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 35 for “"AlphaFold"”.
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Biochemical Characterization of the DUF3328 Protein in the Biosynthesis of Cyclic Peptide Cyclochlorotine
… sequence and structural analyses using AlphaFold suggested that DUF3328 proteins contain a conserved HxxHC(x)nHxxHC motif, a putative metal-binding site. Structural modeling further indicated that DUF3328 proteins form disulfide-linked homodimers, an unusual feature among biosynthetic …
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An investigation of the structure and function of the receptor-type protein tyrosine phosphatase CD148
… To investigate the structure, I analysed the AlphaFold predicted structure of CD148 ECD and also used small-angle X-ray scattering (SAXS). My findings reveal that CD148 adopts an elongated non-globular structure resembling a cylinder. Moreover, it has fewer fibronectin type III (FNIII) domains …
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Computational Discovery of Bacterial Fibrillar Adhesins and Adhesive Domains
… potential novel adhesive domain families. Using AlphaFold2, the structure of these domains was predicted to identify their potential function. The AlphaFold2 release also enabled the detection of FA-like proteins using adhesive and stalk domain structures. Here, the TMalign and Foldseek structure …
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Engineering antimicrobial strains of saccharomyces cerevisiae as industrial platform for non-sterile bioprocesses
… sequence was analyzed using bioinformatic tools. AlphaFold, Clustal Omega, and SNAP2 were used to predict AMP tertiary structures, construct a phylogenetic tree, and analyse mutation effects, respectively.
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Learning the Language of Antibody Hypervariability Through Biological Property Prediction
… regions. Consequently, methods like AlphaFold 2 have relatively weak performance on antibody sequences. In this work, we propose AbMAP (Antibody Mutagenesis-Augmented Processing), a new transfer learning framework that fine-tunes foundational models specifically for antibody-sequence …
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Polypeptide (dis)assembly in bacterial spores and microalgae
… of microalgae. Using early versions of AlphaFold2 that were released during the course of the work, the thesis goes on to add predictions of protein structure to form insights based on information at the molecular level. A comprehensive atlas of the structures of each coat protein was …
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Protein design using artificial intelligence
… problem of protein folding, focusing on AlphaFold and its unprecedented accuracy in predicting protein structures, which rivals experimental methods. The chapter discusses both the innovations brought forth by these models and their technical limitations. Following this, the thesis pivots …
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Developing a Contextual Annotation Framework for Short Linear Motifs in Proteins
… (PTMs), structural context derived from AlphaFold model scores, and the proximity of neighboring motifs. We evaluate each of these metrics using a test dataset sampled from the Eukaryotic Linear Motif (ELM) protein database. Our results indicate that sequence conservation has a consistent …
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Regulation of the histone H3K36 methyltransferase Set2 by the histone chaperone Spt6
… with the Set2 AID, which is in support of the AlphaFold-predicted structure of inactive Set2. Biophysical and analytic approaches reveal that the wild-type Set2 catalytic domain and Set2 AID physically interact, and that the autoinhibition mutants reduce or abolish this interaction. Also, in …
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Chemical Biology Tools for Biochemical and Functional Analysis of Myosin Phosphatase
… we employed mammalian expression systems and AlphaFold modeling to predict structure and optimize expression. A ligand-inducible degron system was developed by fusing PPP1R12C to a destabilized eDHFR domain, allowing rapid, reversible stabilization of the protein with trimethoprim (TMP). This …
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Multilevel frameworks for studying protein energy landscapes
… number of interaction sites. While advances like AlphaFold have improved native structure prediction, understanding thermodynamic stability and folding pathways remains a major challenge. This thesis introduces multilevel computational frameworks that integrate diverse theoretical approaches …
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Regulatory domains of the Arf GEF Sec7 scaffold autoinhibited and active conformations
… in vitro and in vivo. Serendipitously, the AlphaFold predicted structure placed the GEF domain adjacent to the DCB/HUS domain, and we demonstrate this is the active conformation. In this conformation the GEF domain displaces a loop in the DCB/HUS domain we refer to as the “D-loop”. Removal …
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Computational methods for the structure-based design of protein-binding peptides
… peptides. For some of the peptides, I show that AlphaFold can accurately predict the designed structure. Altogether, this work demonstrates the potential of applying structural motifs to the design of protein-binding peptides and highlights important directions for future work.
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Structural and Biochemical Characterization of Glycyl Radical Enzymes Abundant in Mammalian Gut Microbiota
… use newly developed computational tools, such as AlphaFold and bioinformatic approaches, to prioritize and design targeted experiments to hopefully reveal exciting new discoveries about the GRE superfamily. Overall, my research on GREs and their associated proteins will not only add to the field’s …
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Structural And Mechanistic Elucidation Of The EF-hand In LETM1 Ca2+/H+ Antiporter Function
… an approach that leverages the accuracy of AlphaFold to guide nuclear Overhauser effect (NOE) assignments during NMR-based protein structure determination. Overall, these findings provide the first atomic resolution view of the structural dynamics and mechanisms underlying the multi-modal …
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Large Scale Cross-Linking Mass Spectrometry as the Missing Link in the Systems Biology Toolbox
… predicted by computational modellers like AlphaFold. Finally, this thesis reports the use of quantitative XL-MS to explore links between gene function and cellular phenotype, comparing wild-type yeast with a highly pleiotropic deletion strain (Δhpm1) using SILAC multiplexing and PIR …
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Single Molecule Förster Resonance Energy Transfer and Super Resolution Force Spectroscopy Study of Elongation Factor G Evolution, Conformation, and Function
… ribosome. The Thr48 mutations were modeled using AlphaFold predictions and MSAs. This revealed the mutations shifted the conformational balance to two previously reported EF-G conformations, con1 and con2. Predicted ancestral analogues were generated using phylogenetic tree construction. Two …
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Context Dependent Regulation of Dicer Function During Oocyte-to-Embryo Transition
… and serine phosphorylation are modeled in AlphaFold, this suggested that distinct Dicer domains may operate in a coordinated manner to modulate structural conformation and effector recruitment. The totality of the findings here have identified a context dependent …
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Towards Efficient AI for Science in Scalable and High Performance Distributed System
… in diverse fields. Notable examples include AlphaFold, which predicts protein structures, and ClimateX, which enhances weather prediction capabilities. The ability of AI to process large volumes of data, recognize complex patterns with precision, and uncover intricate relationships has made …
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Metabolomic Approaches in Parasitology
… various substrates. Structural modeling based on AlphaFold revealed that alteration of key catalytic residues in Tb927.4.1300 rendered them unsuitable for the catalytic mechanism. Using isotope tracing experiments, I confirmed the inability of T. brucei to convert L-arginine to L-ornithine, …
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