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 33 for “"protein evolution"”.
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Chaperoning viral protein evolution
… 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 …
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Hierarchy of Interactions in Protein Evolution
… For even small systems such as individual protein domains, it has been difficult to comprehensively obtain high quality empirical data of amino acid interactions to distinguish different models for the global pattern of cooperativity. The statistical coupling analysis (SCA) - one approach …
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The Influence of Structural Constraints on Protein Evolution
Few mathematical models of sequence evolution incorporate parameters describingprotein structure, despite its high conservation, essential functional role and the increasingavailability of structural data. The primary goal of my PhD project was to create astructurally aware amino acid substitution …
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Exploring multivalent technologies and strategies for directed protein evolution
Evolution is the continuous adaptation to ever changing environments and pressure for survival of all living species. Directed evolution attempts to mimic this process of natural selection of biological molecules and systems towards a specific function that would otherwise remain untapped by …
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Characterising fitness landscapes of protein evolution by next-generation sequencing
A protein’s amino acid sequence determines its structural, chemical and physical properties, yet how sequence variation influences protein function is still incompletely understood. Protein fitness landscapes powerfully describe the sequence-function relationship by dividing sequence space into …
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Modeling the effects of site-specific amino-acid preferences on protein evolution.
An important goal in the study of protein evolution is understanding which genetic changes that fixed in nature were selected for and why. However, understanding the functional consequence of any given mutation is a challenge because the effects of amino-acid changes are highly idiosyncratic across …
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In silico protein evolution by intelligent design: creating new and improved protein structures
Natural proteins perform a startling diversity of biological functions, but comprise a miniscule fraction of the theoretical sequence-structure space that polypeptides might occupy. The goal of protein design is to identify new free-energy minima in this sequence-structure landscape so as to expand …
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Is Evolution an Algorithm? Effects of local entropy in unsupervised learning and protein evolution
L'abstract è presente nell'allegato / the abstract is in the attachment
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Intrinsic Disorder and Protein Evolution: Amino Acid Composition of Proteins in Last Universal Ancestor
… (1953) are suggested to have appeared early in evolutionary history, and the amino acids associated with codon capture developed late in the course of evolution. The chronological order of appearance of the amino acids proposed by Trifonov (2000) was G/A, V/D, P, S, E/L, T, R, N, K, Q, I, C, H, …
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Protein Folding, Host Cell Proteostasis, and Viral Evolution
… factors that can constrain and potentiate viral evolution. While mutations benefit viruses by generating the diversity required for evolution, they also threaten viral viability because the majority of non-conservative amino acid substitutions cause protein folding defect. Mutations that result …
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Navigating exponentially large spaces in biology : methods for directed evolution and smFRET time series analysis
… This thesis explores two such fields: directed protein evolution and single molecule fluorescence resonance energy transfer analysis. Although the methodologies and applications of the fields differ greatly, they are both limited by a process which scales exponentially with problem size. In the …
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Language Models Predict Drug Resistance from Complex Sequence Variation
… neural language models trained on viral protein sequence evolution have shown promise in their ability to predict viral escape mutations, potentially enabling more intelligent therapeutic design [6]. Hie et al.’s work puts forth the key conceptual advance that viral escape from human …
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Studies on Combining Sequence and Structure for Protein Classification
… is to develop a better understanding of how proteins evolve different structures and functions. A large scale protein clustering can provide a useful platform to identify such principles of protein evolution. Manual classification schemes accurately group homologous proteins, but they are …
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Exploring protein fitness landscapes with new high-throughput technologies
The concept of a protein’s fitness landscape – an abstract space in which related sequences are close together and matched with their fitness – is a useful tool to visualize core principles of protein evolution. Acquiring a new function, for example the laboratory evolution of an enzyme to convert …
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Methods to study protein folding and evolution in vivo
… and quality control factors which maintain protein homeostasis (proteostasis) by actively monitoring protein folding processes in an organelle-specific and dealing with protein misfolding in a stress-responsive manner. While we know that these "proteostasis networks" are capable of …
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Exploring Sequence-Structure-Function Relationships in Proteins Using Classification Schemes
With the rapid growth in the number of available protein sequences and structures, the necessity of interpreting this data in comprehensive and meaningful ways becomes increasingly apparent. Identifying and categorizing the functional, structural, and evolutionary relationships between proteins is …
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Biohydrogen production in Escherichia coli – a synthetic biology approach
… autoradiography, spectroscopy, SEC-MALLS, protein-film voltammetry and H2 production assays. Metabolic engineering of various E. coli strains and directed protein evolution has been carried out to integrate this synthetic hydrogenase activity into cellular metabolism and the resulting …
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The genetic basis of reproductive isolation in house mice: Studies of a European hybrid zone
… region of reduced introgression, a high rate of protein evolution, and restricted expression in the male germ line as criteria, seven candidate genes for reproductive isolation are identified. These results underscore the value of studying natural patterns of introgression in model genetic …
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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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Adapting Proteins for Clinical and Industrial Use
… to pharmaceuticals to biofuel production. Protein engineering is used to make enzymes more readily available, to gain new or improved catalytic function, or optimize properties such as thermostability and enantioselectivity. In this thesis we will discuss the variety of ways proteins can be …
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