Iron is important for human health and serves as a co-factor in a variety of proteins and enzymes. Human serum transferrin (hTF) is an Fe(III) transporter in blood plasma which delivers metal to cells via a receptor-mediated endocytosis. In the first part, crystal structures of FeNFeC-hTF and BiNFeC-hTF have been characterized. The N-lobes of the two structures adopt “partially opened” conformations between holo-hTF’s “closed” and apo-hTF’s “fully-opened” states. The N-lobe of BiNFeC-hTF opens wider than FeNFeC-hTF. Their metal-bound C-lobes are totally closed. Rigid-body movement and different inter-lobal hydrogen bonds for the “partially opened” conformations are observed. The binding affinities of four putative binding residues are in the order: Tyr188>Tyr95>Asp63~His249. In the N-lobe of BiNFeC-hTF, Tyr188, bicarbonate and a nitrilotriacetate (NTA) ion bind to Bi(III), whilst Tyr95 and Asp63 interact with NTA ligand. One (BiNFeC-hTF) or two (FeNFeC-hTF) glycan molecules are identified on the surface area of C-lobe. In the second part, biocoordination chemistry of selected metal ions was investigated using hTF as a template. The Al(III), Fe(III), Ga(III), Dy(III) and Yb(III)-bound hTF exhibit closed conformations in the C-lobe and “fully-opened” conformations in the N-lobe. In these structures, malonate serves as an anion in the C-lobe and provides two tunable ligation sites that lead to a less distorted octahedral coordination geometry. As a result, the large lanthanide ions (Dy(III) and Yb(III)) turn from their favored high coordination numbers (8~12) and fit into the protein’s hexadental pocket. Unexpectedly, in the presence of malonate ion and the excess amount of Dy(III) ion, the Ga(III) can be partially replaced by Dy(III), although Ga(III) has a much higher affinity than Dy(III) towards the protein. The chaperone system in Helicobacter pylorithat helps protein refold is assembled with HspB and HspA. In the third part, preliminary crystallographic work is reported for HspB and HspA. The chaperone HspB has been crystallized under various conditions and currently the diffraction resolution is 6.8Å. The co-chaperone HspA, which binds Bi(III) tightly, although its crystals diffract to 1.6Å, still needs improvement for data collection due to radiation damage.The crystal structure of HspB revealed that HspB presents as a single-ring heptamer, though it is a mixture of dimer, tetramer and a higher oligomer in solution. The interactions between HspB monomers in crystal structure are significantly weaker than that of GroEL (counterpart in Escherichia coli) monomers which may makes the HspB heptamer easier to dissociate in solution. / published_or_final_version / Chemistry / Doctoral / Doctor of Philosophy

Thesis (Ph. D.)--Biology, Georgia Institute of Technology, 2005. / Dr Yury Chernoff, Committee Member ; Dr Jung Choi, Committee Member ; Dr Nick Hud, Committee Member ; Dr Roger Wartell, Committee Member ; Dr Harish Radhakrishna, Committee Member. Vita. Includes bibliographical references.

Doctor of Philosophy / Division of Biology / Jeroen Roelofs / The ubiquitin-proteasome pathway is the major pathway of selective protein degradation in the cell. Disruption of this pathway affects cellular protein homeostasis and contributes to diseases like cancer, and neurodegeneration. The end point of this pathway is the proteasome, a complex protease formed by 66 polypeptides. Structurally, it can be subdivided into the Core Particle (CP) and the Regulatory Particle (RP). The CP harbors the proteolytic sites, whereas, the RP contains six orthologous AAA-ATPases, the Rpt proteins. These Rpt’s are essential for proteasome function and are at the interface between RP and CP. The work in this thesis focuses on the Rpt subunit Rpt5 from yeast. The C-terminal tail of Rpt5 has been shown to contribute to the binding with the CP. However, our study showed it is also essential for the interaction with Nas2, one of nine proteasome-specific chaperones. Thus, Nas2 might function as a regulator of the Rpt5-CP interaction. Further analyses suggested that Nas2 has an additional function in assembly, and that mutating the tail of Rpt5 results in increased binding of the proteasome-associated protein Ecm29 to the proteasome. We showed that Ecm29 binds Rpt5 directly, thereby inducing a closed conformation of the CP substrate entry channel, and inhibiting proteasomal ATPase activity. Consistent with these activities, several proteasome mutant strains showed Ecm29-dependent accumulation of unstable substrates. Thus, Ecm29 is an inhibitor of the proteasome in vivo and in vitro. Interestingly, besides the Rpt5 mutants, several other proteasome mutants show increased levels of Ecm29, suggesting Ecm29 has a role in quality control. Consistent with this, we observed that Ecm29 associates preferably with specific mutants and nucleotide-depleted proteasomes. Based on our data we propose a model, where early in assembly Nas2 binds to the Rpt5 tail inhibiting the Rpt5-CP interaction directly. Later in assembly Ecm29 performs a quality control function, where it recognizes and remains bound to defective proteasomes. By inhibiting these proteasomes Ecm29 prevents the aberrant degradation of proteins.

