Thesis (M.Sc.)--York University, 2005. Graduate Programme in Biology. / Typescript. Includes bibliographical references (leaves 100-108). Also available on the Internet. MODE OF ACCESS via web browser by entering the following URL: http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&res_dat=xri:pqdiss&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&rft_dat=xri:pqdiss:MR19663

Thesis (Ph. D.)--University of Texas at Austin, 2007. / Vita. Includes bibliographical references.

This dissertation describes several strategies used to create diversity in non-immune antibody libraries. Two of the strategies were used to create two separate peptide focused libraries. Both of these strategies used to create these antigen-class focused libraries used a single scaffold antibody gene that contained diversity only in the variable heavy region. The scaffold antibody gene one of the libraries, the M:anti-pep library, was chosen based on hypervariable loop canonical structures that are characteristic of other anti-peptide antibodies. Additionally, all of the contact residues of this antibody are commonly used contact residues in other anti-peptide antibodies. These positions and others were varied to incorporate the natural diversity of other anti-peptide antibodies. The second library, the Hu:anti-pep, is based on a widely used, unique combination of human germline antibody segments that express well in bacterial expression. Positions were chosen for variation based on their usage as contact residues in both anti-peptide and anti-protein antibodies. The diversity was less focused than with the M:anti-pep library, incorporating all 20 amino acids at "high usage" positions and only four amino acids at "low usage" positions. Both libraries were validated by phage display selections against the peptide angiotensin (AT) and neuropeptide Y (NPY). The M:anti-pep library yielded specific antibodies to both peptides with dissociation constants as low as 14 nM against AT and 18 nM against NPY. The Hu:anti-pep library yielded specific clones with higher dissociation constants: 49 nM against NPY and 11 [mu]M against AT. The final strategy used to introduce diversity is widely used for affinity maturation of low affinity, previously selected antibodies. Extremely high rates of mutagenesis (2.2% of the gene to 2.7%) were used to create two libraries of the anti-digoxin antibody 26-10. The libraries had been screened by others in an attempt to examine the effects of highrates of mutagenesis on the directed evolution of an antibody. A total of 91 isolated clones from both libraries were sequenced. Several consensus mutations were identified near the CDRH3 in the isolated clones, indicating that they had a positive, selectable effect. This study confirmed that high-error rate antibody libraries contain more active clones than expected. Combinations of the selected consensus mutations from these libraries provide moderate enhancements to the kinetics and expression of the wild-type antibody in a non-synergistic manner. / text

Thesis (Ph.D.)--York University, 2008. Graduate Programme in Biology. / Typescript. Includes bibliographical references (leaves 243-264). Also available on the Internet. MODE OF ACCESS via web browser by entering the following URL: http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&res_dat=xri:pqdiss&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&rft_dat=xri:pqdiss:NR51693

Immunoglobulin (Ig) gene diversification plays an essential role in adaptive immunity. Faced with a continuous yet varied stream of self, non-self, and possibly harmful molecules, many organisms have mechanisms in their arsenal that have evolved to match the diversity of the antigens they encounter. In humans and mice, developing B and T lymphocytes go through a first round of genomic alteration — V(D)J recombination — in the bone marrow and the thymus, respectively. B cells can subsequently undergo two additional Ig gene diversification processes in secondary lymphoid tissues. Through somatic hypermutation (SHM), Ig variable regions of stimulated germinal center (GC)-forming B cells are mutated and further diversified, enabling affinity maturation. During class-switch recombination (CSR), on the other hand, B cells in the GC or prior to entering the GC recombine Ig constant regions, swapping the IgM-encoding locus for another isotype constant regions gene (e.g., IgG1, IgG3, IgE, IgA) to allow for different effector functions. Both B cell-specific genomic alterations are initiated when the single-stranded DNA (ssDNA) mutator enzyme activation-induced cytidine deaminase (AID) catalyzes the removal of the amino group off deoxycytidine residues, resulting in deoxyuridines and dU:dG mismatches. Low-fidelity cellular responses to the presence of dU, including the mismatch repair (MMR) and the base-excision repair (BER) pathways, are then thought to introduce mutations in SHM and CSR, as well as cause double-strand breaks (DSBs) repaired through canonical and alternative non-homologous end-joining in CSR. Though necessary for proper physiological function, these lymphocyte genome diversification processes are rife with danger for B cells and there is strong selective pressure to carefully orchestrate and target them so as not to threaten the genomic integrity of the cells through breaks or other mutations at non-Ig loci. Yet, these events can still occur, as demonstrated by the implication of AID with translocations found in some cancers (e.g., c- MYC:IGH in Burkitt’s lymphoma). Therefore, the mechanisms underlying AID mutagenic activity targeting to physiological deamination substrates have been the focus of several studies. Protein kinase A (PKA)-dependent phosphorylation of AID at its serine 38 residue has been shown to enable its interaction with replication protein A (RPA) before binding to ssDNA. Others have reported that SPT5 helps target AID to sites of RNA polymerase II (Pol II) stalling, such as the Ig switch sequences. Another cofactor, the RNA exosome complex, helps target the ssDNA mutator AID to both strands of DNA in vivo. The RNA exosome had hitherto been described in the context of RNA processing and degradation as 3’ → 5’ exoribonuclease. Sterile transcript-generating transcription at Ig loci was known to be required for proper AID catalytic activity; the newly described link between the RNA exosome and AID activity raised the prospect that RNA processing, and not mere transcription, might be playing a role in shaping the diversification of the immune repertoire in B lymphocytes. During CSR, transient three-strand structures called R loops are generated. R loops are formed as the nascent transcript invades the DNA duplex, hybridizing to the template strand, and displacing the non-template one. The G-rich nature of the non-template strand is posited to help stabilize the R loop, which allows the ssDNA mutator AID to use the exposed, non-template strand as a substrate. AID must then access the template strand. Here, we investigate the role that the RNA exosome and a potential cofactor, the putative RNA/DNA helicase senataxin (SETX), play in the sequence of biological events that result in CSR while protecting the cell from R-loop accumulation-associated genomic instability.

