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Dissertations / Theses on the topic 'Protein folding studies'

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Published: 4 June 2021

Last updated: 8 February 2022

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1

Vasilkoski, Zlatko. "Protein folding computational studies /." Thesis, Connect to Dissertations & Theses @ Tufts University, 2003.

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Thesis (Ph.D.)--Tufts University, 2003.
Adviser: David L. Weaver. Submitted to the Dept. of Physics. Includes bibliographical references. Access restricted to members of the Tufts University community. Also available via the World Wide Web;

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2

Badcoe, Ian Geoffrey. "Computer studies of protein folding." Thesis, University of Bristol, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.385585.

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3

Nymeyer, Hugh. "Computational studies of protein folding /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC IP addresses, 2001. http://wwwlib.umi.com/cr/ucsd/fullcit?p3022207.

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4

Geierhaas, Christian D. "Computational studies of protein folding." Thesis, University of Cambridge, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.613877.

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5

Perrett, Sarah Elizabeth Dorothy. "Biophysical studies on protein folding." Thesis, University of Cambridge, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.627049.

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6

Hart, Tanya Clare. "Mutational studies of prion protein folding." Thesis, Imperial College London, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.418318.

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7

Wain, Rachel. "Studies of protein folding and aggregation." Thesis, University of Oxford, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.270186.

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8

Woolfson, Derek Neil. "Studies on protein folds and folding." Thesis, University of Cambridge, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.239742.

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9

Matouschek, Andreas T. E. L. "Studies on the folding of barnase." Thesis, University of Cambridge, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.240039.

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10

Eyles, Stephen J. "Studies of protein folding by NMR spectroscopy." Thesis, University of Oxford, 1995. http://ora.ox.ac.uk/objects/uuid:06b8fb16-790c-4b72-80d0-8317920655fe.

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This thesis describes an investigation of the folding and stability of a series of derivatives of the proteins lysozyme and α-lactalbumin which lack one or more of their four native disulphide bridges. Removal of the disulphide bridge which links the N- and C-termini from hen lysozyme results in a three-disulphide derivative (CM^6,127-lysozyme). This has a profound effect on its stability against thermal denaturation, the T_m for unfolding being reduced by 25°C at pH 3.8. Calorimetric measurements performed on this three-disulphide derivative indicate that this reduction in stability may be attributed entirely to an increase in the entropy difference between the native and denatured states. Kinetic refolding studies of CM^6,127-lysozyme using stopped flow optical methods and hydrogen exchange pulse labelling in conjunction with NMR and electrospray ionisation mass spectrometry (ESI-MS) suggest that this reduced stability manifests itself primarily in the α-domain of the protein. A transient intermediate populated during refolding of the unmodified protein can no longer be detected during folding of the derivative resulting in highly cooperative folding under the conditions investigated. The structure and stability of a three- and two-disulphide derivative of the homologous protein, α-lactalbumin have been investigated by NMR spectroscopy. The three-disulphide species, like its lysozyme counterpart, can adopt native structure but this is much more unstable than the intact protein. Removal of a second disulphide bridge, however, destabilises α-lactalbumin to the extent that the native state is no longer formed. Instead, in the presence of Ca²⁺ and high concentrations of salt, a partially structured state is induced which has some elements of tertiary structure present. Novel techniques of ESI-MS have been developed to study protein folding and stability using hydrogen exchange techniques. Applications to the investigation of cooperativity in protein folding, stability in native, partially folded and unfolded states, and the interactions of a partially folded protein with the chaperone GroEL are described.

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11

Itzhaki, Laura Susan. "Spectroscopic studies of protein hydration and folding." Thesis, University of Cambridge, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.284084.

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12

Marianayagam, Neelan Joseph. "Experimental and computational studies of protein folding." Thesis, University of Cambridge, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.619547.

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13

Zerella, Rosa. "Studies of protein folding using peptide models." Thesis, University of Cambridge, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.624162.

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14

Hadfield, David Stuart. "Fluorinated amino acids for protein folding studies." Thesis, University of Sussex, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.366219.

