Protein structure predication is a field of computational molecular modeling with an enormous potential for improvement. Side-chain geometry prediction is a critical component of this process that is crucial for computational protein structure predication as well as crystallographers in refining experimentally determined protein crystal structures. The cornerstone of side-chain geometry prediction are side-chain rotamer libraries, usually obtained through exhaustive statistical analysis of existing protein structures. Little is known, however, about the driving forces leading to the preference or suitability of one rotamer over another. Construction of 3D hydropathic interaction maps for nearly 30,000 tyrosines extracted from the PDB reveals their environments, in terms of hydrophobic and polar (collectively “hydropathic”) interactions. Using a unique 3D similarity metric, these environments were clustered with k-means. In the ϕ, ψ region (–200° < ϕ < –155°; –205° < ψ < –160°) representing 631 tyrosines, clustering reduced the set to 14 unique hydropathic environments, with most diversity arising from favorable hydrophobic interactions. Polar interactions for tyrosine include ubiquitous hydrogen bonding with the phenolic OH and a handful of unique environments surrounding the backbone. The memberships of all but one of the 14 environments are dominated by a single χ1/χ2 rotamer. Each tyrosine residue attempts to fulfill its hydropathic valence. Structural water molecules are thus used in a variety of roles throughout protein structure. A second project involves elucidating the 3D structure of CRIP1a, a cannabinoid 1 receptor (CB1R) binding protein that could provide information for designing small molecules targeting the CRIP1a-CB1R interaction. The CRIP1a protein was produced in high purity. Crystallization experiments failed, both with and without the last 9 or 12 amino acid peptide of the CB1R C-terminus. Attempts were made to use NMR for structure determination; however, the protein precipitated out during data acquisition. A model was thus built computationally to which the CB1R C-terminus peptide was docked. HINT was used in selecting optimum models and analyzing interactions involved in the CRIP1a-CB1R complex. The final model demonstrated key putative interactions between CRIP1a and CB1R while also predicting highly flexible areas of the CRIP1a possibly contributing to the difficulties faced during crystallization.

Ribosomal protein L27 is a component of the eubacterial large ribosomal subunit that has been shown to play a critical role in substrate stabilization during protein synthesis. This function is mediated by the L27 N-terminus, which protrudes into the peptidyl transferase center where it interacts with both A-site and P-site tRNAs as well as with 23S rRNA. We observed that L27 in S. aureus and other Firmicutes is encoded with a short N-terminal extension that is not present in most Gram-negative organisms, and is absent from mature ribosomes. The extension contains a conserved cleavage motif; nine N-terminal amino acids are post-translationally removed from L27 by a site-specific protease so that conserved residues important for tRNA stabilization at the peptidyl transferase center are exposed. We have identified a novel cysteine protease in S. aureus that performs this cleavage. This protease, which we have named Prp, is conserved in all bacteria containing the L27 N-terminal extension. L27 cleavage was shown to be essential in S. aureus; un-cleavable L27 did not complement an L27 deletion. Cleavage appears to play an essential regulatory role, as a variant of L27 lacking the cleavage motif could not complement. Ribosomal biology in eubacteria has largely been studied in E. coli; our findings indicate that there are aspects of the basic biology of the ribosome in S. aureus and other related bacteria that differ substantially from that of E. coli. This research lays the foundation for the development of new therapeutic approaches that target this novel, essential pathway.

