Biological polymers, including proteins and the genome, undergo folding processes crucial for their proper functioning. Even slight changes in the folding structure of these biopolymers can have... Show moreBiological polymers, including proteins and the genome, undergo folding processes crucial for their proper functioning. Even slight changes in the folding structure of these biopolymers can have significant implications, leading to the development of various pathological conditions, such as neurodegenerative diseases and cancer. In this thesis, we leverage the theoretical framework of Circuit Topology and expand its application to real-world scenarios. By employing this approach, we quantify the folding patterns of biological polymers, offering valuable insights for detecting harmful misfolds. Furthermore, this research holds the potential to provide fundamental design principles for molecular engineering in the realm of pharmaceutical applications. Show less
This thesis describes experiments, in which we used an optical-tweezers setup to study a number of biological systems. We studied the interaction between the E. coli molecular chaperone SecB and a... Show moreThis thesis describes experiments, in which we used an optical-tweezers setup to study a number of biological systems. We studied the interaction between the E. coli molecular chaperone SecB and a protein that was being unfolded and refolded using our optical tweezers setup. Our measurements clearly showed that in the presence of SecB, an unfolded protein could not refold. Molecular dynamics simulations were used to successfully explain features that were observed in our unfolding experiments. Our approach enables studies on other chaperones, as well. Next, we aimed to study translocation of single proteins through membranes by the E. coli Sec translocase. We modified an often-used model protein for our experiment. Different used experimental strategies are presented. Future experiments should enable measurements on the translocation of a single protein. The last study was on the packaging of double-stranded DNA by a single bacteriophage phi29. We aimed to study the effect of multivalent cations on the negatively-charged, tightly-packed DNA inside the bacteriophage capsid and in that way on the speed of the packaging process. A special DNA molecule was constructed and used in a number of successful packaging experiments. Future experiments should show the effect of cations on the packaging rate. With Summary in Dutch Show less
This thesis describes experiments, in which we used an optical-tweezers setup to study a number of biological systems. We studied the interaction between the E. coli molecular chaperone SecB and a... Show moreThis thesis describes experiments, in which we used an optical-tweezers setup to study a number of biological systems. We studied the interaction between the E. coli molecular chaperone SecB and a protein that was being unfolded and refolded using our optical tweezers setup. Our measurements clearly showed that in the presence of SecB, an unfolded protein could not refold. Molecular dynamics simulations were used to successfully explain features that were observed in our unfolding experiments. Our approach enables studies on other chaperones, as well. Next, we aimed to study translocation of single proteins through membranes by the E. coli Sec translocase. We modified an often-used model protein for our experiment. Different used experimental strategies are presented. Future experiments should enable measurements on the translocation of a single protein. The last study was on the packaging of double-stranded DNA by a single bacteriophage phi29. We aimed to study the effect of multivalent cations on the negatively-charged, tightly-packed DNA inside the bacteriophage capsid and in that way on the speed of the packaging process. A special DNA molecule was constructed and used in a number of successful packaging experiments. Future experiments should show the effect of cations on the packaging rate. Show less
This thesis describes the peroxidase activity of the electron-transfer protein cytochrome c, and how it is controlled by the protein matrix. It is shown that unfolding cytochrome c has the effect... Show moreThis thesis describes the peroxidase activity of the electron-transfer protein cytochrome c, and how it is controlled by the protein matrix. It is shown that unfolding cytochrome c has the effect to significantly enhance its peroxidase activity of (up to several thousand-fold). This can be achieved by chaotropic agents or by detergents. The hydrogen peroxide-driven inactivation of the heme cofactor of cytochrome c is also characterised. Show less
