The homodimeric hemoglobin (HbI) from the blood clam Scapharca inaequivalvis binds oxygen cooperatively and thus offers a simple model system for studying communication between two chemically identical sites. Although the individual subunits of HbI have the same myoglobin-fold as mammalian hemoglobins, the quaternary assemblage is radically different. Upon oxygen binding by HbI, only small tertiary changes are seen at the subunit interface in contrast to the relatively large quaternary changes observed with mammalian hemoglobins. Analysis of structures of this hemoglobin in the liganded (02or CO) and unliganded states has provided a framework for understanding the role of individual amino acid side-chains in mediating cooperativity. The work presented in this dissertation has directly tested the central tenets of the proposed structural mechanism for cooperativity in HbI, illuminating the key roles played by residue Phe 97 and interface water molecules in intersubunit communication. Heterologous expression of Scapharca dimeric hemoglobin: A synthetic gene has been utilized to express recombinant RbI in Escherichia coli. The HbI apoprotein constitutes 5-10% of the total bacterial protein in this system. Addition of the heme precursor δ-aminolevulinic acid to the expression culture results in a ~3-fold increase in the production of soluble hemoglobin. Recombinant HbI has been successfully purified to homogeneity, resulting in a final yield of 80-100 mg of pure holoprotein from a 12 L expression culture. Analysis of recombinant HbI reveals its oxygen binding properties to be indistinguishable from native HbI. It was necessary to correct a protein sequence error by mutating residue Asn 56 to aspartate in order to obtain diffraction quality crystals, that are isomorphous to native HbI crystals. These recombinant HbI crystals diffract to high resolution, permitting the functional effects of mutant HbI proteins to be correlated with detailed structural analysis.

Proliferation and differentiation are essential processes for the growth and development of higher eukaryotic organisms. Regulation of gene expression is essential for control of cell division and differentiation. Normal eukaryotic cells have a limited proliferative capacity, and ultimately undergo cellular senescence and apoptosis. Terminal differentiation of cells is associated with loss of proliferative capacity and acquisition of specialized functions. Proliferation and differentiation are processes required for the creation and maintenance of diverse tissues both during embryonic development and postnatal life. The cell cycle is the process by which cells reproduce, and requires duplication and segregation of hereditary material. Loss of cell cycle control leads to genetic instability and cancer. Expression of replication-dependent histone genes is tightly coupled to DNA synthesis, thus making histone genes a good model for studying cell cycle regulation. The HiNF-D complex interacts with all five classes (H1, H2A, H2B, H3 and H4) of histone genes in a cell cycle-dependent manner. The CCAAT displacement protein (CDP)/Cux and the tumor suppressor pRB are key components of the HiNF-D complex. However, the molecular interactions that enable CDP/Cux and pRB to form a complex and thus convey cell growth regulatory information onto histone gene promoters are poorly understood. Transient transfection assays show that CDP/Cux represses the histone H4 promoter and that the pRB large pocket domain functions with CDP/Cux as a co-repressor. Direct interaction between CDP/Cux C-terminus and the pRB pocket domain was observed in GST pull-down assays. Furthermore, co-immunoprecipitation assays and immunofluorescence microscopy established that CDP/Cux and pRB form complexes in vivo and associate in situ. pRB interaction and co-repression with CDP/Cux is independent of pRB phosphosphorylation sites, as revealed by GST pull-down assays and transient transfection assays using a series of pRB mutant proteins. Thus, several converging lines of evidence indicate that complexes between CDP/Cux and pRB repress cell cycle-regulated histone gene promoters. CDP/Cux is regulated by phosphorylation and acetylation at the C-terminus, which contains two repressor domains and interacts with histone deacetylase HDAC1. In vivo function of the CDP/Cux C-terminus in development and gene regulation was assessed in genetically targeted mice (Cutl1tm2Ejn, referred to as Cutl1ΔC). The mice express a mutant CDP/Cux protein with a deletion of the C-terminus including the homeodomain. Indirect immunofluorescence microscopy showed that the mutant protein exhibited significantly reduced nuclear localization in comparison to the wildtype protein. Consistent with these data, DNA binding activity of HiNF-D was lost in nuclear extracts derived from mouse embryonic fibroblasts (MEFs) or adult tissues of homozygous mutant (Cutl1 ΔC -/-) mice, indicating the functional loss of CDP/Cux in the nucleus. No significant difference in growth characteristics or total histone H4 mRNA levels was observed between wildtype and Cutl1 ΔC -/- MEFs in culture. However, the histone H4.1 (murine FO108) gene containing CDP/Cux binding sites have reduced expression levels in homozygous mutant MEFs. Stringent control of growth and differentiation appears to be compromised in vivo. Homozygous mutant mice exhibit stunted growth (20-50% weight reduction), a high postnatal death rate of 60-70%, sparse abnormal coat hair and severely reduced fertility. Hair follicle deformities and severely diminished fertility in Cutl1 ΔC -/- mice suggest that CDP/Cux is required for normal development of dermal tissues and reproductive functions. Together the data presented in this dissertation provide new insight into the in vivo functions of CDP/Cux in the regulation of histone gene expression, growth control and differentiation.