The antibody response has evolved under constant pressure to recognize common pathogens and also remain adaptable to novel threats. Given the limited size of the germline antibody repertoire, adaptability requires that some antibodies must be polyspecific for multiple distinct antigens. Despite the profound importance of polyspecificity in the antibody response, the structural features that allow it are not well understood. Antibodies raised against glycoconjugates of Chlamydiaceae LPS oligosaccharides of the inner-core sugar Kdo (3-deoxy-d-manno-oct-2-ulosonic acid) have been shown to cross-react with several inner-core oligosaccharides through conserved recognition of single Kdo residues in a germline-encoded pocket, with additional sugars accommodated by flexible side-chains. Two of these antibodies, S25-2 and S25-39, were observed to bind several Kdo oligosaccharides with an identical binding site conformation, but adopted unique conformations of the heavy chain complementarity determining region loop 3 (CDR H3) in the absence of ligand. Conformational flexibility of germline antibodies is believed to facilitate polyspecificity by generating multiple unique binding sites in a single antibody. This thesis research further explores the conformational flexibility of the antibodies S25-2 and S25-39 to gain insight into mechanisms of antigen recognition and how this feature may allow polyspecificity. This was achieved first by solving structures of S25-39 from crystals grown in unique conditions to observe alternate CDR H3 conformations, and second by designing synthetic Kdo-based antigens so as both to inhibit interaction with the previously observed liganded conformation of S25-2 and S25-39 and to be accommodated by their observed unliganded conformations. These structures reveal an unprecedented level of structural diversity of CDR H3, notably including the exact ‘liganded’ conformation in the absence of ligand. This is the first direct structural evidence that CDR H3 can exist in a conformational equilibrium with antigen binding through a selection mechanism, as opposed to induced fit where antigen causes the observed conformational change. Definitive evidence for binding the synthetic antigens was not obtained, however the resulting structures revealed several additional unique conformations of CDR H3 suggesting that ligands can alter conformational equilibria during crystallization. A unique conformation was also observed with CDR H3 coordinating multiple iodide ions, revealing another potential source of polyspecificity with unique binding paratopes generated by ion coordination. Finally, the unparalleled level of conformational diversity observed for these antibodies highlights the challenges of antibody structure classification and prediction, and stresses the need for additional in-depth studies of conformational diversity and binding mechanisms to advance these fields for therapeutic application. This is the first targeted structural study of flexibility in antibodies and provides insight into their conformational dynamics and antigen-binding mechanisms. These are of fundamental importance in understanding antibody structure and function, a critical consideration in practical applications such as modelling and design of therapeutic or diagnostic antibodies. / Graduate / 2019-11-27

Call number: LD2668 .T4 1985 S78 / Master of Science

Thesis (Ph. D.)--University of Oklahoma. / Bibliography: leaves 115-127.

Thesis (Ph.D.)--University of Alabama at Birmingham, 2009. / Title from PDF title page (viewed on Sept. 9, 2009). Includes bibliographical references.

Thesis (Ph. D.)--Lund University, 1995. / Published dissertation.