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1.
Guerrant, William.
Targeted histone deacetylase inhibition.
Degree: PhD, Chemistry and Biochemistry, 2012, Georgia Tech
URL: http://hdl.handle.net/1853/44907 
► Histone deacetylase (HDAC) inhibitors (HDACi) have demonstrated a wealth of biological effects, including anti-proliferative, anti-inflammatory, anti-parasitic, and cognition-enhancing activities. The recent FDA approvals of the…
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▼ Histone deacetylase (HDAC) inhibitors (HDACi) have demonstrated a wealth of biological effects, including anti-proliferative, anti-inflammatory, anti-parasitic, and cognition-enhancing activities. The recent FDA approvals of the inhibitors SAHA and FK-228 have validated HDACi clinical use in cutaneous T cell lymphoma, while numerous clinical trials are currently ongoing using HDACi against a variety of disease states. While the future of the HDAC field looks increasingly promising, there are lingering issues hindering broader use. Recent data point to dysregulation of specific HDAC isoforms in many disease states. However, most current HDACi are pan-inhibitors, lacking the specificity to target individual isoforms. Adding to this, there are currently 18 identified HDAC isoforms, and most lack a defined crystal structure, further complicating the task of designing isoform-specific inhibitors. Most importantly, HDACi have demonstrated a lack of efficacy against solid tumors in the clinic, a major obstacle to broader use in cancer therapy. Several of these issues could more fully be addressed through specific targeting of HDACi, and could bring HDACi into wider and more efficacious pharmaceutical use. Targeting the specific tissue or organelle where HDAC dysregulation occurs could confer greater efficacy in vivo. To this end, we have created four classes of compounds: (1) aryltriazolyl HDACi that potently inhibit HDAC activity and prostate cancer cell growth, (2) dual-targeted inhibitors of Topoisomerase II and HDAC and (3) dual-targeted inhibitors of Topoisomerase I and HDAC, both of which have potent inhibition against both target enzymes as well as cancer cell lines, and finally (4) macrocyclic HDACi that potently inhibit the growth of lung cancer cell lines and preferentially target lung tissue in vivo.
Advisors/Committee Members: Yomi Oyelere (Committee Chair), Donald Doyle (Committee Member), James Powers (Committee Member), Loren Williams (Committee Member), Yuhong Fan (Committee Member).
Subjects/Keywords: HDAC inhibitors; Drug design; Targeted drug delivery; HDAC; Histone deacetylase; Bifunctional inhibitors; Cancer therapy; Drug delivery systems; Cancer Treatment; Enzymes
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APA (6th Edition):
Guerrant, W. (2012). Targeted histone deacetylase inhibition. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/44907
Chicago Manual of Style (16th Edition):
Guerrant, William. “Targeted histone deacetylase inhibition.” 2012. Doctoral Dissertation, Georgia Tech. Accessed January 23, 2021.
http://hdl.handle.net/1853/44907.
MLA Handbook (7th Edition):
Guerrant, William. “Targeted histone deacetylase inhibition.” 2012. Web. 23 Jan 2021.
Vancouver:
Guerrant W. Targeted histone deacetylase inhibition. [Internet] [Doctoral dissertation]. Georgia Tech; 2012. [cited 2021 Jan 23].
Available from: http://hdl.handle.net/1853/44907.
Council of Science Editors:
Guerrant W. Targeted histone deacetylase inhibition. [Doctoral Dissertation]. Georgia Tech; 2012. Available from: http://hdl.handle.net/1853/44907
Georgia Tech
2.
Das, Prolay.
Long-Range Charge Transfer in Plasmid DNA Condensates and DNA-Directed Assembly of Conducting Polymers.
Degree: PhD, Chemistry and Biochemistry, 2007, Georgia Tech
URL: http://hdl.handle.net/1853/19856
► Long-distance radical cation transport was studied in DNA condensates where linearized pUC19 plasmid was ligated to an oligomer and transformed into DNA condensates with spermidine.…
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▼ Long-distance radical cation transport was studied in DNA condensates where linearized pUC19 plasmid was ligated to an oligomer and transformed into DNA condensates with spermidine. DNA condensates were detected by Dynamic Light Scattering and observed by Transmission Electron Microscopy. Introduction of charge into the condensates causes long-distance charge migration, which is detected by reaction at the remote guanines. The efficiency of charge migration in the condensate is significantly less than it is for the corresponding oligomer in solution. This result is attributed to a lower mobility for the migrating radical cation in the condensate, caused by inhibited formation of charge-transfer-effective states. Radical cation transport was also studied in DNA condensates made from an oligomer sandwiched between two linearized plasmids by double ligation. Unlike the single ligated plasmid condensates, the efficiency of charge migration in the double ligated plasmid-condensates is high, indicative of local structural and conformational transformation of the DNA duplexes.
