+publisher:"University of North Carolina" +contributor:("Wolfenden, Richard")

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University of North Carolina

1. Stockbridge, Randy Buzzell. Insights Into the Catalysis of Phosphoryl Group Transfer by Enzymes.

Degree: Biochemistry and Biophysics, 2010, University of North Carolina

URL: https://cdr.lib.unc.edu/record/uuid:e535ad52-8572-417f-831f-ccf060ad96b8

Enzymes that catalyze phosphoryl group transfer draw from a wide variety of catalytic strategies, including transition state stabilization, acid/base chemistry, juxtaposition, and catalysis by desolvation. In this work, we investigate the rates and thermodynamics of activation of catalyzed and spontaneous phosphoryl group transfer reactions in order to understand the relative importance of those catalytic strategies. Reactions studied include the spontaneous transfer of a phosphoryl group from ATP to methanol in the presence and absence of Mg2+, the corresponding reactions catalyzed by Nacetyl galactosamine kinase, homoserine kinase, and yeast hexokinase, and the hydrolysis of phosphate monoesters and diesters in cyclohexane and other organic solvents. We show that N-acetyl galactosamine kinase, homoserine kinase, and yeast hexokinase accelerate phosphoryl transfer from ATP to an alcohol acceptor group by factors of 1012-1014, relative to the spontaneous transfer of a phosphoryl group from Mg-ATP to methanol, which occurs at a rate of 3.9 x 10-9 s-1M-1. These kinases achieve their rate enhancements by decreasing ΔH‡ to an extent comparable to other enzymes (8-13 kcal./mol), but they also increase TΔS‡ by 6-9 kcal./mol, in accord with the possibility that juxtaposition is a general requirement for bi-substrate enzymes. Consistent with mechanistic suggestions, the relative contributions of ΔH‡ and TΔS‡ to the rate enhancement differ for the three kinases. N-acetyl galactosamine kinase, which lacks a catalytic base, increases TΔS‡ to the greatest extent, whereas homoserine kinase and hexokinase decrease ΔH‡ and seem to rely more heavily on acid/base catalysis or transition state stabilization. We also show that extraction of neopentyl phosphate monoesters and diesters into cyclohexane accelerates their hydrolyses by factors of 2 x 1012 and 4 x 109, respectively. The hydrolysis of the monoester is accelerated to a similar extent in polar solvents like DMSO. For phosphate monoester hydrolysis in cyclohexane, the effect of desolvation was to increase TΔS‡, whereas for phosphate diester hydrolysis in cyclohexane and phosphate monoester hydrolysis in DMSO, the effect of desolvation was to decrease ΔH‡. These rate enhancements approach those generated by many enzymes, and imply that desolvation might be a powerful means of catalysis for phosphate monoesterases and phosphate diesterases. Advisors/Committee Members: Stockbridge, Randy Buzzell, Wolfenden, Richard, University of North Carolina at Chapel Hill.

Subjects/Keywords: School of Medicine; Department of Biochemistry and Biophysics

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Stockbridge, R. B. (2010). Insights Into the Catalysis of Phosphoryl Group Transfer by Enzymes. (Thesis). University of North Carolina. Retrieved from https://cdr.lib.unc.edu/record/uuid:e535ad52-8572-417f-831f-ccf060ad96b8

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Stockbridge, Randy Buzzell. “Insights Into the Catalysis of Phosphoryl Group Transfer by Enzymes.” 2010. Thesis, University of North Carolina. Accessed January 23, 2021. https://cdr.lib.unc.edu/record/uuid:e535ad52-8572-417f-831f-ccf060ad96b8.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Stockbridge, Randy Buzzell. “Insights Into the Catalysis of Phosphoryl Group Transfer by Enzymes.” 2010. Web. 23 Jan 2021.