An optimal antibody response to a thymus-dependent antigen requires cooperation between the B cell and an antigen-specific helper T cell. Major histocompatibility complex restriction of this interaction implies that the helper T cell recognizes antigen on the B cell surface in the context of MHC molecules, and that the antigen-specific B cell gets help by acting as an antigen presenting cell for the helper T cell. However, a number of studies have shown that normal resting B cells are ineffective as antigen presenting cells, implying that the B cell must leave the resting state before it can interact specifically with a helper T cell. On the contrary, other studies, including those using rabbit Ig as antigen, and rabbit globulin-specific mouse T cell lines and hybridomas, show that certain T cell lines can be efficiently stimulated by normal resting B cells. One possibility I considered was that small B cells are unable to process antigens, and that the rabbit Ig-specific T cell lines used above recognize native antigen on the B cell surface. In the majority of cases, experiments with B cell lines and macrophages have shown that antigen presentation requires antigen processing, a sequence of events which includes: internalization of antigen into an acid compartment, denaturation or digestion of antigen into fragments, and the return of processed antigen to the cell surface where it can then be recognized by the T cell in the context of class II molecules of the MHC. The experiments reported here show that the rabbit Ig-specific T cell lines do require an antigen processing step, and that small resting B cells, like other antigen presenting cells, process antigen before presenting it to T cells. Specifically, I show that an incubation of 2-8 hours is required after the antigen pulse before antigen presentation becomes resistant to fixation or irradiation. Shortly after the pulse, the antigen enters a pronase resistant compartment. Chloroquine, which raises the pH of endocytic vesicles, inhibits presentation. In addition, a large excess of antibody to native antigen fails to block presentation of antigen after a 2-8 hour incubation. Also, although membrane Ig, the antigen receptor on the B cell, is required for efficient presentation of antigen at low concentrations, antigen is no longer associated with the B cell receptor at the time of presentation to the T cell. Modulation of membrane Ig by anti-Ig blocks presentation before but not after the antigen pulse.

Endocytosis is important for the regulation of signal transduction and for the movement of essential cellular components from outside the cell to their appropriate intracellular compartment(s). Two established mechanisms of endocytosis are clathrinmediated (CME) and clathrin-independent endocytosis, and they are responsible for internalization of different ligands. In this study, the newly established technique of total internal reflection fluorescent microscopy (TIRF-M) was used, along with standard biochemical and molecular biological tools, to systematically study the sorting and early trafficking of two established ligands of endocytosis, transferrin (Tf) and epidermal growth factor (EGF). TIRF-M studies revealed that Tf binds its receptor that is located in large clathrin arrays positioned just below the surface of the cell and that these large clathrin platforms serves as the major site of CME at the plasma membrane. EGF endocytosis is very different and occurs as follows 1) the liganded EGFR recruits Rab5 to the plasma membrane, 2) Rab5 concentrates around vesicles containing liganded EGFR and 3) these vesicles co-localize with EEA1 enriched endosomes. EEA1 was shown to play a pivotal role in EGF endocytosis, establishing a new role for EEA1 in vesicle trafficking in addition to its role in tethering and fusion. Finally, WDFY2, a new FYVE domain protein was shown to decorate a specific subset of vesicles, upstream of the EEA1 vesicle pool that appear to participate in Tf endocytosis. These studies establish new functions and components of endocytosis that enhances our understanding of this complex process.