Organic monomer units having extended ð-conjugation as part of a long conducting polymer was synthesized and characterized. The monomer units were covalently attached to particular positions in DNA oligonucleotides by either the convertible nucleotide approach or by phosphoramidite chemistry. Successful attachment of the monomer units to DNA were confirmed by mass spectral analysis. The DNA-conjoined monomer units can self assemble in the presence of complementary sequences which act as templates that can control polymer formation and structure. By this method the para-direction of the polymer formation can be enforced and may be used to generate materials having nonrecurring, irregular structures.
Advisors/Committee Members: Dr. Gary B. Schuster (Committee Chair), Dr. David M. Collard (Committee Member), Dr. Donald Doyle (Committee Member), Dr. Marcus Weck (Committee Member), Dr. Uzi Landman (Committee Member).
Subjects/Keywords: DNA charge transfer; Conducting polymers; Radical cation; Self assembly; Conducting polymers; Charge tranfer in biology; Cations; DNA; Self-organizing systems
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APA (6th Edition):
Das, P. (2007). Long-Range Charge Transfer in Plasmid DNA Condensates and DNA-Directed Assembly of Conducting Polymers. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/19856
Chicago Manual of Style (16th Edition):
Das, Prolay. “Long-Range Charge Transfer in Plasmid DNA Condensates and DNA-Directed Assembly of Conducting Polymers.” 2007. Doctoral Dissertation, Georgia Tech. Accessed January 23, 2021.
http://hdl.handle.net/1853/19856.
MLA Handbook (7th Edition):
Das, Prolay. “Long-Range Charge Transfer in Plasmid DNA Condensates and DNA-Directed Assembly of Conducting Polymers.” 2007. Web. 23 Jan 2021.
Vancouver:
Das P. Long-Range Charge Transfer in Plasmid DNA Condensates and DNA-Directed Assembly of Conducting Polymers. [Internet] [Doctoral dissertation]. Georgia Tech; 2007. [cited 2021 Jan 23].
Available from: http://hdl.handle.net/1853/19856.
Council of Science Editors:
Das P. Long-Range Charge Transfer in Plasmid DNA Condensates and DNA-Directed Assembly of Conducting Polymers. [Doctoral Dissertation]. Georgia Tech; 2007. Available from: http://hdl.handle.net/1853/19856
Georgia Tech
3.
Thaler, Tracey Lyn.
Search for Extraterrestrial Life using Chiral Molecules: Mandelate Racemase as a Test Case.
Degree: PhD, Chemistry and Biochemistry, 2007, Georgia Tech
URL: http://hdl.handle.net/1853/14527
► The possible existence of extraterrestrial life forms has been of interest to humans for many millennia. In the past few decades space travel has provided…
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▼ The possible existence of extraterrestrial life forms has been of interest to humans for many millennia. In the past few decades space travel has provided an opportunity to search life outside of Earth. Chiral molecules are critical molecules in Earth-based life and are among the first chemical molecules sought after as proof of potential extraterrestrial life; however, identification of these chiral molecules is difficult due the lack of sensitive instruments. The objective of this work is to develop a benchmark reaction to be used as a guide in the development of instrumentation, such as a polarimeter, to be used in the search for extraterrestrial life. To achieve this objective, to investigate the enzyme mandelate racemase (MR), which catalyzes the racemization between the enantiomers of mandelate. MR is a member of the enolase superfamily, which contains a (alpha/beta)7-b barrel domain, the fold most frequently found among all known protein structures.
