein interactions play an essential role in many biological functions. Prediction and design of these interactions using computational methods requires models that can be used to efficiently sample structural variation. This thesis identifies methods that can be used to sample an important sub-space of protein structure: alpha helices that participate in protein interfaces. Helices, the global structural properties of which can be described with only a few variables, are particularly well suited for efficient sampling. Two methods for sampling helical backbones are presented: Crick parameterization for coiled coils and normal-mode analysis for all helices. These are shown to capture most of the variation seen in the PDB. In addition, these methods are applied to problems in protein structure prediction and design. Normal-mode analysis is used to design novel nanomolar peptide inhibitors of the apoptosis-related Bcl-2 family member, Bcl-xL, and a modification of Crick Parameterization is used to predict the binding orientation of dimeric coiled coils with greater than 80% accuracy. Finally, this study addresses the increase in computational time required by flexible-backbone methods and the use of cluster expansion to quickly map structural energies to sequence-based functions for increased efficiency.
by James R. Apgar.
Ph.D.
Si, Chao. "Theoretical Study of Intermolecular Interactions in Protein-Drug Binding and Protein Folding". University of Toledo / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=toledo1341632548.
Texto completoShih, Yu-Hsuan. "Protein Disaggregation and Degradation by Clp ATPase Nanomachines during Protein Quality Control". University of Cincinnati / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1512045252522582.
Texto completoPhillips, Angela Marie Ph D. Massachusetts Institute of Technology. "Chaperoning viral protein evolution". Thesis, Massachusetts Institute of Technology, 2018. http://hdl.handle.net/1721.1/118276.
Texto completoCataloged from PDF version of thesis. Vita.
Includes bibliographical references.
Preventing viral pandemics and developing effective antiviral therapeutics demands understanding the molecular mechanisms that both potentiate and constrain viral evolution. The rapid evolution of viruses is mediated in part by their high mutation rates, enabling resistance to antiviral drugs, seasonal vaccines, and innate and adaptive immune responses. Fortunately for us, the same mutations responsible for resistance are often biophysically deleterious to viral proteins. Thus, viral evolution is inherently constrained by the proper folding of viral proteins into functional, stable conformations. In cells, protein folding and homeostasis are assisted by complex networks of chaperones and quality control machinery. Though the evolutionary implications of most chaperones and quality control factors remain unexplored, the HSP90 chaperone can buffer and potentiate the phenotypic effects of mutations in endogenous client proteins in bacteria, fungi, plants, and other eukaryotic organisms. Viruses acquire mutations at a rate several orders of magnitude above that of the aforementioned organisms, yet they do not encode any machinery to assist destabilized protein variants to their folded, functional conformations. However, viral proteins are known to interact with host chaperones and quality control machinery. My graduate work has focused on determining whether and how host proteostasis machinery modulates viral protein evolution. First, I employed a serial passaging approach to evolve influenza in host cells with remodeled proteostasis capacities, revealing that cytosolic host proteostasis capacity is indeed a critical determinant of influenza evolutionary trajectories. This work motivated systematic quantification of influenza protein mutational tolerance upon perturbation of host proteostasis, for which I applied deep mutational scanning to comprehensively profile the mutational tolerance of influenza nucleoprotein and hemagglutinin in modulated cytosolic and endoplasmic reticulum (ER) folding environments, respectively. The nucleoprotein work provides the first experimental evidence that host chaperones can enhance the accessibility of biophysically deleterious, adaptive viral protein variants. The hemagglutinin work establishes evolutionary implications for the ER proteostasis machinery, and demonstrates that ER proteostasis mechanisms enhance mutational tolerance across the entire HA protein. Overall, it is clear that host chaperones and quality control machinery crucially impact viral protein fitness, and likely also impact the fitness of endogenous variants.
by Angela Marie Phillips.
Ph. D. in Biological Chemistry
GULOTTA, Maria Rita. "Computational methodologies applied to Protein-Protein Interactions for molecular insights in Medicinal Chemistry". Doctoral thesis, Università degli Studi di Palermo, 2021. http://hdl.handle.net/10447/479127.
Texto completoAngell, Yu Li. "Triazole based peptidomimetics for mimicking protein-protein hot spots". [College Station, Tex. : Texas A&M University, 2007. http://hdl.handle.net/1969.1/ETD-TAMU-1432.