As critical regulators of vesicular trafficking, Rab proteins comprise the largest GTPase family, with thirty-eight functionally distinct members and another twenty isoforms in the human genome. Activated Rab GTPases interact with effector proteins involved in vesicle formation, transport, tethering, docking and fusion. The specificity of Rab interactions with effectors and regulatory factors plays a central role with respect to the fidelity of membrane trafficking. Rab recognition determinants and the mechanisms underlying interactions with structurally diverse regulatory factors and effectors are complex and poorly understood. Using Rab5 mediated endocytic transport as a model system, the work described in this thesis provides insight into the structural basis underlying the interaction of effectors and regulatory factors with Rab GTPases. In addition, structural and biochemical approaches have been used to define how specific Rab5 interacting proteins function in the endocytic and recycling pathways. These results establish novel structural and functional concepts that can be tested using family wide analyses of Rab GTPase recognition determinants and regulatory roles in the cell.

A clear definition of the mechanisms involved in synaptic transmission is of paramount importance for the understanding of the processes governing synaptic efficacy. Despite decades of intense study, these mechanisms remain poorly understood. The work contained in this thesis examines several such mechanisms using the hypothalamic-neurohypophysial system (HNS), a classical preparation for the study of Ca2+-dependent neuropeptide release. The first portion of this thesis is comprised of my efforts to define the cellular machinery essential for the exocytosis of secretory granules isolated from peptidergic neurohypophysial terminals of the HNS. Here, using the planar lipid bilayer model system, I have been able to show that syntaxin alone in the target membrane is sufficient to elicit fusion of modified neurohypophysial secretory granules. Surprisingly, SNAP-25 does not appear to be necessary for this process. This suggests that syntaxin may be able to substitute for SNAP-25 to form functional non-cognate fusion complexes. Additionally, the coupling of amperometric detection with the planar lipid bilayer system has allowed me to confirm these results using native, unmodified secretory granules, and also provides some insight into the kinetics of release in this reconstituted system. This model system should provide a convenient means for the study of additional regulatory factors believed to be involved in secretory vesicle exocytosis. The second and third sections of this thesis involve my examination of the role of presynaptic Ca2+ stores in neuropeptide secretion from isolated peptidergic neurohypophysial terminals (NHT). I initially examined the source of recently discovered ryanodine-sensitive Ca2+ stores in this system. Using Immuno-electron microscopy I have found that ryanodine receptor (RyR) labeling appears to co-localize with large dense core granules. Additionally, I have shown that a large conductance cation channel, with similarities to the RyR, found in the membrane of these granules has the same characteristic response to pharmacological agents specific for the RyR. Further, application of RyR agonists modulates basal neuropeptide release from NHT. These results suggest that the large dense core granules of NHT serve as the source of a functional ryanodine-sensitive Ca2+store. Recent work has revealed that spark-like Ca2+ transients, termed syntillas, can be observed in NHT. These syntillas arise from ryanodine-sensitive intracellular stores. In other neuronal preparations, similar Ca2+ transients have been suggested to affect spontaneous transmitter release. However, such a role for syntillas had yet to be examined. To assess if syntillas could directly trigger spontaneous release from NHT, I used simultaneous Ca2+imaging along with amperometric detection of release. Amperometry was adapted to this system via a novel method of false-transmitter loading. Using this approach I have found no apparent correlation between these two events, indicating that syntillas are unable to directly elicit spontaneous transmitter release. As this finding did not rule out an indirect modulatory role of syntillas on release, I additionally present some preliminary studies examining the ability of ryanodine-sensitive Ca2+ release to modulate vesicular priming. Using immunocytochemistry, I have shown that RyR agonist treatment shifts the distribution of neuropeptides toward the plasma membrane in oxytocinergic NHT, but not in vasopressinergic NHT. RyR antagonists have the opposite affect, again only in oxytocinergic NHT. Further, I have found that application of RyR agonists result in a facilitation of elicited release in NHT using membrane capacitance recording. This facilitation appears to be due primarily to an increase in recruitment of vesicles to the readily-releasable pool. These findings suggest that ryanodine-sensitive Ca2+stores may be involved in vesicular priming in NHTs. Taken together, the work presented in this thesis provides some new and interesting insights into the underlying mechanisms and modulation of transmitter release in both the HNS and other CNS terminals.