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15

Reader, John S. "Folding studies of the #beta#-sheet protein pseudoazurin." Thesis, University of Oxford, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.284456.

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16

Best, R. "High resolution studies of protein folding and dynamics." Thesis, University of Cambridge, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.596604.

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This thesis presents several approaches to the study of the folding and dynamics of proteins, with an emphasis on examples form immunoglobulin-like fold. The first part describes the application of atomic force microscopy to studying the mechanical unfolding of proteins. Most studies to date have used methods such as chemical or thermal denaturation, thus force represents a new type of “denaturant” which adds to the description of the folding energy landscape. Furthermore it is a single-molecule method with the potential to resolve parallel folding pathways, for example. The technique has been used to study the mechanical unfolding of the RNase barnase which has already been extensively characterised by more conventional methods. Barnase is shown to be folded and stable in the protein construct used, yet it unfolds at very low forces compared to proteins with mechanical function (such as titin 127). Phi-value analysis by protein engineering has allowed the detailed characterization of folding pathways by bulk methods. A method is presented and justified which circumvents the large uncertainties in unfolding rates obtained from kinetic fits to AFM data. This has been applied to the domain titin 127, a protein from muscle, showing that the protein unfolds through an intermediate and with a very native-like transition state under force, contrasting with previous bulk studies. The second part of the work concerns the comparison of TNfn3 and FNfn10, belonging to the fibronectin type III superfamily and, like 127, members of the immunoglobulin-like fold. These two domains have very similar structure, yet present a very different response to mutation, which has led to the suggestion that FNfn10 has greater structural “plasticity”. The dynamics of these domains are addressed by means of equilibrium hydrogen exchange measurements, which support the notion that the periphery of FNfn10 is more flexible. The core dynamics have been investigated using recently developed NMR side-chain dynamics experiments, and the results compared to molecular dynamics simulations.

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17

Maynard, Allister J. "NMR studies of protein folding and DNA binding." Thesis, University of Nottingham, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.313244.

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18

Nickson, Adrian Anthony. "Folding studies of a small alpha+beta protein." Thesis, University of Cambridge, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.613173.

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19

Hanazono, Yuya. "Structural studies on the mechanism of protein folding." 京都大学 (Kyoto University), 2014. http://hdl.handle.net/2433/188506.

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20

Clarke, Jane. "Studies of disulphide mutants of barnase." Thesis, University of Cambridge, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.318014.

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21

Wicky, Basile Isidore Martin. "Biophysical studies of protein assemblies." Thesis, University of Cambridge, 2019. https://www.repository.cam.ac.uk/handle/1810/288004.

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Proteins are synthesised as linear polymeric chains. The subtle energetic interplay of interatomic interactions results in chain folding, through which proteins may acquire defined structures. This spatial organisation is encoded by the protein sequence itself; the so-called thermodynamic hypothesis formulated by Anfinsen in 1961. A defined structure is often considered a pre-requisite to protein function, but widespread existence of intrinsically disordered proteins (IDPs) has prompted a re- evaluation of the ways biological function may be encoded into polypeptide chains. Furthermore, proteins often exist as part of multi-component entities, where regulation of assembly is integral to their properties. The interplay between disorder, oligomerisation and function is the focus of this thesis. Some IDPs fold conditionally upon interacting with a partner protein; a process known as coupled folding and binding. What are the biophysical advantages and consequences of disorder in the context of these interactions? A common feature of IDPs is their sequence composition bias, with charged residues being often over-represented. It is therefore tempting to speculate that electrostatic interactions may play a major role in coupled folding and binding reactions. Surprisingly, the opposite was found to be true. Charge-charge interactions only contributed about an order of magnitude to the association rate constants of two contrasting model systems. The lack of pre-formed binding interfaces-a consequence of disorder-might preclude electrostatic acceleration from complementary patches. By looking at the role of the sequence, many studies have taken a protein-centric approach to understanding disorder. Yet there is paucity of data about the effect of extrinsic factors on interactions involving disordered partners. Investigating the role of co-solutes, it was discovered that the kinetic and thermodynamic profiles of coupled folding and binding reactions were sensitive to ion-types. This effect followed the Hofmeister series, and occurred at physiological concentrations of salt. The sensitivity of coupled folding and binding reactions-a consequence of the lack of stability of IDPs-might be advantageous. Given the role of ions in biology, this 'biophysical sensing' could be a mechanism of physiological relevance, allowing modulation of protein-protein interactions involving disordered partners in response to changes in their environments. In cells, signalling networks are often multi-layered, and involve competing protein-protein interactions. The interplay between the biophysical characteristics of the components, and the behaviour of the network were investigated in a model tripartite system composed of folded and disordered proteins. The BCL-2 family regulates the intrinsic pathway of apoptosis through control of mitochondrial outer-membrane permeabilisation; a result of BAK and BAX oligomerisation. Through a shared homology motif (termed BH3), the subtle balance of their interactions determines cellular fate at the molecular level. Characterisation of the model under simple biochemical conditions revealed large differences in affinities among binary interactions; the consequence of the lifetime of the complexes, not their speed of association. A membrane-like environment, re-created using detergents, allows the oligomerisation of BAK and BAX in vitro. Furthermore, investigation of the tripartite system under detergent conditions showed that regulation of the network was the result of competing hetero- and homo-oligomerisation events. Relationships to their biophysical properties were gained by probing their energy landscapes using protein folding techniques. The connection between the biophysical properties of the components of the network and their interactions provides a molecular explanation for the regulation of apoptosis. This thesis offers insights into the ways structured assemblies and environmentally responsive disorder elements may encode functions into proteins.