Activity of the enzyme was measured at low temperatures and in non-aqueous media, as these are the conditions that represent extraterrestrial terrain. We find that mandelate racemase (MR) is active in concentrated ammonium salt solutions and water-in-oil microemulsions in a temperature range between 30C to 70C; however, the enzyme is not active in several organic cryosolvents. The stability of the structure of MR was also explored. Using differential scanning calorimetry (DSC) we observe the unfolding of the enzyme was irreversible and therefore kinetically controlled. We also found proof for divergent evolution of the enolase superfamily, providing evidence for divergent evolution across the MR and muconate lactonizing enzyme (MLE) subfamilies has been demonstrated. However, we also conclude that reactions yielding a polarimetric signal, such as racemizations employed in this work, are suitable as a tool to find signs of life.
Advisors/Committee Members: Andreas Bommarius (Committee Chair), Christoph Fahrni (Committee Member), Donald Doyle (Committee Member), Phillip Gibbs (Committee Member), Rick Trebino (Committee Member).
Subjects/Keywords: Irreversible protein denaturation; Enzymatic reactivity at subzero temperatures; Enolase superfamily; Polarimetric assay
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APA (6th Edition):
Thaler, T. L. (2007). Search for Extraterrestrial Life using Chiral Molecules: Mandelate Racemase as a Test Case. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/14527
Chicago Manual of Style (16th Edition):
Thaler, Tracey Lyn. “Search for Extraterrestrial Life using Chiral Molecules: Mandelate Racemase as a Test Case.” 2007. Doctoral Dissertation, Georgia Tech. Accessed January 23, 2021.
http://hdl.handle.net/1853/14527.
MLA Handbook (7th Edition):
Thaler, Tracey Lyn. “Search for Extraterrestrial Life using Chiral Molecules: Mandelate Racemase as a Test Case.” 2007. Web. 23 Jan 2021.
Vancouver:
Thaler TL. Search for Extraterrestrial Life using Chiral Molecules: Mandelate Racemase as a Test Case. [Internet] [Doctoral dissertation]. Georgia Tech; 2007. [cited 2021 Jan 23].
Available from: http://hdl.handle.net/1853/14527.
Council of Science Editors:
Thaler TL. Search for Extraterrestrial Life using Chiral Molecules: Mandelate Racemase as a Test Case. [Doctoral Dissertation]. Georgia Tech; 2007. Available from: http://hdl.handle.net/1853/14527
4.
Wu, Di.
Discovery and characterization of a signaling molecule regulating somatic embryogenesis in loblolly pine.
Degree: PhD, Chemistry and Biochemistry, 2008, Georgia Tech
URL: http://hdl.handle.net/1853/28252
► myo-Inositol-1,2,3,4,5,6-hexakisphosphate (InsP6), also called phytic acid, is ubiquitous in eukaryotic cells and the most abundant inositol phosphate derivative. Loblolly pine (LP, Pinus taeda) constitutes the…
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▼ myo-Inositol-1,2,3,4,5,6-hexakisphosphate (InsP6), also called phytic acid, is ubiquitous in eukaryotic cells and the most abundant inositol phosphate derivative. Loblolly pine (LP, Pinus taeda) constitutes the primary commercial species in the southern forest of U.S. Somatic embryogenesis (SE) is an effective technique to maintain the desirable genetic composition of the progeny and to accomplish the efficiency of propagation. SE can also serve as a tool for study of plant development. Unlike angiosperm embryos with attached cotyledons as seed storage organs, the diploid conifer embryo is surrounded by the unattached haploid female gametophyte (FG). In LP SE, FG tissue is absent in the embryogenic tissue culture. We found that extracts from early-stage FG stimulate growth and multiplication of early-stage somatic embryos, whereas FG water extracts from late stage contain substance(s) inhibitory to early-stage somatic embryo growth (DeSilva et al., 2007). We now present the isolation and identification of the inhibitory substance as InsP6 by means of water extraction, two gel filtrations and two ion exchange FPLC chromatographies. The results represent the first complete structural characterization of InsP6 from a natural product using LC/MS, LC/MS/MS, exact MS, 1D- and 2D-NMR analyses. We also report that there is a good correlation between the amount of InsP6 purified from FG tissue (1.3 nmoles per full-term FG) and the amount of InsP6 which inhibits somatic embryo growth. This novel approach of isolating and characterizing InsP6 from plant tissue, and investigating its role on SE can allow us to improve SE technology by circumventing current bottleneck, to elucidate enigmatic functions of InsP6 in plants, and most importantly, to utilize this molecule properly.
