The MotA and MotB proteins of E. coli form a MotA4MotB2 complex. Proton flow through a transmembrane channel in the complex powers flagellar rotation. Protonation of Asp-32 of MotB within the channel is proposed to cause a conformational change in the large cytoplasmic loop of MotA, which pushes against FliG in the rotor. MotB is believed to anchor the complex to the cell wall via a conserved sequence that is found in many proteins that bind peptidoglycan. The research presented in this dissertation focused primarily on the formation and activation of the MotAB proton channel. A proposed amphipathic α-helical region, extending from residue 52 through 65 of the periplasmic domain of MotB, was discovered to block proton flow through the channel in its inactive state prior to incorporation into a flagellar motor. The plug is thought to lie parallel to the periplasmic face of the cell membrane and to be removed from the membrane by a conformational change triggered by contact with the motor. Negatively charged residues near the cytoplasmic C-terminus of MotA and positively charged residues at the cytoplasmic N-terminus of MotB were identified as being important for motility. A mutational analysis and subsequent suppressor analysis suggest that these residues may align MotA and MotB to form the MotA4MotB2 complex in the proper position relative to FliG and the rotor. The underlying mechanism for producing MotA and MotB in a 2:1 ratio was also investigated and found to be primarily due to translational coupling of motA and motB. The stop codon of motA and the start codon of motB overlap, allowing the ribosome that has just completed translation of motA to reinitiate and translate motB. The efficiency of reinitiation is about 66%; presumably degradation of excess MotB not in the MotA4MotB2 complex produces the final 2:1 ratio. Research was also conducted to determine whether MotB binds directly to the peptidoglycan layer of the cell wall. Although inconclusive, the preliminary results appear to support this notion. The overall work provides insights into several aspects of the assembly and subsequent activation of the stator component of the bacterial flagellar motor.

The objective of this project was to develop a simple MCNPX model of the human eye to approximate dose delivered from proton therapy. The calculated dose included that due to proton interactions and secondary interactions, which included multiple coulombic energy scattering, elastic and inelastic scattering, and non-elastic nuclear reactions (i.e., the production of secondary particles). After benchmarking MCNPX with a known proton simulation, the proton therapy beam used at Laboratori Nazionali del Sud-INFN was modeled for simulation. A virtual water phantom was used and energy tallies were found to correspond with the direct measurements from the therapy beam in Italy. A simple eye model was constructed and combined with the proton beam to measure dose distributions. Two treatment simulations were considered. The first simulation was a typical treatment scenario-where dose was maximized to a tumor volume and minimized elsewhere. The second case was a worst case scenario to simulate a patient gazing directly into the treatment beam during therapy. Dose distributions for the typical treatment yielded what was expected, but the worst case scenario showed the bulk of dose deposited in the cornea and lens region. The study concluded that MCNPX is a capable platform for patient planning but laborious for programming multiple simulation configurations.

Classical molecular dynamics (MD) simulations are performed to study structural and dynamic properties of water confined within graphite surfaces. The surfaces are separated at distances varying between 7 and 14.5 Å and the water density is held constant at 1g/cc. Results at 298 K show the formation of a well-ordered structure constituted by water layers parallel to the graphite surfaces. The water molecules in the layers in contact with the surface have a tendency to orient their dipole parallel to the surface. Such ice-like structures may have different structural and dynamic properties than those of ice. The calculated mean square displacement reveals that the mobilities of the confined water at a separation of 8 Å become similar to that of low-temperature water (213 K) at the same density, although the structures of water are very different. The temperature at which the mobility of water confined at the separation of 7 Å would become similar to that of bulk low-temperature water was found to be 373K. With respect to the dynamics of confined water, a significant blue shift is observed in the intermolecular vibrational modes associated with the O×××O×××O bending and O×××O stretching of molecules linked by hydrogen bonds. The analysis of the geometry of water clusters confined between two graphite surfaces has been performed using ab initio methods. The ab initio calculations yield two preferential orientations of water molecules which are; 1) one O-H bond points to the surface and the other is parallel; 2) both O-H bonds are parallel to the surface. These orientations agree with those found in our MD simulation results. The calculated energy barriers for proton transfer of the confined H3O+-(H2O) complexes between two graphite model surfaces suggest that the confinement enhances the proton transfer at the separation 6-14.5 Å. When the confinement is high, at a separation of 4 Å, the barrier energies are extremely large. The confinement does not enhance proton transfer when the H3O+-(H2O) complexes are located further from the surfaces by more than 8 Å. As a result, the barrier energies start to increase at the separation of 20 Å.

The MotA and MotB proteins of E. coli form a MotA4MotB2 complex. Proton flow through a transmembrane channel in the complex powers flagellar rotation. Protonation of Asp-32 of MotB within the channel is proposed to cause a conformational change in the large cytoplasmic loop of MotA, which pushes against FliG in the rotor. MotB is believed to anchor the complex to the cell wall via a conserved sequence that is found in many proteins that bind peptidoglycan. The research presented in this dissertation focused primarily on the formation and activation of the MotAB proton channel. A proposed amphipathic α-helical region, extending from residue 52 through 65 of the periplasmic domain of MotB, was discovered to block proton flow through the channel in its inactive state prior to incorporation into a flagellar motor. The plug is thought to lie parallel to the periplasmic face of the cell membrane and to be removed from the membrane by a conformational change triggered by contact with the motor. Negatively charged residues near the cytoplasmic C-terminus of MotA and positively charged residues at the cytoplasmic N-terminus of MotB were identified as being important for motility. A mutational analysis and subsequent suppressor analysis suggest that these residues may align MotA and MotB to form the MotA4MotB2 complex in the proper position relative to FliG and the rotor. The underlying mechanism for producing MotA and MotB in a 2:1 ratio was also investigated and found to be primarily due to translational coupling of motA and motB. The stop codon of motA and the start codon of motB overlap, allowing the ribosome that has just completed translation of motA to reinitiate and translate motB. The efficiency of reinitiation is about 66%; presumably degradation of excess MotB not in the MotA4MotB2 complex produces the final 2:1 ratio. Research was also conducted to determine whether MotB binds directly to the peptidoglycan layer of the cell wall. Although inconclusive, the preliminary results appear to support this notion. The overall work provides insights into several aspects of the assembly and subsequent activation of the stator component of the bacterial flagellar motor.

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Thesis (M.S.)--University of Michigan, 1977.

Thesis (Ph. D.)--University of Wisconsin--Madison, 1989. / Cover title. On t.p. "[square root of]" appears as the square root symbol. Includes bibliographical references (p. 255-262).

Thesis (Ph. D.)--University of Wisconsin--Madison, 1984. / Typescript. Vita. eContent provider-neutral record in process. Description based on print version record. Includes bibliographical references (leaves 87-89).