A sequential series of mutational events is necessary for the development of leukemia. The misexpression of TAL1, a basic helix-loop-helix (bHLH) transcription factor, is the most common mutation in T cell acute lymphoblastic leukemia (T-ALL). Tal1 transgenic mice develop leukemia with a long latency and incomplete penetrance indicating additional mutations are necessary to develop disease. To investigate additional mutational events that potentially contribute to TAL1-expressing T-ALL patients, we sought to identify cooperating mutations in Tal1 transgenic mice. Clinical studies implicated the loss of the INK4a/ARF locus, which encodes two tumor suppressors, p16INK4a and p14ARF, in the majority of T-ALL patients. We demonstrated disease acceleration in tal1/ink4a/arf+/-, tal1/pl6ink4a+/- and tal1/p19arf+/- mice, thereby providing genetic evidence that Tal1 cooperates with loss of either p16Ink4a or p19Arf in leukemogenesis. The cooperation of Tal1 with the loss of or p16Ink4a or p19Arf, is consistent with our observation that Tal1 alters cell cycle regulation in leukemia by promoting S phase induction and apoptosis in vivo. An additional mutational event common in tal1 tumors is activation of the Notch1 signaling pathway. We provide evidence that the majority of tal1 tumors express increased levels of Notch1, and exhibit activating notch1 mutations. Additionally, tal1 tumors display sensitivity to the pharmacologic inhibition of γ-secretase activity in vitro, indicating that γ-secretase inhibitors may prove an efficacious treatment for TAL1-expressing T-ALL patients. Furthermore, we developed a doxycycline-regulated NotchIC T-ALL cell line, which will allow the identification of important Notch1IC target genes in leukemogenesis.

This dissertation addresses the role for Janus Kinase 3 (Jak3) in CD4+ T cell homeostasis and function. Jak3 is a protein tyrosine kinase whose activity is essential for signals mediated by the γc dependent cytokines IL-2, -4, -7, -9, -15, and -21. Previous data have demonstrated that peripheral CD4+ T cells from Jak3-deficient mice have a memory phenotype and are functionally impaired in both proliferative and IL-2 responses in vitro. Interestingly, Jak3/γc activity has been previously shown to play a role in the prevention of T cell anergy. These studies were initiated to more precisely define the role for Jak3/γc cytokines in the prevention of T cell anergy and the maintenance of functional CD4+ T cell responses. We began to address this question by assessing global gene expression changes between wild type and Jak3-/- CD4+ T cells. These data indicate that Jak3-/- CD4+ T cells have an increase in gene expression levels of inhibitory surface receptors as well as immunosuppressive cytokines. Further analyses confirmed that Jak3-deficient T cells express high levels of PD-1, secrete a Trl-type cytokine profile following direct ex vivo activation, and suppress the proliferation of wild type T cells in vitro. These characteristics indicate that CD4+ Jak3-/- T cells share properties with regulatory T cell subsets that have an important role in peripheral tolerance and the prevention of autoimmunity. We next addressed whether these regulatory characteristics were T cell intrinsic or rather the result of expanding in a Jak3-deficient microenvironment characterized by a number of immune abnormalities and a disrupted splenic architecture. Jak3-/- CD4+ T cells proliferate in vivoin a lymphopenic environment and selectively acquire regulatory T cell characteristics in the absence of any additional activation signals. While the precise mechanism by which Jak3-deficient T cells acquire these characteristics remains unclear, our data indicate that one important component is a T cell-intrinsic requirement for Jak3 signaling. These findings indicate several interesting aspects of T cell biology. First, these studies, demonstrate that the homeostatic proliferation of CD4+ T cells is not dependent on signaling via γc-dependent cytokine receptors. And, second, that the weak activation signals normally associated with homeostatic expansion are sufficient to drive Jak3-/- T cells into a non-conventional differentiation program. Previous data indicate that, for wild type T cells, signaling through both the TCR as well as γc-dependent cytokine receptors promote the homeostatic proliferation of T cells in lymphopenic hosts. Since Jak3-/- T cells are unable to receive these cytokine signals, their proliferation is likely to be wholly dependent on TCR signaling. As a consequence of this TCR signaling, Jak3-/- T cells proliferate, but in addition, are induced to up regulate PD-1 and to selectively activate the IL-10 locus while shutting off the production of IL-2. Since this fate does not occur for wild type T cells in a comparable environment, it is likely that the unique differentiation pathway taken by Jak3-/- T cells reflects the effects of TCR signaling in the absence of γc-dependent cytokine signaling. Interestingly, wild type T cells undergoing homeostatic expansion in lymphopenic hosts show many common patterns of gene expression to freshly-purified unmanipulated Jak3-/- T cells. For instance, micro array analysis of gene expression in wild type CD4+ T cells after lymphopenia induced homeostatic expansion show a similar pattern of upregulation in surface markers (PD-1 and LAG-3), and cytokine signaling molecules (IL-10 and IFN-γ cytokine, receptors, and inducible gene targets) to that of Jak3-/- CD4+ T cells immediately ex vivo. These data suggest that the process of homeostatic proliferation normally induces immune attenuation and peripheral tolerance mechanisms, but that full differentiation into a regulatory T cell phenotype is prevented by γc-dependent cytokine signals. Taken together these data suggest that Jak3 plays an important role in tempering typical immune attenuation mechanisms employed to maintain T cell homeostasis and peripheral tolerance.