Advisors/Committee Members: Dr. Sheldon May (Committee Chair), Dr. Donald Doyle (Committee Member), Dr. Gerald Pullman (Committee Member), Dr. James Powers (Committee Member), Dr. Nicholas Hud (Committee Member).
Subjects/Keywords: NMR; LC/MS; FPLC; Female gametophyte; Loblolly pine; Somatic embryogenesis; Myo-inositol hexakisphosphate; Loblolly pine; Somatic embryogenesis; Phytic acid
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APA (6th Edition):
Wu, D. (2008). Discovery and characterization of a signaling molecule regulating somatic embryogenesis in loblolly pine. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/28252
Chicago Manual of Style (16th Edition):
Wu, Di. “Discovery and characterization of a signaling molecule regulating somatic embryogenesis in loblolly pine.” 2008. Doctoral Dissertation, Georgia Tech. Accessed January 23, 2021.
http://hdl.handle.net/1853/28252.
MLA Handbook (7th Edition):
Wu, Di. “Discovery and characterization of a signaling molecule regulating somatic embryogenesis in loblolly pine.” 2008. Web. 23 Jan 2021.
Vancouver:
Wu D. Discovery and characterization of a signaling molecule regulating somatic embryogenesis in loblolly pine. [Internet] [Doctoral dissertation]. Georgia Tech; 2008. [cited 2021 Jan 23].
Available from: http://hdl.handle.net/1853/28252.
Council of Science Editors:
Wu D. Discovery and characterization of a signaling molecule regulating somatic embryogenesis in loblolly pine. [Doctoral Dissertation]. Georgia Tech; 2008. Available from: http://hdl.handle.net/1853/28252
Georgia Tech
5.
McRae, Reagan.
Investigating metal homeostasis in mammalian cells using high resolution imaging techniques.
Degree: PhD, Chemistry and Biochemistry, 2010, Georgia Tech
URL: http://hdl.handle.net/1853/41197
► The primary aim of the work presented in this thesis is to elucidate novel information regarding the uptake, storage, distributions, and functions of both copper…
(more)
▼ The primary aim of the work presented in this thesis is to elucidate novel information regarding the uptake, storage, distributions, and functions of both copper and zinc in mammalian cells by predominantly using a combination of the high resolution imaging modalities, synchrotron radiation X-ray fluorescence microscopy (SXRF) and standard fluorescence imaging. Results from studies using cell permeable, metal ion selective fluorescent probes suggested the presence of labile pools of copper and zinc localized within the mitochondria and Golgi apparatus. Furthermore, SXRF imaging of a cell line defective in the copper transporter, Atox1, revealed intriguing differences in the Cu distribution of Atox1-/- cells compared to the corresponding wild-type cells. Finally, spatially well-resolved SXRF elemental maps of single, adherent mouse cells revealed remarkable changes in the distributions of both zinc and copper as the cells progressed through the cell cycle. Taken together, findings suggested major roles for copper and zinc within a native biological setting.
Advisors/Committee Members: Christoph J. Fahrni (Committee Chair), Donald Doyle (Committee Member), Jake Soper (Committee Member), Nael A. McCarty (Committee Member), Uwe Bunz (Committee Member).
Subjects/Keywords: Microscopy; Imaging; Synchrotron based X-ray fluorescence; Copper; Zinc; Synchrotron radiation
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APA (6th Edition):
McRae, R. (2010). Investigating metal homeostasis in mammalian cells using high resolution imaging techniques. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/41197
Chicago Manual of Style (16th Edition):
McRae, Reagan. “Investigating metal homeostasis in mammalian cells using high resolution imaging techniques.” 2010. Doctoral Dissertation, Georgia Tech. Accessed January 23, 2021.
http://hdl.handle.net/1853/41197.
MLA Handbook (7th Edition):
McRae, Reagan. “Investigating metal homeostasis in mammalian cells using high resolution imaging techniques.” 2010. Web. 23 Jan 2021.
Vancouver:
McRae R. Investigating metal homeostasis in mammalian cells using high resolution imaging techniques. [Internet] [Doctoral dissertation]. Georgia Tech; 2010. [cited 2021 Jan 23].
Available from: http://hdl.handle.net/1853/41197.
Council of Science Editors:
McRae R. Investigating metal homeostasis in mammalian cells using high resolution imaging techniques. [Doctoral Dissertation]. Georgia Tech; 2010. Available from: http://hdl.handle.net/1853/41197
Georgia Tech
6.
