Thesis (Ph. D.)--Rutgers University, 2009. / "Graduate Program in Chemistry." Includes bibliographical references (p. 147-163).

No description available.

Thesis (Ph. D.)--Tufts University, 2003. / Advisers: Klaus Miczek; Joe DeBold. Submitted to the Dept. of Psychology. In title, GABAA is spelled GABA with a subscript A. Includes bibliographical references (leaves 146-183). Access restricted to members of the Tufts University community. Also available via the World Wide Web;

Dissertation (Ph.D.) -- University of Texas Southwestern Medical Center at Dallas, 2008. / Vita. Bibliography: p.121-126

The MDM2 protein regulates the tumour suppressor protein p53, acting as its chaperone, regulating its translation and targeting p53 for degradation by the 26s proteasome via its E3 ligase activity. The E3 ligase activity of MDM2 is dependent on its C-terminal RING domain. E3 ligases containing a RING domain are traditionally thought to catalyse the transfer of ubiquitin from their conjugating enzyme (E2) partner to the target protein, in the final step of the ubiquitination cascade. Various E2 enzymes have been shown to interact with their partner E3 ligases, yet evidence for the interaction between MDM2 and its partner E2, UbcH5α has not yet been shown. It has been reported that the reason for this lack of evidence is that the interaction between the two is highly unstable. Here I show that MDM2 forms a stable isolatable interaction with UbcH5α, the C-terminal tail of MDM2 is not necessary for this interaction. Although RING E3 ligases were not previously thought to interact with ubiquitin, preliminary evidence is emerging that suggests that this interaction is possible indeed I show that MDM2 and ubiquitin form a stable complex. I demonstrate that UbcH5α and ubiquitin both interact with the RING of MDM2, specifically the 20 most C-terminal amino acids of MDM2. My results show that both these proteins can bind this region of the RING simultaneously. I also highlight specific residues including tyrosine 489 and arginine 479 important for UbcH5α and ubiquitin binding respectively and the negative affect that these mutations have on the E3 ligase activity of MDM2 towards p53. Furthermore I show by limited proteolysis and hydrogen deuterium exchange that UbcH5α can be allosterically activated by MDM2. A novel peptide phage display technique linked to next generation sequencing was developed to further confirm an allosteric change and demonstrates that UbcH5α has different binding specificity for peptides when in a free or ligand bound conformation. MDM2 is a popular target for cancer therapeutics due to its dysregulation throughout many cancer types, including 30% of soft tissue sarcomas. Dissecting the mechanism of MDM2 function is an important step in identifying specific drugable interfaces on MDM2 and its interacting partners so that effective therapeutics can be designed.

abstract: G protein-coupled receptors (GPCRs) are known to be modulated by membrane cholesterol levels, but whether or not the effects are caused by specific receptor-cholesterol interactions or cholesterol’s general effects on the membrane is not well-understood. Results from coarse-grained molecular dynamics (CGMD) simulations coupled and structural bioinformatics offer new insights into how cholesterol modulates GPCR function by showing cholesterol interactions with β2AR that agree with previously published data. Additionally, differential and specific cholesterol binding in the CCK receptor subfamily was observed while revealing a previously unreported Cholesterol Recognition Amino-acid Consensus (CRAC) sequence that is also conserved across 38% of class A GPCRs. Mutation of this conserved CRAC sequence of the β2AR affects cholesterol stabilization of the receptor in a lipid bilayer. Serial femtosecond crystallography (SFX) with X-ray free electron lasers (XFELs) has proven highly successful for structure determination of challenging membrane proteins crystallized in lipidic cubic phase, however, as most techniques, it has limitations. Using an optimized SFX experimental setup in a helium atmosphere we determined the room temperature structure of the adenosine A2A receptor (A2AAR) at 2.0 Å resolution and compared it with previous A2AAR structures determined in vacuum and/or at cryogenic temperatures. Specifically, we demonstrated the capability of utilizing high XFEL beam transmissions, in conjunction with a high dynamic range detector, to collect high-resolution SFX data while reducing crystalline material consumption and shortening the collection time required for a complete data set. The results of these studies provide a better understanding of receptor-cholesterol interactions that can contribute to novel and improved therapeutics for a variety of diseases. Furthermore, the experimental setups presented herein can be applied to future molecular dynamics and SFX applications for protein nanocrystal samples to aid in structure-based discovery efforts of therapeutic targets that are difficult to crystallize. / Dissertation/Thesis / Doctoral Dissertation Biochemistry 2020

The studies described in this dissertation examine the effects of F-2,6-P2 and AMP or phosphorylation on the kinetic mechanism of d-PFK. The effect of varied pH on the activation by F-2,6-P2 is also described.