Vancouver:

Stockbridge RB. Insights Into the Catalysis of Phosphoryl Group Transfer by Enzymes. [Internet] [Thesis]. University of North Carolina; 2010. [cited 2021 Jan 23]. Available from: https://cdr.lib.unc.edu/record/uuid:e535ad52-8572-417f-831f-ccf060ad96b8.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Stockbridge RB. Insights Into the Catalysis of Phosphoryl Group Transfer by Enzymes. [Thesis]. University of North Carolina; 2010. Available from: https://cdr.lib.unc.edu/record/uuid:e535ad52-8572-417f-831f-ccf060ad96b8

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of North Carolina

2. Lujan, Scott. Bacterial Conjugation and its Inhibition: The Hows and Whys of Conjugation and What Can be Done to Control It.

Degree: Biochemistry and Biophysics, 2008, University of North Carolina

URL: https://cdr.lib.unc.edu/record/uuid:479d9a87-b137-4371-b5de-c871ab80e258

Conjugation is the primary vehicle for the horizontal transfer virulence factor genes, such as antibiotic resistance, within and between bacterial strains. In certain epicenters, such as hospitals in less developed parts of the world, immune-compromised patients and misuse of antibiotics combine to select for the development and dissemination of these pathogenicity factors via conjugation. Inhibition of conjugation would prove a boon for curbing the creation and spread of new virulent or multi-drug resistant strains. DNA relaxases are the keystone proteins of each conjugative system. TraI is the relaxase of the F plasmid, the archetypal model system for conjugation. Toward revelation and inhibition of relaxase mechanisms, I used bioinformatics and limited proteolysis to find and identify new domains on the F TraI enzyme. I then solved TraI/DNA co-crystal structures that showed a novel DNA binding mode. Based on structure comparisons, sequence conservation, and mutant activity studies, I proposed a mechanism for TraI activity that required the existence of a dual phosphotyrosine intermediate, which has since been observed. I then demonstrated that bisphosphonate compounds mimicking this intermediate are nanomolar in vitro TraI inhibitors. I determined the relaxase structure in complex with one such inhibitor, bound as predicted. We showed that several of these compounds are potent in cell inhibitors of conjugation that often selectively kill conjugation-capable cells, a novel antibiotic paradigm. We showed that oral treatment of gnotobiotic mice with two inhibitors, clodronate and etidronate, decreased the gastrointestinal F+ bacterial load twentyfold without apparent side effects. Beyond the model system, etidronate showed selective in cell potency versus cells harboring a known clinical resistance-bearing R100 plasmid. Etidronate and clodronate are already clinically approved for the treatment of bone loss in humans. Toward more general relaxase inhibition phylogenetic analyses and studies with other medically relevant relaxases, including viral replicative relaxases, are ongoing. Advisors/Committee Members: Lujan, Scott, Redinbo, Matthew R., Wolfenden, Richard, Pielak, Gary J., Matson, Steven, Temple, Brenda.

Subjects/Keywords: School of Medicine; Department of Biochemistry and Biophysics

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Lujan, S. (2008). Bacterial Conjugation and its Inhibition: The Hows and Whys of Conjugation and What Can be Done to Control It. (Thesis). University of North Carolina. Retrieved from https://cdr.lib.unc.edu/record/uuid:479d9a87-b137-4371-b5de-c871ab80e258

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Lujan, Scott. “Bacterial Conjugation and its Inhibition: The Hows and Whys of Conjugation and What Can be Done to Control It.” 2008. Thesis, University of North Carolina. Accessed January 23, 2021. https://cdr.lib.unc.edu/record/uuid:479d9a87-b137-4371-b5de-c871ab80e258.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Lujan, Scott. “Bacterial Conjugation and its Inhibition: The Hows and Whys of Conjugation and What Can be Done to Control It.” 2008. Web. 23 Jan 2021.

Vancouver:

Lujan S. Bacterial Conjugation and its Inhibition: The Hows and Whys of Conjugation and What Can be Done to Control It. [Internet] [Thesis]. University of North Carolina; 2008. [cited 2021 Jan 23]. Available from: https://cdr.lib.unc.edu/record/uuid:479d9a87-b137-4371-b5de-c871ab80e258.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Lujan S. Bacterial Conjugation and its Inhibition: The Hows and Whys of Conjugation and What Can be Done to Control It. [Thesis]. University of North Carolina; 2008. Available from: https://cdr.lib.unc.edu/record/uuid:479d9a87-b137-4371-b5de-c871ab80e258

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

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