Nuclear hormone receptors (NHR) constitute a superfamily of ligand inducible transcriptional activators that enable an organism to regulate development and homeostasis through switching on or off target genes in response to stimuli reflecting changes in environment as well as endocrine. NHRs include classical steroid hormone receptors (GR, AR, ER and MR) and retinoid, thyroid hormone receptors. One long-term goal of our lab is to understand the molecular mechanisms through which the transcriptional activity of NHRs is regulated. Extensive studies in the past few years have revealed that in addition to the dependence on ligand availability, the transcriptional activity of NHRs is also regulated by two types of proteins: co activators and corepressors. In the absence of ligand, many NHRs, including TR and RAR can actively repress target gene transcription with the help of corepressors, proteins that physically interact with both NHRs and histone deacetylases (HDACs). Functional interactions between NHRs and corepressors therefore lead to tightly compact and transcriptionally non-permissive chromatin structures after the removal of obstructive acetyl groups from histone tails by HDACs. On the other hand, ligand binding stabilizes NHRs in a conformation that favors interaction with proteins other than corepressors; many of these proteins are able to potentiate the transcriptional activity of NHRs through various mechanisms, such as histone acetylation, chromatin remodeling and recruitment of basal transcription machinery and are collectively termed coactivators. Two highly related corepressors, SMRT (silencing mediator of retinoid and thyroid hormone receptors) and N-CoR (nuclear receptor corepressor), have been cloned. This research in corepressor SMRT started by a systematic study of its subcellular localization. We found that SMRT predominantly forms a specific nuclear punctuate structure that does not appear to overlap with any other well-known subnuclear domains/speckles. Although our searching for specific sequence signals that may determine the specific speckle localization of SMRT did not yield conclusive results, we discovered the colocalization of unliganded RAR and certain HDACs, including HDAC1, 3,4 and 5, in the SMRT nuclear speckles. Moreover, SMRT is likely to be the organizer of such speckles since it appears to be able to recruit other proteins into these speckles. The presence of HDAC1 in the SMRT speckles suggests a direct association between these two proteins, which has not been detected by previous biochemical analyses. Interestingly, HDAC1 point mutants that are completely defective in deacetylase activity failed to locate to SMRT nuclear speckles, while another partially active mutant maintained the colocalization. These discoveries may indicate SMRT nuclear speckles as novel nuclear domains involved in transcriptional repression. More physiologically relevant support for this hypothesis arises from study of HDAC4 and 5. HDAC4 and 5 are potent inhibitors of transcriptional activator MEF2C. Nuclear presence of HDAC4/5 can block the activation of MEF2C, which is required during muscle differentiation. Normally, HDAC4 is predominantly located in cytoplasm. However, we found that in the presence of SMRT overexpression, HDAC4 was found mostly in SMRT nuclear speckles. This accumulation enhanced HDAC4 mediated inhibition on MEF2C transcriptional activity in a transient transfection assay. SMRT overexpression also resulted in accumulation of HDAC5 in the SMRT nuclear speckles compared to the nuclear diffuse distribution in the absence of SMRT. Again, this accumulation of HDAC5 in nuclear speckles correlated with enhanced inhibition of MEF2C. Taken together, our study suggested that instead of being merely a corepressor for NHRs, SMRT might function as an organizer of a nuclear repression domain, which may be involved in a broad array of cellular processes. In contrast to the limited number of corepressors, numerous co activators have been identified; the SRC (or p160) family is relatively well studied. This family includes three highly related members, SRC-1, TIF2/GRIP1, RAC3/AIB1/ACTR/p/CIP. Similar domain structures are shared among these factors, with the most highly conserved region, the bHLH-PAS domain found within the N terminal ~400 amino acid residues. This study of RAC3 aims to identify the function of the highly conserved N terminal bHLH-PAS domain by isolating interacting proteins through yeast two-hybrid screening. One candidate gene isolated encodes the C terminal fragment of the human homologue of the yeast protein MMS19. Functional studies of this small fragment revealed that it specifically interacted with human estrogen receptors (ERs) and inhibited ligand induced transcriptional activity of ERs in the transient transfection assay. Then we cloned the full-length human MMS19 cDNA and characterized the hMMS19 as a weak coactivator for estrogen receptors in the transient transfection assay. Furthermore, when tested on separate AF-1 or AF-2 of ERs, hMMS19 specifically enhanced AF-1 but had no effect on AF-2. These results identified hMMS19 as a specific coactivator for ER AF-1.

