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Synthetic studies towards a novel reverse turn peptidomimeticParr, Ian Barrie January 1995 (has links)
No description available.
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Chemistry of 4-azalysine and its derivativesMahajan, Anju January 2000 (has links)
No description available.
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Synthetic applications of morpholinone templatesCurrie, G. S. January 1996 (has links)
No description available.
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Asymetric synthesis using coordination complexesCox, M. A. January 1987 (has links)
No description available.
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Structural and Functional Insights on Regulation by Phenolic CompoundsShahinas, Dea 26 February 2009 (has links)
The shikimate pathway is a primary metabolic pathway involved in the synthesis
of aromatic compounds in plants, fungi, apicomplexan parasites and microbes.
The absence of this pathway in animals makes it ideal for the synthesis of
antimicrobial compounds and herbicides. Additionally, its branching into indole
hormone synthesis and phenylpropanoid secondary metabolism makes this
pathway attractive for metabolic engineering. Here, the focus is on the first step
of the shikimate pathway catalyzed by DAHP synthase. This step consists of the
condensation of phosphoenol pyruvate and erythrose-4-phosphate to make
DAHP, which undergoes another six catalytic steps to synthesize chorismate, the
precursor of the aromatic amino acids. Arabidopsis thaliana contains three DAHP
synthase isozymes, which are known to indirectly regulate downstream pathways
in response to wounding and pathogen stress. The model presented here
proposes that DAHP synthase isozymes are regulated by the end products
tyrosine, tryptophan and phenylalanine.
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Structural and Functional Insights on Regulation by Phenolic CompoundsShahinas, Dea 26 February 2009 (has links)
The shikimate pathway is a primary metabolic pathway involved in the synthesis
of aromatic compounds in plants, fungi, apicomplexan parasites and microbes.
The absence of this pathway in animals makes it ideal for the synthesis of
antimicrobial compounds and herbicides. Additionally, its branching into indole
hormone synthesis and phenylpropanoid secondary metabolism makes this
pathway attractive for metabolic engineering. Here, the focus is on the first step
of the shikimate pathway catalyzed by DAHP synthase. This step consists of the
condensation of phosphoenol pyruvate and erythrose-4-phosphate to make
DAHP, which undergoes another six catalytic steps to synthesize chorismate, the
precursor of the aromatic amino acids. Arabidopsis thaliana contains three DAHP
synthase isozymes, which are known to indirectly regulate downstream pathways
in response to wounding and pathogen stress. The model presented here
proposes that DAHP synthase isozymes are regulated by the end products
tyrosine, tryptophan and phenylalanine.
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Optimization of in vitro transcription/translation conditions for in vitro compartmentalization studies and synthesis of 4-fluorohistidineRing, Christine 01 January 2017 (has links)
Genetic code expansion allows the incorporation of non-canonical amino acids with a variety of new functional groups: fluorescent amino acids,1-3 azides,4-6 alkynes,5-10 and photocrosslinkers.4,11,12 This incorporation requires the evolution of new tRNA/aminoacyl tRNA sythetase pairs. Traditionally screenings of novel tRNA/aminoacyl tRNA synthetase pairs have been done in vivo. While these in vivo screenings have proven robust, they are limited in multiple ways: non-canonical amino acids (ncAAs) must be nontoxic and bioavailable. Furthermore, library size is limited by transformation efficiency. Lastly, in vivo screenings require substantial amounts of the target ncAA, which is often not available in large masses. In vitro screenings bypass these limitations: toxicity and bioavailibilty are no longer concerns. Library size can be expanded by several orders of magnitude as we are no longer limited by transformation efficiency. Lastly, because in vitro transcription/translation reactions are routinely conducted on the μL scale, ncAA usage can be minimized. We set out to use in vitro compartmentalization to further expand the code. In an in vitro compartmentalization screening, the water droplets in a water-in-oil emulsion serve as separate reaction chambers in which individual library members are transcribed and translated. Here we report optimization of S30 transcription/translation reactions. Optimizations include cell lysis method, reaction temperature, template amount, and T7 RNA polymerase amounts. Yields remained low and we transistioned into the use of PURExpress.
Fluorohistidines are isosteric with histidine, but not isoelectronic.13 This change in environment results in a reduction of pKa. We set out to synthesize 4-fluorohistidine to use as a pH probe in several target proteins. A synthesis of 4-fluorohistidine was published in 1973.14,15 We were able to improve upon this synthesis by reducing cost and improving yield of a key step in the reaction. Next, small peptides with polyhistidine tags were translated in vitro using our 4-fluorohistidine. We are calling this polyhistidine tag incorporating 4-fluorohistidine our “hexafluorohistag.” Because of the reduced pKa of the 4-fluorohistidine, the hexafluorohistag showed affinity to Nickel-NTA resin even at reduced pH. This allowed for the purification of hexafluorohistagged peptides in the presence of traditional polyhistidine-tagged peptides.
