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 16 of 16 for “"flexible loop"”.
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Advances in structure and small molecule docking predictions for crystallized G-Protein coupled receptors
… coupled receptors: structure predictions of the flexible loop domains and docking into these receptors. The prediction of loop structure has been long worked on in the context of native, globular proteins. In this work it is extended to transmembrane proteins, which requires an explicit …
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An investigation of the structure and function of the receptor-type protein tyrosine phosphatase CD148
… and features an interesting, unstructured flexible loop. The AlphaFold prediction correlated well with the experimental SAXS data. With regards to the second aim, I tested an RPTP inhibitor, AKB-9778 (Razuprotafib), on CD148 phosphatase activity, whole blood in vitro thrombogenicity and …
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Improving the Performance of Parallel Loops in OpenCilk
For good performance, parallel loop scheduling must achieve low scheduling overheads and multidimensional locality in nested loops. This thesis explores both challenges and contributes an extension to randomized work-stealing for first-class loop support that reduces scheduling overheads. …
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From ribosomal rotation to autism and cancer
… this process in yeast ribosomes through a flexible loop located within 13 Å of the peptidyltransferase center. While deletion of the entire loop is lethal, viable mutants in this region were found to promote opposing effects on the natural equilibrium between the two conformational …
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Human testis angiotensin-converting enzyme: crystal structure of a glycosylation mutant and investigation of a putative hinge-mechanism by normal mode analysis
… suggests the functional conservation of three flexible loop regions, as well as the sequence conservation of three constrained regions, involved in the hinge. Normal mode analysis reveals the intrinsic flexibility of tACE, and further suggests that a putative open form of tACE would behave …
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Characterization of vacuolating cytotoxin A of helicobacter pylori in cell binding and cellular activity
… W603, and R647, each situated in a different flexible loop a series of flexible loops are aligned adjacently in a linear fashion along a single edge of the extended beta-helix structure of VacA. These residues were shown to facilitate VacA interactions with plasma membrane SM. Based on our …
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Mechanistic study and protein engineering of a dye-decolorizing peroxidase from Thermomonospora curvata for enhanced and expanded functions
… this work, we identified a key surface-exposed loop residue, Glu293, as a target for tuning substrate access and radical stability. Replacing E293 with glycine (E293G) enhanced peroxidase activity toward small-sized substrates, likely due to increased heme accessibility through an expanded …
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Assembly of Iron-Sulfur Clusters In Vivo
… formation. In silico studies showed that a flexible loop containing the conserved LPPVK motif, which is responsible for interactions with HscA, may facilitate cluster exposure to either mediate its delivery to acceptor proteins or participation in the construction of [4Fe-4S] clusters. …
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Elucidating TRPA1 Ion Channel Aberrations in Oesophageal Adenocarcinoma.
… in coarse- grain (CG) resolution reveal a flexible hinging of the otherwise rigid ARD. OAC point mutations are located on the predicted flexible loop, and I hypothesize that these mutations alter protein dynamics and flexibility. CG-MD simulations of the full-length protein embedded in a …
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NMR application and development : study of the ribosomal RNA-L11 complex
… not only induces a rigidification of a flexible loop in the C-terminal domain but a sizeable reorientation of the N-terminal domain. The domain orientation in the free L11 shows some similarity to that of ribosome bound L11 in complexes with EF-G. Upon binding to RNA based on chemical …
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Investigating the role of ICL3 in β1-adrenergic receptor activation
… there is little known about the intracellular loop 3 (ICL3) – connecting transmembrane helices 5 and 6. It is usually truncated in crystallographic studies as it interferes with the lattice formation and is replaced with T4 lysozyme to enhance crystal contacts. In some active state crystal …
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A computational approach for identification and development of novel inhibitors targeting viral polymerases
… conformational change upon ligand binding. The flexible loop regions and in general the flexibility of the structure have a critical functional role in enzymes, but those features and their connection with the functionality of protein are hard to retrieve from xray, NMR techniques and cryoEM …
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Structure- and Ligand-Based Design of Novel Antimicrobial Agents
… bacterial crystal structures are available, the flexible loop regions that enclose <em>p</em>ABA during binding and contain key sulfonamide resistance sites have yet to be visualized in their functional conformation. To gain a new understanding of the structural basis of sulfonamide resistance, …
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Defining the mechanisms of microbial sensing among members of the toll-like receptor 2 sub-family
… was mapped to amino acid residues located in the flexible loop of LRR11. Additionally, the amino acids F314, P315, Q316 and V339, within LRRs 11 and 12, were each found to be necessary for the sensing of triacylated lipopeptides by TLR1. More importantly, mutation of these same critical residues …
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Molecular modeling and simulations of viruses: structure, dynamics and antibody design
… to determine the atomic structure of highly-flexible capsid domains, which could not be solved using a single experimental method, and to unravel the molecular mechanisms of host-pathogen interactions. Furthermore, we have recently integrated MD simulation into a de novo antibody design …