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 60 for “"protein families"”.
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Charting environmental protein families through planetary metagenomes
Η μεταγονιδιωματική αλληλούχηση επιτρέπει τη μελέτη μικροβιακών και ιικών κοινοτήτων απευθείας από περιβαλλοντικά δείγματα, συμπεριλαμβανομένων ακραίων περιβαλλόντων όπου οι καλλιεργητικές προσεγγίσεις συχνά δεν είναι εφικτές. Ωστόσο, ο μεγάλος όγκος και η υψηλή ποικιλομορφία των μεταγονιδιωματικών …
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Conservation of Electrostatically Mediated Function Across Protein Families and Superfamilies
… conserved electrostatic properties across enzyme families and superfamilies that, despite sequence and structural differences, have maintained function. In order to completely understand how function is conserved across a enzyme family or superfamily, we investigate the conserved and varying …
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Crystallographic and Modeling Studies Suggest that the SKICH Domains from Different Protein Families Share a Common Ig-like Fold but harbor substantial Structural Variations
TAX1BP1 is a pleiotropic multi-domain protein involved in many important biological processes such as signal transduction, cell growth and apoptosis, transcriptional coactivation, membrane trafficking, neurotransmission and autophagy. The N-terminus of TAX1BP1 contains a SKICH domain implicated in …
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Modeling Evolutionary Constraints and Improving Multiple Sequence Alignments using Residue Couplings
Residue coupling in protein families has received much attention as an important indicator toward predicting protein structures and revealing functional insight into proteins. Existing coupling methods identify largely pairwise couplings and express couplings over amino acid combinations, which do …
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Deep Learning Based Proteomic Language Modelling for in-silico Protein Generation
A protein is a biopolymer of amino acids that encodes a particular function. Given that there are 20 amino acids possible at each site, even a short protein of 100 amino acids has $20^{100}$ possible variants, making it unrealistic to evaluate all possible sequences in sequence level space. This …
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Protein structure determination using evolutionary information
… to optimize its sequence to perform a task. For protein-coding genes, the task includes folding, stability, and function. The record of the evolutionary process, which in itself is probabilistic, is contained within a multiple sequence alignment. A statistical model that accurately describes …
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Using Co-evolutionary Information to Improve Protein Language Modelling
Protein engineering has the potential to solve complex global problems in medicine, clean energy, and manufacturing. However, current protein engineering efforts are hampered by a lack of supervised data. We help recitify this issue by developing supervised models that perform well in …
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Structural and Functional Studies of Nucleoside Transporters
… cell possesses two evolutionarily unrelated protein families of nucleoside transporters, the concentrative nucleoside transporters and the equilibrative nucleoside transporters. We aimed to elucidate their transport mechanisms using X-ray crystallography and biochemical assays. We solved …
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Community Classification of the Protein Universe
Protein family databases are an important resource for biologists seeking to characterise the function of proteins, the structure of their domains, and their localisation within the cell. Operating a protein family database requires the identification of families, and the curation of literature …
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Identifying The Structure Of Genomic Islands In Prokaryotes
… prokaryotic and phage genomes via patterns of protein families across many species. A pattern is a sequence of protein families that is found to frequently occur in the genomes of a number of species. Here the large data set available from the IslandViewer4 database and protein families from …
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Gas migration inside proteins: Mechanism, characterization, and applications
"Gas migration inside proteins is a little-studied yet very important topic for many classes of proteins such as globins, oxygenases, and oxidases, which store oxygen gas or use it for enzymatic purposes. One reason why this process has not received prominent attention in recent years was because …
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Cardiovascular Characterization of Cx40/Panx1 Single and Double Knockout Mice
Connexins (Cxs) and pannexins (Panxs) are protein families that form large-pore channels which exist at the plasma membrane for both intracellular and extracellular signaling. Given their potential for overlapping cellular signaling functions we proposed that mice lacking both a connexin and a …
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Proteomic Profiling of Animal Models of Motor Neuron Disease and Muscular Dystrophy
… and/or liquid chromatography for largeQscale protein separation, and labelQfree mass spectrometry basedQproteomics are highly suitable to determine changes in the isoform expression pattern of muscle and testis proteins. The work presented outlines major categories of protein families that …
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Extracellular Contractile Injection Systems (eCIS) - Characterization of Conserved Phage Tail-like Structures in Streptomyces
… I show that all eCIS are comprised of nine core protein families and are closely related to contractile phage tails, a relationship emphasized by the discovery of rare eCIS-like prophages that are the likely evolutionary link between the two. I classify eCIS into six distinct groups and show that …
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A lentiviral system for RNAi transgenesis and the Ena/VASP triple-knockout defines neuronal and non-neuronal functions in mouse development
… employs complex expression patterns of expanded protein families to achieve the complexity and specificity required in mammalian development. For example, the Drosophila axon guidance ligands, Netrin and Slit, have recently been implicated in the development of several mammalian organ systems. …
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Computational prediction of coiled-coil interaction structure specificity
The alpha-helical coiled coil is a protein sequence and structural motif that consists of two or more helices in a parallel or antiparallel orientation supercoiling around a central axis. Coiled coils have been observed in a wide range of protein families, and many studies have focused on their …
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Toward Structural and Functional Predictions from Biological Sequences
Biological sequences, including DNA and protein sequences, are believed to encode sufficient information to determine the structure and function of biological molecules, which in turn decide the phenotypic traits of animals. Deciphering the biological sequences is an important and multiscale …
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INSIGHTS INTO POLYMERISATION OF FTSZ AND OTHER CYTOMOTIVE FILAMENTS
Protein filaments are used in different ways to organise other molecules in space and time within cells. Some proteins form filaments that couple hydrolysis of nucleotides to their polymerisation cycle in order to power the directed movement of other molecules, these filaments are termed …
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Models and analysis of yeast mating response : tools for model building, from documentation to time-dependent stimulation
… (Saccharomyces cerevisiae) have revealed many protein families and regulatory motifs also found in higher eukaryotes. This thesis develops several computational and experimental approaches that facilitate characterization of cellular signaling systems, and tests these approaches using yeast …
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Biochemical Characterization of the DUF3328 Protein in the Biosynthesis of Cyclic Peptide Cyclochlorotine
… the Domains of Unknown Function 3328 (DUF3328) protein family and investigates its role in cyclochlorotine biosynthesis. Through transcriptomic sequencing and CRISPR/Cas9 knockout experiments, I revealed that CctP2 is essential for chlorination and CctR is required for hydroxylation. …
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