In mammalian cells newly synthesised proteins are translocated across the ER membrane and their subsequent folding is facilitated by an array of folding factors present in the lumen. These include the lectins calreticulin and calnexin, which form complexes with ERp57 to generate glycoprotein specific molecular chaperones. ERp57 is a member of the protein disulphide isomerase (PDI) family and its binding to ER lectins can be reconstituted in vitro. I have exploited this approach to define the regions of ERp57 that are necessary and sufficient for its specific interaction with calreticulin and calnexin. Truncated forms of ERp57, chimeric proteins containing various domains of ERp57 and PDI (which does not interact with calreticulin) and ERp57 b' domain point mutants have been constructed. By analysing the interactions of ERp57 derivatives with calreticulin using both cross-linking and binding assays I have been able to provide detailed insights into the molecular basis for the specific assembly of these components within the ER lumen. My results indicate that the b and b' domains of ERp57 are necessary, but not sufficient for binding to both calreticulin and calnexin. The more stringent binding assay revealed that the a' domain of ERp57 significantly enhanced binding to biotin-tagged calreticulin. The ERp57 C-terminal extension also increased binding to biotin-tagged calreticulin, perhaps by playing a role in the overall stability of the ERp57. In addition, the ERp57 b' domain point mutants show that certain amino acids in this domain, in particular residues F280, V283 and F299, may be crucial for binding to calreticulin, consistent with the principal lectin-binding site being located in the b' domain. However, the binding region clearly extends into other domains, in particular the b and a' domains.

Poly-Q expanded exon 1 of huntingtin (Q103) fused to GFP is toxic to yeast cells containing endogenous yeast prions, [PIN+] ([RNQ+]) and/or [PSI+], which presumably serve as aggregation nuclei. Propagation of yeast prions is modulated by the chaperones of Hsp100/70/40 complex. While some chaperones were reported to influence poly-Q aggregation in yeast, it was not clear whether they do it directly or via affecting yeast prions. Our data show that while dominant negative Hsp104 mutants antagonize poly-Q aggregation and toxicity by eliminating endogenous yeast prions, some mutant alleles of Hsp104 decreases size and ameliorate toxicity of poly-Q aggregates without affecting prion propagation. Elevated levels of the yeast Hsp40 proteins, Ydj1 and Sis1, exhibit opposite effects on poly-Q aggregation and toxicity without influencing prion propagation. Among the yeast Hsp70s, only overproduction of Ssa4 antagonized poly-Q toxicity. We have also isolated dominant Anti-poly-Q-toxicity (AQT) mutants counteracting poly-Q toxicity only in the absence of the major ubiquitin-conjugating enzyme Ubc4. Prion forming potential of other Q-rich proteins and influence of Q and P-rich regions on prion propagation were also studied. Our data connects poly-Q aggregation and toxicity to the stress defense pathway in yeast. As many stress-defense proteins are conserved between yeast and mammals, our data shed light on possible mechanisms modulating poly-Q aggregation and toxicity in mammalian cells.

Thesis (doctoral)--Swedish University of Agricultural Sciences, 2001. / Abstract inserted. Includes bibliographical references.

Thesis (Ph. D.)--University of Washington, 2003. / Vita. Includes bibliographical references (leaves 174-188).

Thesis (Ph.D.)--University of Wollongong, 2006. / Typescript. Includes bibliographical references: leaf 228-250.

Thesis (Ph.D.)--University of Wollongong, 2003. / Typescript. Includes bibliographical references: leaf 247-274.

Thesis (M. S.)--Biology, Georgia Institute of Technology, 2006. / Jung Choi, Committee Member ; Yury Chernoff, Committee Chair ; kirill.lobachev@biology.gatech.edu, Committee Member.