Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 20 of 95 for “"Protein domains"”.
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Functional Sorting of Evolutionary Effects in Protein Domains
… But for the comparatively more conservative protein domain data, the absence of enough variations makes these general methods incompetent. The other problem lies at the difficulty of discerning the difference between positive selection and relaxation of functional constraint; both processes …
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Dynamics and Turnover of Lipid and Protein Domains in Cells and Supported Bilayers
<p>Protein and lipid clustering is an important mechanism for cell processes such as exo- and endo-cytosis and creating functional signaling complexes. It has been seen that both lipids and proteins are involved with the formation of cluster domains on cell membranes, yet little is known about the …
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De Novo Design And Engineering Of Functional Metal And Porphyrin-Binding Protein Domains
… of two functional cofactor-binding protein domains. First, a hybrid computational/experimental method was developed with the aim of algorithmically generating a suite of porphyrin-binding protein sequences with minimal mutual sequence information. This method was explored by …
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Insights into the evolution of protein domains give rise to improvements of function prediction
… in public databases has turned the prediction of protein function into a challenging research field. Traditional annotation methods are often error-prone due to the small subset of proteins with experimentally verified function. Goal of this thesis was to analyse the function and evolution of …
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Characterizing Multivalent Interactions Between Folded Protein Domains and Intrinsically Disordered Regions or Peptide Substrates
<p>Protein-protein interactions (PPIs) play central roles in most biological processes. Studying PPIs is a fundamental step in understanding the molecular basis of cellular processes such as cell-cell contact, enzyme activity, and transient assembly of signaling complexes or cellular structures. In …
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1q21.1 syndrome: A perspective on Structural Variant detection & the evolutionary profile of associated protein domains
Pese a que el síndrome 1q21.1 ha sido descrito clínicamente, sus causas genéticas se desconocen. Esta región es altamente repetitiva y por ello requiere tecnologías de secuenciación basadas en long reads para poder genotipar a sus pacientes de forma precisa. Además, 1q21.1 comprende múltiples …
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Effects of Protein Domains on Localization of Penicillin-Binding Proteins 2a and 2b in Bacillus Subtilis
… with a defined morphology. Penicillin-binding proteins (PBPs) catalyze the polymerization of the peptidoglycan in Bacillus subtilis. PBP2a and PBP2b are class B PBPs which have been known to have transpeptidase activities and they localize at different positions on the cell membrane. PBP2a …
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Exploring the function and evolution of proteins using domain families
Proteins are frequently composed of multiple domains which fold independently. These are often evolutionarily distinct units which can be adapted and reused in other proteins. The classification of protein domains into evolutionary families facilitates the study of their evolution and function. In …
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GPU-Optimized Graph Theory Analysis of Allosteric Protein Signaling Networks
… we performed MD simulations of several protein-RNA complex, where we abstracted the residues and their interactions as nodes and edges, respectively, to characterize the molecular interaction network. We then systematically compare the change in the betweenness upon the deletion of the …
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Fluorescence characterization of protein and lipid dynamics
… techniques were used to study the motion of protein domains in adenylate kinase, and to characterize the formation of myelin in neuron Schwann cell co-cultures. Domain motion upon substrate binding was examined in adenylate kinase using fluorescence resonance energy transfer. The process of …
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Integration and analysis of protein evolutionary relationships and small molecule bioactivity data
Interactions of small organic molecules and proteins have been studied extensively in the search of therapeutic drugs. Historically, the interaction partners have been attributed to separate scientific disciplines: small organic molecules to the domain of chemistry, proteins to the domain of …
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Functional Dissection of Arabidopsis Thaliana Resistance Gene RPS2
… loci that interact with RPS2 and RPM1 and domains within RPS2 that modify expression and strength of the resistance response. Further characterization and cloning of the RPS2- and RPM1-interacting loci, conjoined with functional analysis of RPS2 protein domains such as the LRRs and the NBS, …
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Molecular recognition in plant immunity
… disease-resistance genes, which generally encode proteins with nucleotide-binding and leucine-rich repeat domains (NB-LRRs). NB-LRRs are a large of proteins found in both plants and animals, with plant NB-LRRs further classified by the presence of N-terminal coiled-coil or toll-interleukin …
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Protein potentials and domains : re-use and composability
Protein-protein interactions are one of the cornerstones of biological processes throughout the cell. Unfortunately, lack of available data precludes many possible approaches to modeling these fundamental interactions at scale. This thesis focuses on a specific set of protein domains, known as …
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Analysis of variation in protein domain families and interfaces
… availability of over 110,000 three-dimensional protein structures allows the structural context of many SNPs to be examined in atomic detail. Interfaces are essential sites for protein function and adaptation, and key in a majority of biological processes. A computational framework, ProIntVar, …
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Foundation Models for Protein Phenotype Prediction
Understanding the roles of human proteins remains a major challenge, with approximately 20% of human proteins lacking known functions and more than 40% missing context-specific functional insights. Even well-annotated proteins are often poorly characterized in diverse biological contexts, disease …
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Structural analysis of phosphorylation hotspots and kinase target preferences.
… sensing and adapting to changes in conditions. Protein post-translational regulation is one of the fastest mechanism used by cells to relay signals from sensors to effectors during such adaptations. Mass spectrometry allows for the study of posttranslational modifications on a very large scale …
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Structural investigations of adenosylcobalamin-dependent enzyme maturation
… of these metallocofactors often relies on proteins known as metallochaperones that transport, modify, and/or insert the metallocofactor for its target metalloenzyme. This thesis focuses on the maturation of methylmalonyl-CoA mutase (MCM). In humans, MCM is the only known adenosylcobalamin …
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Engineering protein self-assembly for biosensing applications
Protein self-assembly is a promising bottom-up approach to create biological materials with programmable functionalities, particularly for biotechnological applications. This approach leverages engineering recombinant protein building blocks, derived from natural or artificially designed proteins, …
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Hyper-Plastic Structural Evolution Of The PEX Domain - A Model Of Evolutionary Exaptation And Neofunctionalization At The Molecular Level
… biochemical and physiological aspects of proteins. Tertiary protein structural domains are assumed to be features of proteins whose bio-historical relationships can be traceable over relevant evolutionary space. The phylogenetics of protein domains, including their genesis, duplication, …
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