The promoter sequence of the mouse high affinity neurotensin receptor, Ntr-1, gene was cloned and characterized, sequences required for positive regulation in N1E-115 cells were localized, and at least two different peptides from these cells were shown to make specific contacts within the most potent positive regulatory element. A mouse neuroblastoma cell line, N1E-115, treated with 1.5% DMSO for 72 hours induces gene expression of both endogenous Ntr-l, and reporter constructs driven by the NTR-1 promoter, by 3 - 4 fold. The sequence ofthe NTR-1 promoter has no canonical TATA box, but is GC rich and contains consensus SP1, CACCC, CRE, and initiator elements. These elements are located within a 193 base positive regulatory region required for DMSO responsive activity and contains the transcriptional start site. Detailed mutational analysis of this region revealed that a CACCC box and the central region of a large GC rich palindrome are crucial cis-regulatory elements for DMSO induction. The SP1 element, an NGFI-A-related element, and the 5' end of the positive regulatory region are required for maintaining basal expression in N1E-115 cells. Cell type differences in the cis-regulatory elements that mediate both DMSO induction and maintenance of basal expression are observed. Characterization of proteins in N1E-115 cells that make specific contacts within the CACCC element identified at least two peptides with predicted sizes of 57 kd and 97 kd. Two dimensional UV crosslinking indicates that these proteins might contribute to inducible gel shift complexes that require the CACCC element. Several previously characterized CACCC binding proteins, belonging to the Kruppel-like family of transcription factors, were tested by supershift analysis for their ability to contribute to NTR-1 CACCC complexes. In fact, a protein closely related to SP1 does bind the CACCC element in N1E-115 cells, but of the other Kruppel-like protein tested, only BKLF contributes to a minor complex in N1E-115 cells. These results provide evidence for the complex regulation of Ntr-1 gene expression mediated by the cooperation of several cis-regulatory elements including a CACCC Kruppel-like binding element.

CP1 (encoded by the gene CEP1) is a sequence-specific DNA-binding protein of Saccharomyces cerevisiae that recognizes a sequence element (CDEI) found in both yeast centromeres and gene promoters. Strains lacking CP1 are viable but exhibit defects in growth, chromosome segregation, and methionine biosynthesis. To investigate the basis of the methionine requirement, a YEp24-based yeast genomic DNA library was screened for plasmids which suppressed the methionine auxotrophy of a cep1 null mutant. The suppressing plasmids contained either CEP1 or DNA derived from the PHO4 locus. PHO4 encodes a factor which positively regulates transcription of genes involved in phosphate metabolism via an interaction with CDEI-like elements within the promoters of these genes. Subcloning experiments confirmed that suppression correlated with increased dosage of PHO4. PHO4c, pho80, and pho84 mutations, all of which lead to constitutive activation of the PHO4 transcription factor, also suppressed cep1 methionine auxotrophy. The suppression appeared to be a direct effect of PHO4, not a secondary effect of PHO regulon derepression, and was dependent on a second transcriptional regulatory protein encoded by PHO2. Spontaneously arising extragenic suppressors of the cep1 methionine auxotrophy were also isolated; approximately one-third of the them were alleles of pho80. While PHO4 overexpression suppressed the methionine auxotrophy of a cep1 mutant, CEP1 overexpression failed to suppress the phenotype of a pho4 mutant; however, a cep1 null mutation suppressed the low-Pi growth deficiency of a pho84 mutant. The results suggest that CP1 functions as a transcriptional regulator of MET genes, and that activation of PHO4 restores expression to those genes transcriptionally-disabled by the cep1mutation. The results also suggest the existence of a network that cross-regulates transcription of genes involved in methionine biosynthesis and phosphate metabolism. A direct molecular approach to investigate CP1's role in MET gene expression was also taken. CDEI sites are associated with the promoter regions of most MET genes, but only MET16, the gene encoding PAPS reductase, has been shown to require CP1 for expression; both PAPS reductase activity, and MET16 mRNA are absent in cep1 mutants. Results of the present study demonstrate that CP1 participates in two systems which regulate expression of MET16, one triggered by methionine starvation and requiring the transactivator MET4 (pathway-specific control), and the other triggered by starvation for many different amino acids and requiring GCN4 (general control). CP1 was shown to mediate its regulatory function through the upstream CDEI site, and to act directly or indirectly to modulate the chromatin structure of the MET16 promoter. In addition, the pho80 mutation was found to partially restore MET16 expression to the cep1 strain, confirming the proposed nature of PHO4 suppression. A second methionine biosynthetic gene MET25, was also analyzed. Like MET16, MET25 was found to be regulated by both pathway-specific and general control mechanisms, but in contrast to MET16, CP1 only participated in the pathway-specific response of this gene. The results demonstrate that CP1, possibly by modulating changes in chromatin structure, assists the regulatory proteins MET4 and GCN4 in activating transcription of MET genes.

