The translocation of a biopolymer through a narrow pore exists in universal cellular processes, such as the translocations of nascent proteins through ribosome and the degradation of protein by ATP-dependent proteases. However, the molecular details of these translocation processes remain unclear. Using computer simulations we study the translocations of a ubiquitin-like protein into a pore. It shows that the mechanism of co-translocational unfolding of proteins through pores depends on the pore diameter, the magnitude of pulling force and on whether the force is applied at the N- or the C-terminus. Translocation dynamics depends on whether or not polymer reversal is likely to occur during translocation. Although it is of interest to compare the timescale of polymer translocation and reversal, there are currently no theories available to estimate the timescale of polymer reversal inside a pore. With computer simulations and approximate theories, we show how the polymer reversal depends on the pore size, r, and the chain length, N. We find that one-dimensional transition state theory (TST) using the polymer extension along the pore axis as a reaction coordinate adequately predicts the exponentially strong dependence of the reversal rate on r and N. Additionally, we find that the transmission factor (the ratio of the exact rate and the TST rate) has a much weaker power law dependence on r and N. Finite-size effects are observed even for chains with several hundred monomers. If metastable states are separated by high energy-barriers, transitions between them will be rare events. Instead of calculating the relative energy by studying those transitions, we can calculate absolute free energy separately to compare their relative stability. We proposed a method for calculating absolute free energy from Monte Carlo or molecular dynamics data. Additionally, the diffusion of a knot in a tensioned polymer is studied using simulations and it can be modeled as a one-dimensional free diffusion problem. The diffusion coefficient is determined by the number of monomers involved in a knot and its tension dependence shows a maximum due to two dominating factors: the friction from solvents and “local friction” from interactions among monomers in a compact knot. / text

published_or_final_version / abstract / Pathology / Doctoral / Doctor of Philosophy

Successful bacterial circular chromosome segregation requires that any dimeric chromosomes, which arise by crossing over during homologous recombination, are converted to monomers. Resolution of dimers to monomers requires the action of the XerCD site-specific recombinase at dif in the chromosome replication terminus region. This reaction requires the DNA translocase, FtsK(C), which activates dimer resolution by catalysing an ATP hydrolysis-dependent switch in the catalytic state of the nucleoprotein recombination complex. We show that a 62-amino-acid fragment of FtsK(C) interacts directly with the XerD C-terminus in order to stimulate the cleavage by XerD of BSN, a dif-DNA suicide substrate containing a nick in the 'bottom' strand. The resulting recombinase-DNA covalent complex can undergo strand exchange with intact duplex dif in the absence of ATP. FtsK(C)-mediated stimulation of BSN cleavage by XerD requires synaptic complex formation. Mutational impairment of the XerD-FtsK(C) interaction leads to reduction in the in vitro stimulation of BSN cleavage by XerD and a concomitant deficiency in the resolution of chromosomal dimers at dif in vivo, although other XerD functions are not affected.

Thesis (Ph. D.)--University of California, Riverside, 2009. / Includes abstract. Title from first page of PDF file (viewed March 18, 2010). Includes bibliographical references. Issued in print and online. Available via ProQuest Digital Dissertations.

The chromosomes involved in twenty reciprocal translocations in G. hirsutum were reidentified by means of a specially designed crossing program. Each translocation line was crossed to appropriate monosomic, monotelodisomic, and/or translocation lines. The F₁ hybrids were then scored cytologically to verify the original chromosome identification. These twenty reciprocal translocations now become the cytogenetic tester set for G. hirsutum. Seed stocks for each verified translocation line will be maintained at, and distributed by, the University of Arizona. Nineteen of the twenty heterozygous translocations had a modal chiasma frequency per quadrivalent of four. Fourteen of these translocation lines formed predominantly ring multivalents at MI, and the remaining five translocations usually formed multivalents with at least one interstitial chiasma. One translocation line, which was originally produced by an interspecies cross, formed predominantly chains at MI. This increased amount of chaining in the quadrivalent is probably the result of interspecific chromosome material within the translocation reducing the chiasma frequency. The orientation of the centromeres in quadrivalents is influenced by the size of the chromosomes involved in the reciprocal translocation, and the constraints imposed by the chiasmata within the chromosome arms. Ten of the twenty reciprocal translocations studied formed predominantly alternate orientations at MI. Eight of these ten translocation lines were reciprocal translocations between two A subgenome chromosomes. This suggests that the large A subgenome chromosomes allow the quadrivalent to be more flexible, resulting in easy reorientation to the stable alternate configuration. Proximal chiasma formation influences the orientation and probable involvement of the homologous centromeres in spindle formation. Lines in which a high frequency of multivalents with interstitial chiasma were observed had a significantly lower frequency of multivalents with either one or two centromeres not involved in spindle formation of 3:1 orientations. In most of the heterozygous translocations, identification of each chromosome within the quadrivalent at MI was not possible. Estimation formulae were developed to estimate the positions of the breakpoints and the genetic lengths of each segment defined by multivalents in these translocations.

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

Thesis (Ph. D.)--University of Hong Kong, 2007. / Title proper from title frame. Also available in printed format.

Thesis (M.S.)--Brandeis University, 2009. / Title from PDF title page (viewed on May 29, 2009). Includes bibliographical references.

Thesis (M.Sc.)--University of Alberta, 2009. / A thesis submitted to the Faculty of Graduate Studies and Research in partial fulfillment of the requirements for the degree of Master of Science in Experimental Oncology, Department of Oncology. Title from pdf file main screen (viewed on July 30, 2009). Includes bibliographical references.

Thesis (MSc (Genetics))--University of Stellenbosch, 200 5. / The Lr19 translocation is associated with deleterious agronomic effects and as a result modified forms of the translocation have been derived by different researchers in an attempt to remove the genes responsible.