Urs, Aarti N.
Reciprocal binding of sphingosine and phosphatidic acid to steroidogenic factor 1 regulates the transcription of CYP17.
Degree: MS, Biology, 2005, Georgia Tech
URL: http://hdl.handle.net/1853/7638
► Steroidogenic factor (SF1) is an orphan nuclear receptor that is essential for steroid hormone-biosynthesis and endocrine development. Recent studies have demonstrated that phospholipids are ligands…
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▼ Steroidogenic factor (SF1) is an orphan nuclear receptor that is essential for steroid hormone-biosynthesis and endocrine development. Recent studies have demonstrated that phospholipids are ligands for SF1. In the present study our aim was to identify endogenous ligands for SF1 and characterize their functional significance in mediating cAMP-dependent transcription of human CYP17. Using mass spectrometry we show that in H295R adrenocortical cells SF1 is bound to sphingosine (SPH) under basal conditions and that cAMP stimulation decreases the amount of SPH bound to the receptor. We also show that silencing both acid and neutral ceramidases using siRNA induces CYP17 mRNA expression, suggesting that SPH acts as an inhibitory ligand. In vitro analysis of ligand binding using scintillation proximity assays show that several sphingolipids and phospholipids, including phosphatidic acid (PA), can compete with [3H]SPH for binding to SF1, suggesting that SF1 may have more than one ligand and binding specificity may change with the changes in intracellular fluxes of phospholipids. Further, phosphatidic acid (PA) induces SF1-dependent transcription of CYP17 reporter constructs. Inhibition of diacyglycerol kinase (DAGK) activity using R59949 and silencing DAGK- expression attenuates SF1-dependent CYP17 transcriptional. We propose that PA is an activating ligand for SF1 and that cAMP-stimulated activation of SF1 takes place by displacement of SPH.
Advisors/Committee Members: Marion Sewer (Committee Chair), Alfred Merrill (Committee Member), Donald Doyle (Committee Member), Harish Radhakrishna (Committee Member).
Subjects/Keywords: CYP17; Sphingosine; Phosphatidic acids; Steroidogenic factor 1; Transcription factors; Steroid hormones Synthesis; Sphingosine; Pregnenolone; Phospholipids; Ligands
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APA (6th Edition):
Urs, A. N. (2005). Reciprocal binding of sphingosine and phosphatidic acid to steroidogenic factor 1 regulates the transcription of CYP17. (Masters Thesis). Georgia Tech. Retrieved from http://hdl.handle.net/1853/7638
Chicago Manual of Style (16th Edition):
Urs, Aarti N. “Reciprocal binding of sphingosine and phosphatidic acid to steroidogenic factor 1 regulates the transcription of CYP17.” 2005. Masters Thesis, Georgia Tech. Accessed January 23, 2021.
http://hdl.handle.net/1853/7638.
MLA Handbook (7th Edition):
Urs, Aarti N. “Reciprocal binding of sphingosine and phosphatidic acid to steroidogenic factor 1 regulates the transcription of CYP17.” 2005. Web. 23 Jan 2021.
Vancouver:
Urs AN. Reciprocal binding of sphingosine and phosphatidic acid to steroidogenic factor 1 regulates the transcription of CYP17. [Internet] [Masters thesis]. Georgia Tech; 2005. [cited 2021 Jan 23].
Available from: http://hdl.handle.net/1853/7638.
Council of Science Editors:
Urs AN. Reciprocal binding of sphingosine and phosphatidic acid to steroidogenic factor 1 regulates the transcription of CYP17. [Masters Thesis]. Georgia Tech; 2005. Available from: http://hdl.handle.net/1853/7638
Georgia Tech
7.
Gotz, Marion Gabriele.
Design, synthesis, and evaluation of irreversible peptidyl inhibitors for clan CA and clan CD cysteine proteases.
Degree: PhD, Chemistry and Biochemistry, 2004, Georgia Tech
URL: http://hdl.handle.net/1853/8072
► Cysteine proteases are a class of proteolytic enzymes, which are involved in a series of metabolic and catabolic processes, such as protein turnover, digestion, blood…
(more)
▼ Cysteine proteases are a class of proteolytic enzymes, which are involved in a series of metabolic and catabolic processes, such as protein turnover, digestion, blood coagulation, apoptosis, fertilization and cell differentiation, and the immune response system. The development of novel potent and selective inhibitors for cysteine proteases has therefore gained increasing attention among medicinal chemists. In this thesis we have reported the design, synthesis, and evaluation of several peptidyl inhibitors for clan CA and clan CD cysteine proteases.