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Applications of generalised supply-demand analysisChristensen, Carl David 03 1900 (has links)
Thesis (MSc)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: Supply-demand analysis (SDA) is a tool that allows for the control, regulation
and behaviour of metabolic pathways to be understood. In this framework, reactions
are grouped into reaction blocks that represent the supply and demand of a
metabolic product. The elasticities of these supply and demand blocks can be used
to determine the degree of control either block has over the flux in the pathway
and the degree of homoeostasis of the metabolic product that links the blocks. Rate
characteristic plots, on which the rates of supply and demand blocks are plotted as
functions of the concentration of the linking metabolite, represent a powerful visual
tool in this framework.
Generalised supply-demand analysis (GSDA) allows for the analysis of metabolic
models of arbitrary size and complexity without prior knowledge of the regulatory
structure of the pathway. This is achieved by performing SDA on each variable
metabolite in a pathway instead of choosing a single linking metabolite. GSDA also
provides other benefits over SDA as it allows for potential sites of regulation and
regulatory metabolites to be identified. Additionally it allows for the identification
and quantification of the relative contribution of di erent routes of regulation from
an intermediate to a reaction block.
Moiety-conserved cycles present a challenge in performing in silico SDA or GSDA,
as the total concentration of a moiety must remain constant, thereby limiting the
range of possible concentrations of the metabolites between which it cycles. The first
goal of this thesis was to develop methods to perform GSDA on two-membered and
interlinked moiety-conserved cycles. We showed that by expressing the members
of a moiety-conserved cycle as a ratio, rather than individual metabolite concentrations,
we can freely vary the ratio without breaking moiety conservation in a
GSDA. Furthermore, we showed that by linking the concentrations of the members
of two interlinked two-membered moiety-conserved cycles to a “linking metabolite”,
we could vary the concentration of this metabolite, within constraints, without breaking moiety conservation.
The Python Simulator for Cellular Systems (PySCeS) is a software package developed
within our group that provides a variety of tools for the analysis of cellular
systems. The RateChar module for PySCeS was previously developed as a tool to
perform GSDA on kinetic models of metabolic pathways by automatically generating
rate characteristic plots for each variable metabolite in a pathway. The plots
generated by RateChar, however, were at times unclear when the models analysed
were too complex. Additionally, invalid results where steady-states could not be
reached were not filtered out, and therefore appeared together with valid results on
the rate characteristic plots generated by RateChar. We therefore set out to improve
upon RateChar by building plotting interface that produces clear and error-free rate
characteristics. The resulting RCFigure class allows users to interactively change
the composition of a rate characteristic plot and it includes automatic error checking.
It also provides clearer rate characteristics with e ective use of colour.
Using these tools two case studies were undertaken. In the first, GSDA was used to
investigate the regulation of aspartate-derived amino acid synthesis in Arabidopsis
thaliana. A central result was that the direct interaction of aspartate-semialdehyde
(ASA), a metabolite at a branch point in the pathway, with the enzyme that produces
it only accounts for 7% of the total response in the flux of supply. Instead,
89% of the observed flux response was due to ASA interacting with of the downstream
enzymes for which it is a substrate. This result was unexpected as the ASA
producing enzyme had a high elasticity towards ASA.
In a second case study moiety-conserved cycles in a model of the pyruvate branches
in lactic acid bacteria were linearised using the above mentioned method. This
served to illustrate how multiple reaction blocks are connected by these conserved
moieties. By performing GSDA on this model, we demonstrated that the interactions
of these conserved moieties with the various reaction blocks in the pathway,
led to non-monotonic behaviour of the rate characteristics of the supply and demand
for the moiety ratios. An example of this is that flux would increase in
response to an increase in product for certain ranges. This thesis illustrates the power of GSDA as an entry point in studying metabolic
pathways, as it can potentially reveal properties of the regulation and behaviour of
metabolic pathways that were not previously known, even if these pathways were
subjected to previous analysis and a kinetic model is available. In general it also
demonstrates how e ective analysis tools and metabolic models are vital for the
study of metabolism. / AFRIKAANSE OPSOMMING: Vraag-en-aanbod analise (VAA) is ’n analisemetode wat mens in staat stel om
die beheer, regulering en gedrag van metaboliese paaie beter te verstaan. In
hierdie raamwerk word reaksies gegroepeer as reaksieblokke wat die aanbod
(produksiestappe) en die aanvraag (verbruik-stappe) van ’n metaboliese produk
verteenwoordig. Vanaf die elastisiteite van hierdie aanbod- en aanvraag-blokke
kan die graad van beheer van elkeen van die blokke oor die fluksie, asook die
graad van homeostase van die metaboliese koppelingsintermediaat, bereken word.