This body of work details the exploitation of an incredibly powerful neural culture system, which enables the in vitrostudy of events involved in peripheral nervous system (PNS) development. Using a myelinating dorsal root ganglion (DRG) explant culture system, node of Ranvier formation and maintenance and the associated generation and maturation of myelin segments was examined. In addition, Schwann cell (SC) development, dynamics, and migration were extensively studied. First, in characterizing these cultures, the discrete axonal localization of specific ankyrin isoforms was revealed. Ankyrins are peripheral membrane proteins that immobilize classes of integral membrane proteins to the spectrin based-membrane skeleton. Ankyrins interact with proteins such as the voltage-dependent/gated sodium channel (vgsc) and members of the L1 family of cell adhesion molecules. These interactions are physiologically relevant to the formation of membrane specializations involved in axon guidance and the initiation and propagation of action potentials. We examined ankyrinB and ankyrinG expression in cultured DRG explants, which allowed visualization of individual axons. AnkyrinB and ankyrinG exhibited differential localizations to specific axonal populations. This was evident as early as one day in vitro and persisted over time. In mature pre-myelinated cultures, axons having an apparent diameter of less than 1 µm predominantly expressed ankyrinB, whereas axons having a diameter greater than or equal to 1 µm predominantly expressed ankyrinG (based on immunocytochemical reactivity). When myelination was induced, ankyrinGwas appropriately localized to sites of nodal development flanked by myelinating glial processes in the large caliber axons. These observations suggest that axons destined for myelination may express a distinct complement of peripheral, and perhaps integral, membrane proteins as compared to those observed in non-myelinated axons. These distinguishing features may play a role in the selection of axons for myelination. This work was followed with defining the role axo-glial interactions play in organizing domains along the axon being myelinated. Nodes of Ranvier are specialized, highly polarized axonal domains crucial to the propagation of saltatory action potentials. In the PNS, axon-glial cell contacts have been implicated in SC differentiation and the formation of nodes of Ranvier. SC microvilli establish axonal contact at mature nodes, and their components have been observed to localize early to sites of developing nodes. However, a role for these contacts in node formation remains controversial. Using the myelinating explant culture system, we observed that SCs reorganize and polarize microvillar components, such as the ezrin-binding phosphoprotein 50kDa (EBP50)/regulatory co-factor of the sodium-hydrogen exchanger isoform 3 (NHERF-1), actin, and the activated ezrin, radixin, and moesin (ERM) family of proteins, concomitant with myelination in response to inductive signals. These components were targeted to the SC distal tips where live cell imaging revealed novel, dynamic growth cone-like behavior. Further, localized activation of the Rho signaling pathway at SC tips gave rise to these microvillar component-enriched “caps” and influenced the efficiency of node formation. Extending these findings, a more profound examination of SC dynamics was undertaken. This was a particularly important experimental transition, as SC motility is crucial in the development and regeneration of the PNS. The seemingly equivalent bipolarity of mature SCs represents a conundrum in terms of directed motility. Fluorescence time-lapse microscopy of transfected SCs within the myelinating DRG explants revealed a novel cycling of these cells between static, bipolar and motile, unipolar morphologies via asymmetric process retraction and extension. Concentrations of PIP2 (phosphatidylinositol (4,5)-bisphosphate), activated ERMs, and EBP50 delineated the transitory asymmetry associated with the generation and neuron-like migration of the unipolar cell. EBP50 over-expression enhanced unipolar SC migration, suggesting a new role for this adaptor protein in cell motility. Further, the ERMs themselves were found to be essential to both motility and process dynamics with ERM disruption yielding a dysfunctional, multipolar SC phenotype. We propose this novel form of motility may be associated with the correct alignment and spacing of SCs along axons prior to elaboration of the myelin sheath. These compiled studies present significant advances in understanding and examining axo-glial interactions in the PNS. This work establishes the foundation for further, novel exploration of normal PNS development and the regeneration and repair mechanisms involved in PNS injury and disease states.