We have continued the investigation of dipeptidyl vinyl sulfones as potent and selective inhibitors for dipeptidyl peptidase I (DPPI), a lysosomal cysteine protease, which is involved in the processing of intracellular proteases, such as granzymes. We have found that DPPI tolerates negatively charged amino acid residues in the P2 position with inhibition rates of 7,600 M-1s-1. Dipeptidyl vinyl sulfones with positively charged amino acid residues at the P1 position, however, do not inhibit DPPI at all.
A second project focused on the epoxidation of the double bond of the vinyl sulfone moiety of the dipeptidyl vinyl sulfones. Instead of epoxidizing the double bond, we found that an isomerization had occurred. The newly formed compounds were determined to be allyl sulfones. We tested this new class of inhibitors with clan CA proteases and obtained inhibition rates of 560 M-1s-1 for Cbz-Leu-Phe-AS-Ph with calpain I.
Two new classes of compounds for the clan CD protease S. mansoni legumain were designed, synthesized, and evaluated. Aza-peptidyl epoxides were found to be potent and selective inhibitors of S. mansoni legumain with IC50’s as low as 45 nM. Aza-peptide Michael acceptors were derived from the aza-peptide epoxide design and synthesized in an analogous fashion. The aza-peptide Michael acceptors inhibited S. mansoni legumain with even lower IC50’s, as low as 10 nM. However, the aza-peptide Michael acceptors react with thioalkylating agents contained in the buffer, such as DTT. The rates of degradation were determined spectroscopically, and half-lives of 3 to 20 minutes were measured. This observation gave us insights into the enzymatic mechanism and allowed us to determine the point of attack for the legumain active site cysteine thiol.
Advisors/Committee Members: Dr. James C. Powers (Committee Chair), Dr. Donald Doyle, Dr. Nicholas Hud, Dr. Niren Murthy, and Dr. Suzanne Shuker (Committee Members).
Subjects/Keywords: Allyl sulfone; Aza-peptide; Biosynthesis; Cysteine protease; Cysteine proteinases; Irreversible inhibitors; Protease inhibitors; Sulphones; Vinyl sulfone
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APA (6th Edition):
Gotz, M. G. (2004). Design, synthesis, and evaluation of irreversible peptidyl inhibitors for clan CA and clan CD cysteine proteases. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/8072
Chicago Manual of Style (16th Edition):
Gotz, Marion Gabriele. “Design, synthesis, and evaluation of irreversible peptidyl inhibitors for clan CA and clan CD cysteine proteases.” 2004. Doctoral Dissertation, Georgia Tech. Accessed January 23, 2021.
http://hdl.handle.net/1853/8072.
MLA Handbook (7th Edition):
Gotz, Marion Gabriele. “Design, synthesis, and evaluation of irreversible peptidyl inhibitors for clan CA and clan CD cysteine proteases.” 2004. Web. 23 Jan 2021.
Vancouver:
Gotz MG. Design, synthesis, and evaluation of irreversible peptidyl inhibitors for clan CA and clan CD cysteine proteases. [Internet] [Doctoral dissertation]. Georgia Tech; 2004. [cited 2021 Jan 23].
Available from: http://hdl.handle.net/1853/8072.
Council of Science Editors:
Gotz MG. Design, synthesis, and evaluation of irreversible peptidyl inhibitors for clan CA and clan CD cysteine proteases. [Doctoral Dissertation]. Georgia Tech; 2004. Available from: http://hdl.handle.net/1853/8072
Georgia Tech
8.
Roberts, Lezah Wilette.
Effect of Netropsin on One-electron Oxidation of DNA.