Texto completoLong, Jiafu. "Supramodular nature of neuronal scaffolding proteins /". View abstract or full-text, 2004. http://library.ust.hk/cgi/db/thesis.pl?BICH%202004%20LONG.
Texto completoIncludes bibliographical references (leaves 167-184). Also available in electronic version. Access restricted to campus users.
Ryan, Jeremy Adam. "Design and synthesis of probes for detection of protein-protein interaction and RNA localization". Thesis, Massachusetts Institute of Technology, 2005. http://hdl.handle.net/1721.1/33657.
Texto completoIncludes bibliographical references.
The use of the ketone biotin - benzophenone-biotin hydrazide system for detecting the formation of cyan fluorescent protein and NF-kappaB p50 dimers was assessed. A series of benzophenone-based probes were synthesized and tested for photocrosslinking activity to investigate the efficiency of photocrosslinking in these systems. Three series of small molecule probes were synthesized for the selection of ribozymes from a random sequence pool. Solid-phase immobilized fluorescein and fluorescein phosphates were synthesized for the indirect selection of a fluorescein phosphatase ribozyme. A corresponding thiophosphate analog was created for the in-gel selection of a thiophosphatase ribozyme via APM-PAGE. Finally, a series of fluorescein-nucleoside phosphate conjugates was designed and synthesized for use in the solution phase preparation of a fluorogenic ribozyme substrate, and later immobilization of this substrate on a silyl resin for direct ribozyme selection.
by Jeremy Adam Ryan.
S.M.
Sarkar, Mohosin M. "Engineering Proteins with GFP: Study of Protein-Protein Interactions In vivo, Protein Expression and Solubility". The Ohio State University, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=osu1261418776.
Texto completoFüllen, Georg Karl-Heinz. "Protein engineering and pattern recognition". Thesis, Massachusetts Institute of Technology, 1994. http://hdl.handle.net/1721.1/17354.
Texto completoWavreille, Anne-Sophie Marie. "SRC homology 2 domain proteins binding specificity from combinatorial chemistry to cell-permeable inhibitors /". Columbus, Ohio : Ohio State University, 2006. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1164738844.
Texto completoCheng, Yu-Chia. "Effects of salts on the phase behavior of proteins and protein mixtures". Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file, 281 p, 2008. http://proquest.umi.com/pqdweb?did=1456290961&sid=10&Fmt=2&clientId=8331&RQT=309&VName=PQD.
Texto completoReyes, Samuel Onofre J. "Expanding beta-turn analogs for mimicking protein-protein hot spots". Thesis, [College Station, Tex. : Texas A&M University, 2006. http://hdl.handle.net/1969.1/ETD-TAMU-1748.
Texto completoBrophy, Megan Brunjes. "Bioinorganic Chemistry of the Human Host-Defense Protein Calprotectin". Thesis, Massachusetts Institute of Technology, 2015. http://hdl.handle.net/1721.1/98823.
Texto completoVita. Cataloged from PDF version of thesis.
Includes bibliographical references.
The human innate immune system responds to bacterial and fungal pathogens by releasing the metal-chelating protein calprotectin (CP) at sites of infection and in the upper layers of the epidermis. CP is a Mn(II)- and Zn(ll)-binding protein. The work described in this thesis elucidates the metal-binding properties of CP, and correlates these properties with in vitro growth inhibition of bacteria and fungi. We report that the metal-binding properties of CP are modulated by Ca(ll), and we propose a working model in which CP responds to physiological Ca(Il)-ion gradients to become a potent Zn(ll)- and Mn(Il)-chelating agent in the extracellular space. Individual chapter summaries follow. Chapter 1: Bioinorganic Chemistry of the Host Pathogen Interaction. Transition metal ions are required for all forms of life. During the course of infection, pathogenic microorganisms must acquire transition metals from the host. Three metals of interest from this standpoint are iron, zinc, and manganese. This chapter describes bacterial metal-ion homeostasis machineries, and metal-requiring processes with a focus on Zn(II) and Mn(II). This chapter then highlights the S100 family of Ca(ll)-binding proteins and discuses the Zn(Il)-, Cu(ll)-, and Mn(Il)-binding properties of S100B, S100A12, S100A7, S10OA15, and S100A8/S100A9. Finally, an overview of the scope of this thesis is presented. Chapter 