Glioblastoma multiforme (GBM) is a grade IV astrocytoma and is the most aggressive malignant primary brain tumor in adults. Without treatment, patients are expected to survive an average of three months. Conversely, current treatment regimens only extend survival to 12-14 months. Characteristically, GBM tumors are highly proliferative, invasive and stop responding to treatments relatively fast due to therapy resistance. Interestingly, GBM also exhibits high metabolic activity but manages to maintain a low level of reactive oxygen species (ROS). These ROS neutralization capabilities are sustained by system Xc–, a sodium-independent, electro neutral transporter that is found in the plasma membrane of GBM cells. System Xc– is composed of a regulatory heavy subunit (4F2hc) linked to a 12 transmembrane domain catalytic light chain subunit (xCT) that mediates the uptake of L-cystine into the cell, and L-glutamate out of the cell, at a 1:1 ratio. Imported cystine is quickly reduced to L- cysteine, the rate limiting substrate in glutathione (GSH) synthesis. Glutathione is a major antioxidant in the central nervous system that is responsible for maintaining intracellular redox homeostasis by neutralizing ROS by direct and indirect methods. The function of chemo and radiation therapy is to generate significant levels of ROS that tigger the cell to undergo apoptosis. High intracellular GSH levels in cancer cells are associated with drug resistance and detoxification of alkylating agents such as temozolomide (TMZ). Therefore, system Xc– represents a potential target to reduce glioma cell survival and reduce tumor progression. Sulfasalazine is an FDA approved drug in the treatment of arthritis and Crohne’s disease and has been shown to inhibit system Xc–. In vitro SASP studies demonstrated a strong antitumor potential in preclinical mouse models of malignant glioma. However, two clinical trials using sulfasalazine with standard chemo and radiation therapy to treat GBM patients were terminated due to off-target effects. Both results showed high toxicity and no change in the overall survival of patients. These studies demonstrate the need for a more effective inhibitor of system Xc–. To further elucidate the role of system Xc– in GBM survival, stable xCT knock-down and over-expressing U251 glioma cells were generated. These lines were characterized for survival, proliferation, apoptosis and resistance to oxidative and genotoxic insult. As expected xCT-knockdown cells exhibited lower GSH levels, increased intracellular ROS and markers for apoptosis after oxidative and genotoxic insult. The xCT-over-expressing cells displayed higher levels of GSH, increased resistance to hydrogen peroxide and various chemotherapy drugs including TMZ. An interesting unforeseen result of xCT over-expression in glioma cells was an increase in the metabolic activity as a result of increased mitochondria. Using xCT-modified glioma lines stably, we demonstrate for the first time that system XC– over-expression not only promotes survival under oxidative stress but may also decreases sensitivity to chemotherapy treatment and increase metabolic properties. Therefore, therapeutic manipulation of this transporter either alone or in combination with other treatments may improve clinical outcome in patients diagnosed with GBM.

The ability of incorporation non-canonical amino acids (ncAAs) using translation offers researchers the ability of extend the functionality of proteins and peptides for many applications including synthetic biology, biophysical and structural studies, and discovery of novel ligands. Here we describe the three projects where the addition of ncAAs to in vitro translation systems creates useful chemical biology techniques. In the first, a fluorinated histidine derivative is used to create a novel affinity tag that allows for the selective purification of peptides from a complex mixture of proteins. In the second, the high promiscuity of an editing-deficient valine-tRNA synthetase (ValRS T222P) is used to demonstrate ribosomal translation of 13 ncAAs including those with novel side chains, α,α disubstitutions, and cyclic β amino acids. Lastly, a couple of these amino acids are integrated into the powerful ligand discovery tool of mRNA display for the discovery of helical peptide ligands.