Degree: PhD, Chemistry and Biochemistry, 2005, Georgia Tech
URL: http://hdl.handle.net/1853/7228
► One electron oxidation of DNA has been studied extensively over the years. When a charge is injected into a DNA duplex, it migrates through the…
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▼ One electron oxidation of DNA has been studied extensively over the years. When a charge is injected into a DNA duplex, it migrates through the DNA until it reaches a trap. Upon further reactions, damage occurs in this area and strand cleavage can occur. Many works have been performed to see what can affect this damage to DNA. Netropsin is a minor groove binder that can bind to tracts of four to five A:T base pairs. It has been used in the studies within to determine if it can protect DNA against oxidative damage, caused by one-electron oxidation, when it is bound within the minor groove of the DNA. By using a naphthacenedione derivative as a photosensitizer, several DNA duplexes containing netropsin binding sites as well as those without binding sites, were irradiated at 420 nm, analyzed, and visualized to determine its effect on oxidative damage. It has been determined netropsin creates a quenching sphere of an average of 5.8 * 108 Šwhether bound to the DNA or not. Herein we will show netropsin protects DNA against oxidative damage whether it is free in solutions or bound within the minor groove of a DNA duplex.
Advisors/Committee Members: Gary B. Schuster (Committee Chair), Donald Doyle (Committee Member), Laren Tolbert (Committee Member), Nicholas V. Hud (Committee Member), Roger Wartell (Committee Member).
Subjects/Keywords: Photosensitizer; Charge transfer; Netropsin; TQ; DNA; Electron transfer; One-electron oxidation; Photosensitization, Biological; Charge transfer in biology; DNA Analysis; Oxidation, Physiological
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APA (6th Edition):
Roberts, L. W. (2005). Effect of Netropsin on One-electron Oxidation of DNA. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/7228
Chicago Manual of Style (16th Edition):
Roberts, Lezah Wilette. “Effect of Netropsin on One-electron Oxidation of DNA.” 2005. Doctoral Dissertation, Georgia Tech. Accessed January 23, 2021.
http://hdl.handle.net/1853/7228.
MLA Handbook (7th Edition):
Roberts, Lezah Wilette. “Effect of Netropsin on One-electron Oxidation of DNA.” 2005. Web. 23 Jan 2021.
Vancouver:
Roberts LW. Effect of Netropsin on One-electron Oxidation of DNA. [Internet] [Doctoral dissertation]. Georgia Tech; 2005. [cited 2021 Jan 23].
Available from: http://hdl.handle.net/1853/7228.
Council of Science Editors:
Roberts LW. Effect of Netropsin on One-electron Oxidation of DNA. [Doctoral Dissertation]. Georgia Tech; 2005. Available from: http://hdl.handle.net/1853/7228
Georgia Tech
9.
Watkins, Jason Derrick.
X-ray structures of p22 c2 repressor-dna complexes: the mechansism of direct and indirect readout.
Degree: PhD, Chemistry and Biochemistry, 2008, Georgia Tech
URL: http://hdl.handle.net/1853/26709
► The P22 c2 repressor protein (P22R) binds to DNA sequence-specifically and helps direct the temperate lambdoid bacteriophage P22 to the lysogenic developmental pathway. To gain…
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▼ The P22 c2 repressor protein (P22R) binds to DNA sequence-specifically and helps direct the temperate lambdoid bacteriophage P22 to the lysogenic developmental pathway. To gain insight into its DNA binding mechanism, we solved the 1.6 Å x-ray structure of the N-terminal domain (NTD) of P22R in a complex with a DNA fragment containing the synthetic operator sequence [d(ATTTAAGATATCTTAAAT)]2 This operator has an A-T at position 9L and T-A at position 9R and is termed DNA9T.
Van der Waals interactions between protein and DNA appear to confer sequence-specificity. The structure of the P22R NTD – NA9T complex suggests that sequence-specificity arises substantially from interaction of a valine with a complementary binding cleft on the major groove surface of DNA9T. The cleft is formed by four methyl groups on sequential base pairs of 5' TTAA 3'. The valine cleft is intrinsic to the DNA sequence and does not arise from protein-induced DNA conformational change. Protein-DNA hydrogen bonding plays a secondary role in specificity.
Advisors/Committee Members: Loren D. Williams (Committee Chair), Donald Doyle (Committee Member), Nicholas V. Hud (Committee Member), Roger Wartell (Committee Member), Stephen Harvey (Committee Member).