Snelheidskenmerk-grafieke, waarop die snelhede van die vraag- en aanbod-blokke
as funksies van die konsentrasie van die koppelingsmetaboliet uiteengesit word,
verteenwoordig ’n kragtige visuele hulpmiddel in hierdie raamwerk.
Veralgemeende vraag-aanbod analise (VVAA), die veralgemeende vorm van VAA,
maak dit moontlikommetaboliese modelle van arbitrêre grootte en kompleksiteit te
analiseer sonder enige vooraf-kennis van die regulatoriese struktuur van die paaie.
Die prosedure is om VAA op elk van die veranderlike metaboliete in die pad uit
te voer, eerder as om ’n enkele koppelingsmetaboliet te kies. VVAA het ook ander
voordele bo VAA aangesien dit potensiële setels van regulering en regulatoriese
metaboliete kan identifiseer. Daarbenewens kan dit die relatiewe bydrae van verskillende
regulerings-roetes van vanaf ’n intermediaat na ’n reaksieblok identifiseer
en hulle kwantifiseer.
Groep-gekonserveerde siklusse bied ’n uitdaging vir in silico VAA of VVAA, aangesien
die totale konsentrasie van die gekonserveerde groep konstant moet bly. Dit
beperk die waardes van moontlike konsentrasies van die metaboliete wat die siklus
uitmaak. Die eerste doelstelling van hierdie tesis was dus om metodes te ontwikkel
waarmee VVAA op tweeledige en saamgebonde groep-gekonserveerde siklusse
uitgevoer kan word. Deur die lede van groep-gekonserveerde siklusse eerder as
verhoudings uit te druk in plaas van as individuele metabolietkonsentrasies, het
ons gewys dat ons hierdie verhouding vrylik kan varieer sonder om die groep-konservering te breek in ’n VVAA. Ons het ook gewys dat die konsentrasies van die
lede van ’n saamgebonde groep-gekonserveerde siklus gekoppel kan word aan ’n
“koppelingsmetaboliet”, waarvan die konsentrasie dan binne perke gevarieer kan
word sonder om die groep-konservering te breek.
Die “Python Simulator for Cellular Systems” (PySCeS) is ’n programmatuur-pakket
wat binne ons navorsingsgroep ontwikkel is met die doel om sellulêre sisteme
numeries te analiseer. Die RateChar module vir PySCeS was reeds voor die aanvang
van hierdie projek ontwikkel om VVAAop kinetiese modelle van metaboliese paaie
uit te voer deur outomaties snelheidskenmerke vir elke veranderlikke metaboliet te
genereer. Die grafieke wat deur RateChar gegenereer is, was egter soms onduidelik
wanneer die modelle te groot of kompleks geraak het. Daarbenewens is ongeldige
resultate, waar ’n bestendige toestand nie bereik kon word nie, nie uitgefiltreer nie,
en het dus saam met geldige resultate op die snelheidskenmerke verskyn. Een van
die doelstellings was dus om RateChar te verbeter deur ’n koppelvlak vir grafieke
te ontwikkel wat duidelike en foutlose snelheidskenmerke kon produseer. Dit het
gelei tot die RCFigure klas wat outomatiese foutopsporing uitvoer en gebruikers
in staat stel om op ’n interaktiewe wyse die samestelling van ’n snelheidskenmerkgrafiek
te verander. Dit bied ook duideliker snelheidskenmerke deur e ektief van
kleur gebruik te maak.