2: Calcium Ion Gradients Modulate the Zinc(Il) Affinity and Antibacterial Activity of Human Calprotectin. Calprotectin (CP) is a human neutrophil protein that is produced and released by neutrophils at sites of infection, where it prevents the growth of microorganisms by sequestering bioavailable zinc(II) and manganese(II). In this chapter, we present metalbinding studies to elucidate the Zn(ll)-binding properties of CP. We report unique optical absorption and EPR spectroscopic signatures for the interfacial His 3Asp and His 4 sites of human CP by using Co(II) as a spectroscopic probe. Zinc competition titrations employing colorimetric and fluorimetric Zn(II) sensors establish that CP coordinates two Zn(II) ions / CP heterodimer. The Ca(ll)-insensitive Zn(ll) sensor ZP4 is used to determine the Kd of CP for Zn(II) in Ca(Il)-deplete and Ca(Il)-replete conditions. These competition titrations afford apparent Kdsitel = 133 58 pM and Kdsite2 = 185 219 nM in the absence of Ca(II). In the presence of excess Ca(Il) these values decrease to Kd,sitel 5 10 pM and Kd,site2 : 240 pM. In vitro antibacterial assays indicate that the metal-binding sites and Ca(ll)-replete conditions are required to inhibit the growth of Gram-negative and Gram-positive bacteria. We propose a model in which Ca(II) ion gradients modulate the antibacterial activity and Zn(Il)-binding properties of human CP. Chapter 3: High-Affinity Manganese Coordination by Human Calprotectin Is Calcium- Dependent and Requires the Histidine-Rich Site at the Dimer Interface. In this chapter, we report that the His 4 motif at the S10OA8/S100A9 dimer interface of CP is required for high-affinity Mn(II) coordination. We identify a low-temperature EPR spectroscopic signal for this site that is consistent with high-spin Mn(II) in an octahedral coordination sphere. This site could be simulated with zero-field splitting parameters D = 270 MHz and EID = 0.30 (E = 81 MHz). This analysis, combined with studies of mutant proteins, suggests that (A8)Hisl7, (A8)His27, (A9)His9l, (A9)His95 and two as-yet unidentified ligands coordinate Mn(ll) at site 2. These studies support a model in which CP responds to Ca(ll) ion gradients to become a potent metal-ion chelator in the extracellular space. Chapter 4: Contributions of the C-terminal Tail of S100A9 to High-Affinity Manganese Binding by Human Calprotectin. This chapter examines the role of the S100A9 C-terminal tail to high-affinity Mn(ll) coordination by human CP. We present a 16-member mutant family with mutations in the S100A9 C-terminal tail (residues 96-114), which houses three histidine and four acidic residues, to evaluate its contribution to Mn(ll) sequestration. These studies confirm that two His residues at positions 103 and 105 complete the octahedral coordination sphere of CP in solution. Appendix 1: Sequence Alignments of Transition-Metal Binding S100 Proteins. Sequence alignments of S100A7, S100A8, S100A9, S100A12, S100A15, and S100B proteins from multiple organisms are presented. Appendix 2: Characterization of CP Mutant Proteins by Circular Dichroism and Analytical Size Exclusion Chromatography. Additional characterization of CP and mutant proteins employed in Chapters 2-4 is presented. Appendix 3: Structures of Sensors Used In this Work. The structures of Zincon, MagFura-2, Zinpyr-1, and Zinpyr-4 are presented. Appendix 4: Manganese Binding Properties of Human Calprotectin under Conditions of High and Low Calcium. This appendix represents a collaborative work with the Drennan Lab (MIT) and Britt Lab (UC Davis) to study the Mn(Il)-CP complex in low- and high-Ca(II) conditions. We report a crystal structure of Mn(Il)-, Ca(Il)-, and Na(l)-bound CP with Mn(II) exclusively coordinated to the His6 motif. Electron spin-echo envelope modulation and electron-nuclear double resonance experiments demonstrate that the six coordinating histidine residues are spectroscopically equivalent. The observed 15N ( = %/h)y perfine couplings (A) arise from two distinct classes of nitrogen atoms: the coordinating E-nitrogen of the imidazole ring of each histidine (A = [3.45, 3.71, 5.91] MHz) and the distal 6-nitrogen (A = [0.11, 0.18, 0.42] MHz). In the absence of Ca(II), the affinity of CP for Mn(II) drops by two to three orders of magnitude, and Mn(II) coordinates to the His6 site as well as other sites on the protein.
by Megan Brunjes Brophy.