Subjects/Keywords: P22 repressor; Direct readout; Indirect readout; Protein binding; DNA-protein interactions; Van der Waals forces
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APA (6th Edition):
Watkins, J. D. (2008). X-ray structures of p22 c2 repressor-dna complexes: the mechansism of direct and indirect readout. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/26709
Chicago Manual of Style (16th Edition):
Watkins, Jason Derrick. “X-ray structures of p22 c2 repressor-dna complexes: the mechansism of direct and indirect readout.” 2008. Doctoral Dissertation, Georgia Tech. Accessed January 23, 2021.
http://hdl.handle.net/1853/26709.
MLA Handbook (7th Edition):
Watkins, Jason Derrick. “X-ray structures of p22 c2 repressor-dna complexes: the mechansism of direct and indirect readout.” 2008. Web. 23 Jan 2021.
Vancouver:
Watkins JD. X-ray structures of p22 c2 repressor-dna complexes: the mechansism of direct and indirect readout. [Internet] [Doctoral dissertation]. Georgia Tech; 2008. [cited 2021 Jan 23].
Available from: http://hdl.handle.net/1853/26709.
Council of Science Editors:
Watkins JD. X-ray structures of p22 c2 repressor-dna complexes: the mechansism of direct and indirect readout. [Doctoral Dissertation]. Georgia Tech; 2008. Available from: http://hdl.handle.net/1853/26709
10.
Shaffer, Hally A.
Engineering the pregnane X receptor and estrogen receptor alpha to bind novel small molecules using negative chemical complementation.
Degree: PhD, Chemistry and Biochemistry, 2011, Georgia Tech
URL: http://hdl.handle.net/1853/39620
► Nuclear receptors are ligand-activated transcription factors that play significant roles in various biological processes within the body, such as cell development, hormone metabolism, reproduction, and…
(more)
▼ Nuclear receptors are ligand-activated transcription factors that play significant roles in various biological processes within the body, such as cell development, hormone metabolism, reproduction, and cardiac function. As transcription factors, nuclear receptors are involved in many diseases, such as diabetes, cancer, and arthritis, resulting in approximately 10-15% of the pharmaceutical drugs presently on the market being targeted toward nuclear receptors. Structurally, nuclear receptors consist of a DNA-binding domain (DBD), responsible for binding specific sequences of DNA called response elements, fused to a ligand-binding domain (LBD) through a hinge region. The LBD binds a small molecule ligand. Upon ligand binding, the LBD changes to an active conformation leading to the recruitment of coactivator (CoAC) proteins and initiation of transcription. As a result of their involvement in disease, there is an emphasis on engineering nuclear receptors for applications in gene therapy, drug discovery and metabolic engineering.
Advisors/Committee Members: Bahareh Azizi (Committee Chair), Donald Doyle (Committee Chair), Andreas Bommarius (Committee Co-Chair), Loren Williams (Committee Co-Chair), Adegboyega Oyelere (Committee Member), Nick Hud (Committee Member), Sheldon May (Committee Member).
Subjects/Keywords: Nuclear receptors; Chemical complementation; Negative chemical complementation; Yeast-two hybrid selection; Pregnane X receptor; Estrogen receptor; Pregnane; Protein engineering; Nuclear receptors (Biochemistry); Transcription factors; Yeast Genetics
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Shaffer, H. A. (2011). Engineering the pregnane X receptor and estrogen receptor alpha to bind novel small molecules using negative chemical complementation. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/39620
Chicago Manual of Style (16th Edition):
Shaffer, Hally A. “Engineering the pregnane X receptor and estrogen receptor alpha to bind novel small molecules using negative chemical complementation.” 2011. Doctoral Dissertation, Georgia Tech. Accessed January 23, 2021.
http://hdl.handle.net/1853/39620.
MLA Handbook (7th Edition):
Shaffer, Hally A. “Engineering the pregnane X receptor and estrogen receptor alpha to bind novel small molecules using negative chemical complementation.” 2011. Web. 23 Jan 2021.
Vancouver:
Shaffer HA. Engineering the pregnane X receptor and estrogen receptor alpha to bind novel small molecules using negative chemical complementation. [Internet] [Doctoral dissertation]. Georgia Tech; 2011. [cited 2021 Jan 23].
Available from: http://hdl.handle.net/1853/39620.
Council of Science Editors:
Shaffer HA. Engineering the pregnane X receptor and estrogen receptor alpha to bind novel small molecules using negative chemical complementation. [Doctoral Dissertation]. Georgia Tech; 2011. Available from: http://hdl.handle.net/1853/39620
. 
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