The CB1 cannabinoid receptor is a G-protein coupled receptor highly expressed throughout the central nervous system, that has been suggested as a target for the treatment of various disorders, including anxiety, pain and neurodegeneration. Despite the wide therapeutic potential of CB1, development of potential drug candidates has long been hindered by concerns about adverse effects, rapid tolerance development and abuse potential. Ligands that produce biased signaling have been proposed as a strategy to dissociate therapeutic and adverse effects for a variety of G-protein coupled receptors. Biased signaling involves selective activation of a signaling transducer in detriment of another, mainly involving selective activation of G-protein signaling or b-arrestin signaling. However, biased signaling at the CB1 receptor is poorly understood due to the lack of strongly biased agonists. The development of biased agonists would be aided by understanding the molecular mechanism that leads to biased signaling. Although the structure of CB1 has been resolved in the inactive state and in the canonical active state, which allows G-protein signaling, little is known about the alternative active state that allows b-arrestin biased signaling. Therefore, we set out to investigate molecular and pharmacological tools that could shed light on the mechanism of CB1 biased signaling and to characterize novel allosteric ligands with a biased signaling profile. Using molecular dynamics stimulation of CB1 bound to a ORG27569, an allosteric ligand that stimulates b-arrestin signaling and inhibits G-protein signaling, we proposed single amino acid mutations that were predicted to impact b-arrestin signaling, and expressed wild-type and mutated CB1 receptor in HEK293 cells to measure signaling through different signaling transducers. We found that N7.49 and Y7.53, two amino acids in the highly conserved NPXXY motif, were essential for b-arrestin recruitment and signaling, but mutating them to Ala and Phe, respectively, did not impact G-protein signaling. We also found that I2.43, a functionally conserved amino acid on transmembrane helix 2, negatively regulates a switch in the rotameric position of Y7.53, as mutating I2.43 to Ala reduced steric hindrance upon Y7.53 and enhanced b-arrestin1 recruitment and signaling, while mutating it to Thr, a polar residue that would further hinder Y7.53, partially inhibited b-arrestin recruitment. Therefore, we concluded that N7.49 and Y7.53 form a hydrogen bond network along with D2.50 that is essential for the alternative active state that stimulates b-arrestin biased signaling. N7.49 acts as a fulcrum on which transmembrane helix 7 can bend, and Y7.53 acts as a rotamer toggle switch, stabilizing conformational changes on the intracellular end of transmembrane helix 7. This is the first record of a molecular mechanism for CB1 b-arrestin biased signaling involving the NPXXY motif. Due to the highly conserved character of these residues, it is possible that this mechanism can also be applied to other class A G-protein coupled receptors. In addition, we characterized novel biased allosteric ligands that stimulate or inhibit b-arrestin1 signaling. Two ORG27569 analogs were found to enhance orthosteric agonist induced b-arrestin1 recruitment and extracellular-signal regulated kinase 1/2 phosphorylation (pERK), with no effect on G-protein signaling. Two pregnenolone analogs absent of the steroid scaffold were found to inhibit pERK signaling independent of Gprotein signaling, indicating that they hinder b-arrestin dependent signaling. Since these analogs are believed to mediate their effects via stimulation or inhibition of conformational changes on transmembrane helix 7, our findings support a role for this domain on the alternative active state of CB1. In contrast, a GAT211 analog, GAT1601, had no effect on recruitment of b-arrestin1, but stimulated G-protein signaling and slightly enhanced barrestin2 recruitment. This compound binds to an allosteric site, where it stimulates the canonical active state of CB1 by facilitating the outward movement of transmembrane helix 6. Altogether, the results presented in this dissertation suggest that CB1 b-arrestin biased signaling is regulated by the NPXXY motif, which stimulates conformational changes on the transmembrane helix 7/helix 8 elbow, and that stimulating or hindering these conformational changes can enhance or disrupt CB1 b-arrestin biased signaling. However, facilitating the movement of transmembrane helix 6 favors G-protein biased signaling. Our findings provide molecular and pharmacological tools that will be of great importance to structure guided drug design and to future studies on the functional consequences of biased signaling at the CB1 receptor.

No description available.

No description available.