In mammals a single receptor protein binds both insulin-like growth factor II (IGF-II) and mannose 6-phosphate (Man 6-P) containing ligands, most notably lysosomal enzymes. However, in chick embryo fibroblasts IGF-II binds predominantly to a type 1 IGF receptor, and no IGF-II/Man 6-P receptor has been identified in this species. In order to determine if chickens possess an IGF-II/Man 6-P receptor, an affinity resin (pentamannosyl 6-phosphate (PMP) Sepharose) was used to purify receptors from chicken membrane extracts by their ability to bind mannose 6-phosphate. Then 125I-IGF-II was used to evaluate their ability to bind IGF-II. These experiments demonstrate that nonmammalian Man 6-P receptors lack the ability to bind IGF-II, suggesting that the ability to bind IGF-II has been gained recently in evolution by the mammalian Man 6-P receptor. The second area of study involves the serum form of the IGF-II/Man 6-P receptor. This receptor had been detected in the serum of a number of mammalian species, yet its structure, function, regulation, and origin were unknown. Initial studies, done with Dr. R. G. MacDonald, showed that the serum receptor is truncated such that the C-terminal cytoplasmic domain of the cellular receptor is removed. These studies also demonstrate a regulation of serum receptor levels with age, similar to that seen for the cellular receptor, and that the serum form of the receptor existed in several forms which appeared intact under nonreducing conditions, but as multiple proteolytic products upon reduction. Finally, these studies demonstrated that both the cellular and serum IGF-II/Man 6-P receptors are capable of binding IGF-II and Man 6-P simultaneously. In studies on the serum form of the IGF-II/Man 6-P receptor that I have conducted independently, the regulation of the serum IGF-II/Man 6-P and transferrin receptors by insulin has been demonstrated. In these studies, insulin injected into rats subcutaneously resulted in a time and dose dependent increase in serum receptor levels. Finally, to investigate the relationship of the serum IGF- II/Man 6-P receptor to the cellular form of the receptor, pulse chase experiments were performed. These experiments demonstrate that the soluble (serum form released into the medium) receptor is a major degradation product of the cellular receptor. Furthermore, the lack of detectable amounts of the lower Mr soluble receptor intracellularly and the parallel relationship of cell surface and soluble receptor suggest that the proteolysis is occurring from the cell surface. Finally, a number of experiments suggest that the degradation rate depends upon the conformation state of the receptor: binding of IGF-II or Man 6-P makes the receptor more susceptible to proteolysis while the presence of lysosomal enzymes prevents receptor proteolysis. In summary, the serum form of the IGF-II receptor is a proteolytic product of the cellular form of the receptor. The rate of release depends upon the number of receptors at the cell surface and the binding state of the receptor. In circulation, the receptor retains the ability to bind both types of ligands, it thus may serve as an IGF binding protein and/or a lysosomal enzyme binding protein. These results suggest a model whereby the cellular receptor is proteolytically cleaved by a plasma membrane protease to produce a short membrane anchored fragment and the serum receptor. In vivo this pathway serves as the major degradative pathway of the IGF-II/Man 6-P receptor, with the serum form being cleared from circulation by further degradation and reuptake.