Met hierdie ontwikkelde gereedskap is twee gevallestudies onderneem. In die
eerste is VVAA gebruik om die regulering van aspartaat-afgeleide aminosuursintese
in Arabidopsis thaliana te bestudeer. Die belangrikste resultaat was dat die direkte
interaksie van aspartaat-semialdehied (ASA), ’n metaboliet by ’n vertakkingspunt
in die pad, met die ensiem wat dit produseer, slegs vir 7% van die totale respons in
die aanbod-fluksie verantwoordelik was. Daarteen was 89% van die waargenome
fluksierespons die gevolg van die interaksie van ASA met drie van die stroomafensieme,
waarvoor dit ’n substraat is. Hierdie resultaat was onverwag aangesien
die ensiem wat ASA produseer ’n hoë elastisiteit teenoor ASA toon. In ’n tweede gevallestudie is die groep-gekonserveerde siklusse in ’n model van
die pirovaat-takke in melksuurbakterie-metabolisme gelineariseer deur gebruik
te maak van die bo beskrewe metode. Dit illustreer hoe verskeie reaksieblokke
verbind word deur hierdie gekonserveerde groepe. M.b.v. ’n VVAA van hierdie
model het ons gedemonstreer dat die interaksies van die gekonserveerde groepe
met die verskeie reaksieblokke in die pad kan lei tot nie-monotoniese gedrag van
die snelheidskenmerke van die vraag- en aanbod-reaksies vir die verhouding van
die gekonserveerde groep-komponente. ’n Voorbeeld hiervan is die onverwagte waarneming dat die fluksie toeneem met toenemende produk-konsentrasie oor
sekere gebiede.
Hierdie tesis illustreer die krag van VVAA as ’n beginpunt vir die studie van
metaboliese paaie, aangesien dit onbekende regulatoriese eienskappe en gedragspatrone
kan ontbloot, selfs al is die paaie vantevore m.b.v. kinetiese modelle geanaliseer.
Oor die algemeen demonstreer dit die noodsaaklikheid van e ektiewe analisegereedskap
en metaboliese modelle vir die bestudering van metabolisme. / National Research Foundation
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Asymmetric Synthesis of C-Glycosylated Amino Acids : Incorporation in Collagen Glycopeptides and Evaluation in a Model for Rheumatoid ArthritisGustafsson, Tomas January 2005 (has links)
<p>This thesis describes stereoselective syntheses of four amino acids, three of which are C-glycosidic analogues of glycosylated amino acids. The overall goal of the project was to probe the interactions between MHC molecules, glycopeptide antigens and T cell receptors, that are essential for development of collagen induced arthritis. Collagen induced arthritis is a frequently used mouse model for rheumatoid arthritis, an autoimmune disease that attacks joint cartilage and leads to a painful and eventually crippling condition.</p><p>The thesis is based on four studies. The first study describes the synthesis of hydroxylysine, an amino acid that is found in collagen and is an important constituent of the glycopeptide proposed as an antigen in collagen induced arthritis. During the synthesis of hydroxylysine some new insight into the mechanism of the reductive opening of <i>p</i>-methoxybenzylidene acetals was obtained.</p><p>The remaining three studies deals with the synthesis of C-glycosidic analogues of glycosylated amino acids, hydroxy norvaline, threonine and hydroxylysine.The synthesis of each amino acid required control of several stereogenic centra and utilizes a variety of approaches such as use of stereoselective reactions, chiral auxilaries, chiral templates and asymmetric catalysis.</p><p>The C-glycosidic analogues of galactosylated hydroxynorvaline and hydroxylysine were incorporated in glycopeptides from type II collagen and evaluated in T cell response assays. It was found that the T cells were stimulated by the C-glycopeptides, but that higher concentrations were required than for the native O-glycopeptide</p>
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Asymmetric Synthesis of C-Glycosylated Amino Acids : Incorporation in Collagen Glycopeptides and Evaluation in a Model for Rheumatoid ArthritisGustafsson, Tomas January 2005 (has links)
This thesis describes stereoselective syntheses of four amino acids, three of which are C-glycosidic analogues of glycosylated amino acids. The overall goal of the project was to probe the interactions between MHC molecules, glycopeptide antigens and T cell receptors, that are essential for development of collagen induced arthritis. Collagen induced arthritis is a frequently used mouse model for rheumatoid arthritis, an autoimmune disease that attacks joint cartilage and leads to a painful and eventually crippling condition. The thesis is based on four studies. The first study describes the synthesis of hydroxylysine, an amino acid that is found in collagen and is an important constituent of the glycopeptide proposed as an antigen in collagen induced arthritis. During the synthesis of hydroxylysine some new insight into the mechanism of the reductive opening of p-methoxybenzylidene acetals was obtained. The remaining three studies deals with the synthesis of C-glycosidic analogues of glycosylated amino acids, hydroxy norvaline, threonine and hydroxylysine.The synthesis of each amino acid required control of several stereogenic centra and utilizes a variety of approaches such as use of stereoselective reactions, chiral auxilaries, chiral templates and asymmetric catalysis. The C-glycosidic analogues of galactosylated hydroxynorvaline and hydroxylysine were incorporated in glycopeptides from type II collagen and evaluated in T cell response assays. It was found that the T cells were stimulated by the C-glycopeptides, but that higher concentrations were required than for the native O-glycopeptide
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