Ph. D. in Biological Chemistry
Higgs, C. "A computational study of the G-protein-G-protein coupled receptor interaction". Thesis, University of Essex, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.324216.
Texto completoLee, John Edwin 1965. "Molecular orientation distributions in adsorbed protein films". Diss., The University of Arizona, 1997. http://hdl.handle.net/10150/282448.
Texto completoLopac, Senja Katarina. "Polymer chemistry effects on protein release and immune activation". [Ames, Iowa : Iowa State University], 2008.
Buscar texto completoMorimoto, Koichi. "Studies on Highly Sensitive Enzyme Immunoassays by Protein Chemistry". Kyoto University, 1997. http://hdl.handle.net/2433/157104.
Texto completoKyoto University (京都大学)
0048
新制・論文博士
博士(農学)
乙第9633号
論農博第2147号
新制||農||747(附属図書館)
学位論文||H9||N3072(農学部図書室)
UT51-97-L210
(主査)教授 井上 國世, 教授 松野 隆一, 教授 廣瀬 正明
学位規則第4条第2項該当
Whelan, Helen A. "Calmodulin Dependent Protein Kinase II - A Sulfhydryl Chemistry Study /". The Ohio State University, 1995. http://rave.ohiolink.edu/etdc/view?acc_num=osu148793151262033.
Texto completoDowman, Luke James. "Expanding the Scope of Peptide and Protein Modification Chemistry". Thesis, University of Sydney, 2020. https://hdl.handle.net/2123/23402.
Texto completoBietlot, Henri P. "Characterization of the insecticidal protein from Bacillus thuringiensis: The importance of DNA-protein interactions". Thesis, University of Ottawa (Canada), 1993. http://hdl.handle.net/10393/6598.
Texto completoBrenner, Rachel Natanya. "Structure/function studies of protein phosphatases". Thesis, Massachusetts Institute of Technology, 1995. http://hdl.handle.net/1721.1/37550.
Texto completoSeneviratne, Herana Kamal. "Towards Understanding Dirigent Protein Function". Thesis, Washington State University, 2017. http://pqdtopen.proquest.com/#viewpdf?dispub=10269677.
Texto completoPlants produce a dazzling collection of chemical compounds with great structural and functional diversity that are known as specialized metabolites which have important roles in plant defense responses. Most significantly, these chemical entities serve as rich and important source of biologically active pharmaceuticals. Although much has been known about the immense importance of these specialized metabolites, little is known about how they are produced in plants.
The evolution of the biochemistry of vascular plants depend extensively upon unique phenoxy radical-radical coupling reactions to produce different chemical compounds. In this regard, a group of proteins called dirigent proteins (DPs) control the stereoselectivities of above-mentioned coupling processes to engender a class of specialized metabolites known as lignans. In particular, lignans represent a large class of plant specialized metabolites which exhibit a broad range of physiological functions and potential medicinally important therapeutic properties. Even though there are many dirigent homologs in the plant kingdom, we do not know the precise functions of these homologous proteins.
This dissertation describes the elucidation of the biochemical function of a dirigent homolog, i.e. PsDRR206 and localization of phytoalexin pathway in pea (Pisum sativum) pods using high-resolution mass spectrometry techniques. From the studies described herein, the metabolite associated with PsDRR206 gene was identified as pinoresinol monoglucoside. Additionally, the localization of selected phytoalexins including pinoresinol monoglucoside as well as (+)-pisatin was determined as the endocarp epidermal cell layer of pea pod tissue. The results from these studies provide new insights for plant biochemistry research through gaining the knowledge of important biological processes occurring in nature.
Pham, Thi Minh Hai. "Protein extraction using reverse micelles". Thesis, University of Greenwich, 2015. http://gala.gre.ac.uk/18122/.
Texto completoSchmitt, Jaclyn L. "Understanding timing| Conservation between the circadian protein period and the C. elegans developmental timing protein lin-42". Thesis, University of California, Santa Cruz, 2014. http://pqdtopen.proquest.com/#viewpdf?dispub=1551325.