Deoxycytidylate (dCMP) hydroxymethylase (CH) catalyzes the formation of 5-hydroxymethyl-dCMP (Hm5CMP) from dCMP and methylene tetrahydrofolate (CH2THF), analogous to the reaction between dUMP and CH2THF catalyzed by thymidylate synthase (TS), an enzyme of known structure. The amino acid sequence identity between invariant TS residues and CH is at least 50%. Most of the residues which contact the dUMP and CH2THF in TS are conserved in CH. It is hypothesized that CH is homologous to TS in both structure and mechanism. The project described in this thesis tests this hypothesis. In-vitro studies on catalysis by CH variants. The roles of three residues in catalysis by CH have been tested using site-directed mutagenesis. Conversion of Cys148 to Asp, Gly or Ser decreases CH activity at least 105 fold, consistent with a nucleophilic role for Cys148 (analogous to the catalytic Cys in TS). In crystalline TS, hydrogen bonds connect O4 and N3 of bound dUMP to the side chain of an Asn; the corresponding CH residue is Asp179. Conversion of Asp179 in CH to Asn reduces kcat/KM for dCMP by 104 fold and increases kcat/KM for dUMP 60 fold, changing the nucleotide specificity of the enzyme. Other studies have shown that the specificity of TS was changed from dUMP to dCMP by conversion of the appropriate Asn to Asp. Based on the crystal structure of TS, a Glu residue (also conserved in CH) is proposed to catalyze formation of the N5 iminium ion methylene donor by protonation of N10 of CH2THF. In CH and TS, overall turnover and tritium exchange are tightly coupled. Replacement of Glu60 in CH or Glu58 in TS uncouples these catalytic steps. Conversion the Glu60/58 to Gln or Asp results in a 5-50 fold decrease in the ability to catalyze tritium exchange, consistent with an inability to catalyze formation of the N5 iminium ion, but also results in a 104-105 decrease in product formation. This suggests that Glu60/58is also involved in a step in catalysis after nucleotide and folate binding and proton removal from carbon 5 of the nucleotide. Isotope effect studies. The observed value of the α-secondary tritium inverse equilibrium isotope effect (EIE = 0.8) on formation of the complex between FdUMP, CH2THF and both wild-type CH and CH(D179N) indicates that carbon 6 of FdUMP is sp3 hybridized (tetrahedral) in the ternary complex. This is consistent with the hypothesis that that carbon 6 is bonded to Cys148 in the complex. Removal of Cys148in CH prevents complex formation with FdUMP. Lack of an observed α-secondary tritium kinetic isotope effect (KIE) for position 6 of dCMP for both enzymes suggests that the intrinsic KIE is masked by other rate-limiting steps or that rehybridization follows the first irreversible step. An observed KIE on carbon 6 of dUMP by CH(D179N) suggests the rate-limiting steps for the two nucleotide substrates is different. In-vivo studies catalysis by CH variants. In order to prevent recombination between CH deficient T4 phage and plasmid borne copies of CH variants, the gene coding for CH, gene 42, was deleted from the T4 chromosome. The T4Δ42 phage requires wild-type CH expressed from a plasmid to kill their host cell. CH variants C148G, D179N, E60Q, and E60D, all which exhibit at least 2000 fold lower activity in vitro, do not complement the T4Δ42 phage in vivo. Interchanging the functional domains of CH and TS. It is proposed that shortening the C-terminal loop seen in the structure of TS changes the solvent structure of the CH active-site such that it becomes more hydrated. Differences in the solvent structure of the active-site may account for differences in the catalytic specificity between CH and TS, respectively, hydration versus reduction. In order to test the hypothesis that these catalytic differences between TS and CH lie within the C-terminal portion of the enzyme, the N-terminus of the CH(D179N) variant was fused to the C-terminus of the wild-type TS to create a chimeric CH/TS enzyme. The chimeric enzyme was predicted to have specificity for dUMP and a active-site solvent structure similar to that for wild-type TS. However, the resulting protein cannot be overproduced to significant levels and does not have any detectable TS activity in vivo.