No description available.

Thesis (Ph. D.)--Ohio State University, 2007. / Title from first page of PDF file. Includes bibliographical references (p. 93-119).

Thesis (Ph. D.)--University of Alberta, 2010. / Title from pdf file main screen (viewed on Jan. 18, 2010). A thesis submitted to the Faculty of Graduate Studies and Research in partial fulfillment of the requirements for the degree of Doctor of Philosophy, Department of Biochemistry, University of Alberta. Includes bibliographical references.

Thesis (Ph. D.)--Hong Kong University of Science and Technology, 2003. / Includes bibliographical references (leaves 130-138). Also available in electronic version. Access restricted to campus users.

published_or_final_version / Chinese Medicine / Doctoral / Doctor of Philosophy

In this work we analyse aspects of dynamics and organization of biological membranes from a physical prospective [i.e. perspective]. We provide an analysis of the process of self-assembly and spatial organization of membrane proteins. We illustrate the analysis by considering a channel activated by membrane tension called mechanosensitive channels (MS), in E. coli and the twin arginine translocation system (Tat). We analyse the mechanism of formation of oligomeric protein complexes formed by identical subunits. By derivation of a mathematical approach based on Smoluchowski coagulation equation, we study the deficiency of the process of complex formation, taking into account both irreversible aggregation, as well as fragmentation. We find that a small fragmentation rate increases the efficiency of the formation process, however if the fragmentation rate vanishes the irreversible process is very inefficient. Our second aim is to determine how the spatial organization can affect the function of channels, which are regulated by elastic forces. We map these short-range interactions into a discretized system, from which we obtain the spatial distribution of the channels and its effect on the gating dynamics. We find that organized channels activate at lower membrane tensions, but possess a delay in the reaction time. In the last part we determine how the formation of transient pores on the membrane depends on the dynamics of its assembly process. We analyse the pores formed by the Tat complex, which is responsible for protein transport through the membrane. This system functions by polimerization in response to a signal of transport demand from a protein in the cell cytoplasm. The direct correlation of the size of the assembled pore and the size of the protein determines the speed of the translocation process. Using a differential equation approach we obtain that the flux of a given protein depends quadratically on its size.

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Biochemical and structural studies of membrane protein usually require their stabilization in solution with detergents. However, purified membrane proteins often show reduced activity and stability in traditional detergents. Lipopeptide detergents (LPDs) are a new class of engineered amphiphiles that from small micelles and mimic the lipid bilayer more closely than traditional detergents. An LPD molecule consists of an α-helical peptide with fatty acyl chains covalently attached to both ends. These molecules self-assemble into cylindrical micelles with a hydrophilic exterior and a hydrophobic interior made up of the fatty acyl chains. Here we present the biophysical and biochemical properties of a model bacterial ABC transporter, MsbA, in different LPD variations. Four types of LPD molecules have been synthesized and have been categorized as original LPD, LPD5Q, LPD2, and LPD4 based on the peptide sequence. Dynamic light scattering, thermal aggregation, and ATPase activity were used to measure the biophysical properties of MsbA in LPDs and in a traditional detergent, n-decyl-β-D-maltoside (DM). The results show that MsbA-LPD particles are monodisperse with small hydrodynamic radii. When compared to DM, MsbA is thermodynamically more stable and has higher catalytic activity in LPDs. Membrane proteins have favorable biophysical properties in LPDs, suggesting that these detergents resemble the native lipid bilayer environment more closely. We also present crystal structures of three LPDs: LPD-12, LPD5Q-14 and LPD- 14. These structures reveal that LPD micelles are highly ordered with varying oligomeric states. The octomeric structure of the LPD-12 micelle is composed of four sets of antiparallel coiled-coil dimers, while the LPD5Q-14 micelle assembles as a nonamer of three trimers each with an “up-up-down” topology. The LPD-14 micelle, on the other hand, is a dodecamer of three tetramers with all helices assuming an antiparallel orientation. Overall, the structures of LPDs show highly ordered detergent micelles that are made up of repeated building blocks. Based on these results, we propose that LPDs can sample multiple conformational states, but the number of accessible conformations is significantly reduced relative to traditional detergents. Our results show that LPDs are an alternative platform for in vitro studies of membrane proteins. Future studies will focus on the crystallization of membrane proteins in LPDs and the further characterization of these complexes.