Ligands of the human monoamine transporters encompass a wide range of both illicit and therapeutic drugs that act upon neural circuitry related to reward, motivation, and the processing of salient stimuli. The present study utilizes two methods for analyzing transporter substrates and inhibitors in order to characterize activity and assess potency. The first measures transient changes in intracellular calcium as a surrogate for transporter activity by harnessing the electrical coupling of monoamine transporters and L-type calcium channels. This is used to analyze novel chimera of the strong hDAT inhibitors methylphenidate and 𝛼-PPP in order to assess the contribution of specific moieties to potency. The observed reduction in potency suggests that methylphenidate may bind to the transporter in a manner distinct from 𝛼-PPP, as chimera would otherwise be expected to show similar activity to parent compounds. These results highlight the importance of 𝛼-carbon substituents and the relatively small contribution of beta-carbon groups to inhibitor potency at hDAT, while the lack of activity at hSERT suggests potency is not strongly influenced by beta-carbon or N-alkyl substituents. In order to further characterize drug-transporter interaction, a method was developed to analyze the kinetics of binding and unbinding using both known and novel hNET ligands, including a series of N-alkyl derivatives of 4-methylamphetamine. The study emphasizes the importance of both association and dissociation kinetics to affinity and sets up a methodological framework with two ways for determining Kd, with notable advantages over current models. The results indicate that lengthening the N-alkyl chain of 4-methylamphetamine leads to a decrease in potency and a shift in activity from substrate to blocker, with the results of N-propyl 4-methylamphetamine in particular indicating the potential existence of multiple low-affinity binding sites, each with distinct on and off kinetics. The implications of these results help elucidate the mechanism of action of transporter ligands and set up a framework for future studies that can more specifically classify the interaction between transporters and inhibitors or releasing agents.

DNA damage can cause genome instability, which may lead to human cancer. The most common form of DNA damage is DNA base damage, which is efficiently repaired by DNA base excision repair (BER). Thus BER is the major DNA repair pathway that maintains the stability of the genome. On the other hand, BER mediates DNA demethylation that can occur on the promoter region of important tumor suppressor genes such as Breast Cancer 1 (BRCA1) gene that is also involved in prevention and development of cancer. In this study, employing cell-based and in vitro biochemical approaches along with bisulfite DNA sequencing, we initially discovered that an oxidized nucleotide, 5’,2-cyclo-2-deoxyadenosine in DNA duplex can either cause misinsertion by DNA polymerase β (pol β) during pol β-mediated BER or inhibit lesion bypass of pol β resulting in DNA strand breaks. We then explored how a T/G mismatch resulting from active DNA demethylation can affect genome integrity during BER and found that pol β can extend the mismatched T to cause mutation. We found that AP endonuclease 1 (APE1) can use its 3'-5' exonuclease to remove the mismatched T before pol β can extend the nucleotide preventing a C to T mutation. The results demonstrate that the 3'-5' exonuclease activity of APE1 can serve as a proofreader for pol β to prevent mutation. We further explored the effects of exposure of environmental toxicants, bromate and chromate on the DNA methylation pattern on the promoter region of BRCA1 gene with bisulfite DNA sequencing. We found that bromate and chromate induced demethylation of 5-methylcytosines (5mC) at the CpG sites as well as created additional methylation at several unmethylated CpG sites at BRCA1 gene in human embryonic kidney (HEK) 293 cells. We further demonstrated that the demethylation was mediated by pol β nucleotide misinsertion and an interaction between pol β and DNA methyltransferase 1 (DNMT1) suggesting a cross-talk between BER and DNA methyltransferases. We suggest that DNA base damage and BER govern the interactions among the environment, the genome and epigenome, modulating the stability of the genome and epigenome and disease development.