Effect of Molecular Crowding on Cellular Metabolism

Henrik Seir Thoke

Effect of Molecular Crowding on Cellular Metabolism

Henrik Seir Thoke

Institut for Biokemi og Molekylær Biologi

Publikation: Afhandling › Ph.d.-afhandling

Abstract

I denne afhandling præsenterer jeg en opsummering af mit samlede forskningsarbejde i emnet glykolytiske oscillationer i gær, udført i perioden januar 2015 - januar 2018. Resultaterne, der er opsummeret i fire artikler, indikerer at cytoplasma generelt, og oscillerende glykolyse specifikt, ikke kan fuldt ud forstås fra en beskrivelse af fortyndede systemer. Vores resultater passer bedre med Gilbert Lings "Association Induction Hypothesis", der i højere grad fokuserer på det specifikke miljø der dannes i en koncentreret blanding af ioner, protein og vand så som cytoplasmaen. Baseret på denne hypotese er vi i stand til at forklare vores eksperimentelle resultater, samt udfærdige en ny model for glykolytiske oscillationer der har et termodynamisk fundament.

Afhandlingen begynder med en præsentation af Lings hypotese i mod den historiske baggrund (kapitel 1 of 2), og fortsætter med en beskrivelse af det glykolytiske oscillationer i gær der er det primært benyttede modelsystem (kapitel 3). Kapitel 4 fokuserer på teoretiske overvejelser angående dipolær relaksation og effekten på fluoroforer, hvilket er den primært benyttede eksperimentelle metode benyttet igennem afhandlingen. Til slut vil jeg i kapitel 5 give en kort introduktion til hver af de fire artikler, der er vedhæftede som appendikser. Dette kapitel indeholder også en kort opsummering af mit eksperimentelle bidrag til en anden artikler, der stadig er under udarbejdelse. Grundet mit begrænsede bidrag til denne artikel skal denne artikel ikke anses som en del af denne afhandling, trods den er en del af det arbejde jeg har udført i løbet af min ph.d.

Originalsprog	Engelsk
Bevilgende institution	Syddansk Universitet
Vejledere/rådgivere	Olsen, Lars Folke, Hovedvejleder Bagatolli, Luis, Bivejleder Hansen, Per L., Bivejleder, Ekstern person
Udgivelsessted	Odense
Udgiver	Syddansk Universitet. Det Naturvidenskabelige Fakultet
Status	Udgivet - jan. 2018

Note vedr. afhandling

Afhandlingen kan læses på SDUs bibliotek. 

4 Tidsskriftartikel

Inductive effects in amino acids and peptides: Ionization constants and tryptophan fluorescence
Lara-Popoca, J., Thoke, H. S., Stock, R. P., Rudino-Pinera, E. & Bagatolli, L. A., dec. 2020, I: Biochemistry and Biophysics Reports. 24, 9 s., 100802.
Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

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Is a constant low-entropy process at the root of glycolytic oscillations?
Thoke, H. S., Olsen, L. F., Duelund, L., Stock , R. P., Heimburg, T. & Bagatolli, L., sep. 2018, I: Journal of Biological Physics. 44, 3, s. 419-431
Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

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The dynamics of intracellular water constrains glycolytic oscillations in Saccharomyces cerevisiae
Thoke, H. S., Thorsteinsson, S., Stock , R. P., Bagatolli, L. & Olsen, L. F., 24. nov. 2017, I: Scientific Reports. 7, 12 s., 16250.
Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

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Citationsformater

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title = "Effect of Molecular Crowding on Cellular Metabolism",

abstract = "In this thesis I present a summary of my work done during my Ph.D. in the period January 2015 - January 2018 on the subject of glycolytic oscillations in yeast. The results which are summarized in four articles, suggest that the cytoplasm in general, and oscillatory glycolysis in particular, cannot be treated in the framework of dilute system theory. Specifically our results are more consistent with Gilbert Ling{\textquoteright}s {"}Association Induction Hypothesis{"}, which to a greater extent considers the specific environment created by a concentrated ion-protein-water solution, such as the cytoplasm. Based on this hypothesis we manage to explain all of our experimental results, and create a new model for glycolytic oscillations in yeast founded in thermodynamics.I begin by a presentation of the Association Induction Hypothesis against the historical background (chapters 1 and 2), and continue with a description of my used model system of glycolytic oscillations in yeast (chapter 3). Chapter 4 is reserved for theoretical considerations of fluorescent response to dipolar relaxation, which is the primary experimental method used throughout my work. Finally chapter 5 provides a brief introduction to each of the four articles attached in the appendices. These articles, of which two are presently published, one is in review and the last is in the final stages of preparation, are the main outcome of my scientific work on the subject of molecular crowding and oscillating glycolysis performed during my Ph.D.Ph.D.Additionally chapter 5 contains the essence of my experimental contribution to another paper, which as of yet is a work in progress. Due to my limited contribution this paper should not be considered a part of this thesis, but it is part of the work I have contributed in the Ph.D. period.",

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AB - In this thesis I present a summary of my work done during my Ph.D. in the period January 2015 - January 2018 on the subject of glycolytic oscillations in yeast. The results which are summarized in four articles, suggest that the cytoplasm in general, and oscillatory glycolysis in particular, cannot be treated in the framework of dilute system theory. Specifically our results are more consistent with Gilbert Ling’s "Association Induction Hypothesis", which to a greater extent considers the specific environment created by a concentrated ion-protein-water solution, such as the cytoplasm. Based on this hypothesis we manage to explain all of our experimental results, and create a new model for glycolytic oscillations in yeast founded in thermodynamics.I begin by a presentation of the Association Induction Hypothesis against the historical background (chapters 1 and 2), and continue with a description of my used model system of glycolytic oscillations in yeast (chapter 3). Chapter 4 is reserved for theoretical considerations of fluorescent response to dipolar relaxation, which is the primary experimental method used throughout my work. Finally chapter 5 provides a brief introduction to each of the four articles attached in the appendices. These articles, of which two are presently published, one is in review and the last is in the final stages of preparation, are the main outcome of my scientific work on the subject of molecular crowding and oscillating glycolysis performed during my Ph.D.Ph.D.Additionally chapter 5 contains the essence of my experimental contribution to another paper, which as of yet is a work in progress. Due to my limited contribution this paper should not be considered a part of this thesis, but it is part of the work I have contributed in the Ph.D. period.

M3 - Ph.D. thesis

PB - Syddansk Universitet. Det Naturvidenskabelige Fakultet

CY - Odense

ER -

Effect of Molecular Crowding on Cellular Metabolism

Abstract

Note vedr. afhandling

Fingeraftryk

Relaterede publikationer

Inductive effects in amino acids and peptides: Ionization constants and tryptophan fluorescence

Is a constant low-entropy process at the root of glycolytic oscillations?

The dynamics of intracellular water constrains glycolytic oscillations in Saccharomyces cerevisiae

Citationsformater