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Understanding the interaction of antibodies and transcription factors with their ligands through structural biology
Škerlová, Jana
Understanding protein function highly benefits from the knowledge of its three-dimensional structure, especially in the case of protein-ligand complexes. Structural biology methods such as X-ray crystallography, SAXS and NMR are therefore widely used for structural studies of protein-ligand interaction. In this work, these methods were used to understand two biological processes involving protein interactions: X-ray structural analysis was used to study binding of effector molecule to a prokaryotic transcription factor. NMR and SAXS techniques were used to study interaction of a monoclonal antibody with its protein antigen. Transcriptional regulator DeoR negatively regulates the expression of catabolic genes for the utilization of deoxyribonucleosides and deoxyribose in Bacillus subtilis. DeoR comprises an N-terminal DNA-binding domain and a C-terminal effector-binding domain (C-DeoR), and its function is regulated by binding of a small-molecular effector deoxyribose-5-phosphate. We determined crystal structures of C-DeoR both in the free form and in complex with deoxyribose-5-phosphate. Structural analysis revealed unique covalent binding of effector molecule through a reversible Schiff-base double bond with an effector-binding-site lysine residue. The physiological nature of this binding mode was...
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Protein engineering as a tool for the production of antibody derivatives
Šulc, Josef ; Bařinka, Cyril (advisor) ; Mikulecký, Pavel (referee)
This thesis deals with production and properties of disulfide-stabilized single-chain variable fragments of the 5D3 antibody (dsscFv), which specifically recognizes and binds to glutamate carboxypeptidase II (GCPII), an antigen closely related to the prostate carcinoma processes and other tumor diseases. Small antibody fragments are in current focus of development of diagnostic and therapeutic reagents. However, compromised stability of antibody derivatives often results in low production yield or loss of function. Introduction of structural changes by protein engineering is often used to solve the issue. The aim of the study was based on enhancement of protein stability by the introduction of interdomain disulfide bond into the structure of single-chain variable fragment. The effect of modification was evaluated by estimation of production yield and affinity of studied protein. The aforementioned antibody derivative was produced using an Escherichia coli expression system, using specific signal sequences leading the production to the bacterial periplasm. The attempted stabilization was carried out by introducing mutations at LV-G44 and HV-G100 positions, replacing glycines with cysteines. The binding affinity of the derivative for human GCPII was determined using ELISA. This thesis also shows a solved 3D...
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Understanding the interaction of antibodies and transcription factors with their ligands through structural biology
Škerlová, Jana
Understanding protein function highly benefits from the knowledge of its three-dimensional structure, especially in the case of protein-ligand complexes. Structural biology methods such as X-ray crystallography, SAXS and NMR are therefore widely used for structural studies of protein-ligand interaction. In this work, these methods were used to understand two biological processes involving protein interactions: X-ray structural analysis was used to study binding of effector molecule to a prokaryotic transcription factor. NMR and SAXS techniques were used to study interaction of a monoclonal antibody with its protein antigen. Transcriptional regulator DeoR negatively regulates the expression of catabolic genes for the utilization of deoxyribonucleosides and deoxyribose in Bacillus subtilis. DeoR comprises an N-terminal DNA-binding domain and a C-terminal effector-binding domain (C-DeoR), and its function is regulated by binding of a small-molecular effector deoxyribose-5-phosphate. We determined crystal structures of C-DeoR both in the free form and in complex with deoxyribose-5-phosphate. Structural analysis revealed unique covalent binding of effector molecule through a reversible Schiff-base double bond with an effector-binding-site lysine residue. The physiological nature of this binding mode was...
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Understanding the interaction of antibodies and transcription factors with their ligands through structural biology
Škerlová, Jana ; Maloy Řezáčová, Pavlína (advisor) ; Hrabal, Richard (referee) ; Obšil, Tomáš (referee)
Understanding protein function highly benefits from the knowledge of its three-dimensional structure, especially in the case of protein-ligand complexes. Structural biology methods such as X-ray crystallography, SAXS and NMR are therefore widely used for structural studies of protein-ligand interaction. In this work, these methods were used to understand two biological processes involving protein interactions: X-ray structural analysis was used to study binding of effector molecule to a prokaryotic transcription factor. NMR and SAXS techniques were used to study interaction of a monoclonal antibody with its protein antigen. Transcriptional regulator DeoR negatively regulates the expression of catabolic genes for the utilization of deoxyribonucleosides and deoxyribose in Bacillus subtilis. DeoR comprises an N-terminal DNA-binding domain and a C-terminal effector-binding domain (C-DeoR), and its function is regulated by binding of a small-molecular effector deoxyribose-5-phosphate. We determined crystal structures of C-DeoR both in the free form and in complex with deoxyribose-5-phosphate. Structural analysis revealed unique covalent binding of effector molecule through a reversible Schiff-base double bond with an effector-binding-site lysine residue. The physiological nature of this binding mode was...
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