Texto completoTiming of development, metabolic regulation, and longevity are crucial elements in optimizing physiological functions to, and within, our environment. The synchronization of our internal clocks to the twenty-four hour day of our environment aids in anticipatory and protective measures on the molecular level. Dysregulation of this internal clock, known as the circadian clock, has been linked to various cancers, diabetes and heart failure. Mental ailments such as alcoholism and bipolarism can be magnified through dysregulation of our circadian rhythms. The output of circadian time keeping is still being explored, including the link to longevity. To further our understanding of clock functions through molecular structure, comparisons between biological time keeping methods are vital. On the molecular level of the circadian clock, one of the core negative feedback loop proteins is PERIOD. The complex timing of PERIOD transcription and protein accumulation directly contributes to setting the circadian clock. Within PERIOD protein, the functions of the homo- and heterodimerizing PERIOD-ARNT-SIM (PAS) domain to facilitate nuclear localization, and possibly many of the PERIOD output functions, are still being understood. Another protein that contains this canonical PAS domain is the nematode C. elegans development timing protein LIN-42. Although C. elegans are not known to have circadian rhythms, LIN-42 shares many motif and functional similarities to PERIOD. The development of C. elegans larva is repressively regulated, or gated, by LIN-42. Additionally, LIN-42 regulates entry into quiescent states during larval devolvement when environmental conditions are stressful. Considering the functions of LIN-42 within development of specialized stem cells, known as seam cells, and the recent discovery of the functions of PERIOD within the development of our own stem cells; a molecular comparison of LIN-42 and PERIOD will facilitate our understanding of the associated output functions of these proteins. Specifically the N-terminal regions of PER and LIN-42 share well-folded structural domains, and are the focus of this thesis. The forms of PERIOD and LIN-42 that share the most sequence and functional homology are PER2 and LIN-42b. Direct comparison of the similarities and differences between these two proteins on the molecular level will shed light on biological time keeping.
Watkins, Andrew M. "An in silico pipeline for the design of peptidomimetic protein-protein interaction inhibitors". Thesis, New York University, 2016. http://pqdtopen.proquest.com/#viewpdf?dispub=10188557.
Texto completoProtein-protein interactions have historically been branded “undruggable” due to their intrinsic challenges above and beyond protein-small molecule interactions. Incrementally, system after system has been approached by a variety of specialized design strategies. Still, the vast majority of interactions are intractable, and the profusion of individualized strategies leave few general approaches that might be able to extend to recalcitrant systems.
The ecosystem of tools available for developing inhibitors of protein-protein interactions suggests a potential modular strategy for proceeding from protein structure to plausible interaction inhibitors. My dissertation describes an analysis of all the protein-protein interactions containing key interfacial structural motifs found in protein structures catalogued by the Protein Data Bank. This work provides both data on extant protein interactions and specific conclusions regarding directions for further peptidomimetic design. We describe the incorporation of our lab’s peptidomimetic scaffolds into Rosetta and the validation of those methods against valuable biological systems. Finally, I chronicle substantial extension to Rosetta’s capacity to accurately model and design peptidomimetic structures.
Male, Abigail. "Identification of inhibitors of protein-protein interactions essential for virulence in pathogenic bacteria". Thesis, University of Southampton, 2014. https://eprints.soton.ac.uk/369351/.
Texto completoLuechapanichkul, Rinrada. "Determination of the Sequence Specificity and Protein Substrates of Protein Phosphatases". The Ohio State University, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=osu1398868380.
Texto completoFriedli, Georges-Louis. "Interaction of deamidated soluble wheat protein (SWP) With other food proteins and metals". Thesis, University of Surrey, 1996. http://epubs.surrey.ac.uk/2204/.
Texto completoStiving, Alyssa Quencer. "Development of Surface-Induced Dissociation, Ion Mobility, and Ultraviolet Photodissociation to Characterize Peptide, Protein, and Protein Complex Structure". The Ohio State University, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=osu1587409993097519.
Texto completoCooper, Jahan. "Optimizing the Potency of a Bicyclic Peptide Inhibitor of the Ras-Raf Protein-Protein Interaction via Combinatorial Screening". The Ohio State University, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=osu152570020664904.
Texto completoMealman, Tiffany Diane. "Metal Transfer And Protein-Protein Interactions In The CusCFBA CU(I)/AG(I) Efflux System Of E. Coli". Diss., The University of Arizona, 2012. http://hdl.handle.net/10150/312754.
Texto completo