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22

Platt, Geoffrey W. "Protein engineering studies of the Î²-hairpin of ubiquitin." Thesis, University of Nottingham, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.289450.

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23

Bemporad, Francesco. "Folding and aggregation studies in the acylphosphatase-like family /." Firenze : Firenze University Press, 2009. http://digital.casalini.it/9788884539465.

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24

Beaumont, Ellen Sarah. "Refolding studies on 2-oxoacid dehydrogenase multienzyme complexes." Thesis, University of Glasgow, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.360171.

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25

Farood, Amjad. "Kinetic studies of the folding of the protein bacteriorhodopsin." Thesis, Imperial College London, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.285497.

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26

Clark, Jennifer. "Single molecule studies of protein folding, aggregation and translocation." Thesis, University of Leeds, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.496544.

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27

Aguilar, Ximena. "Folding and interaction studies of subunits in protein complexes." Doctoral thesis, Umeå universitet, Kemiska institutionen, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-84726.

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Proteins function as worker molecules in the cell and their natural environment is crowded. How they fold in a cell-like environment and how they recognize their interacting partners in such conditions, are questions that underlie the work of this thesis. Two distinct subjects were investigated using a combination of biochemical- and biophysical methods. First, the unfolding/dissociation of a heptameric protein (cpn10) in the presence of the crowding agent Ficoll 70. Ficoll 70 was used to mimic the crowded environment in the cell and it has been used previously to study macromolecular crowding effects, or excluded volume effects, in protein folding studies. Second, the conformational changes upon interaction between the Mediator subunit Med25 and the transcription factor Dreb2a from Arabidopsis thaliana. Mediator is a transcriptional co-regulator complex which is conserved from yeast to humans. The molecular mechanisms of its action are however not entirely understood. It has been proposed that the Mediator complex conveys regulatory signals from promoter-bound transcription factors (activators/repressors) to the RNA polymerase II machinery through conformational rearrangements. The results from the folding study showed that cpn10 was stabilized in the presence of Ficoll 70 during thermal- and chemical induced unfolding (GuHCl). The thermal transition midpoint increased by 4°C, and the chemical midpoint by 0.5 M GuHCl as compared to buffer conditions. Also the heptamer-monomer dissociation was affected in the presence of Ficoll 70, the transition midpoint was lower in Ficoll 70 (3.1 μM) compared to in buffer (8.1 μM) thus indicating tighter binding in crowded conditions. The coupled unfolding/dissociation free energy for the heptamer increased by about 36 kJ/mol in Ficoll. Altogether, the results revealed that the stability effect on cpn10 due to macromolecular crowding was larger in the individual monomers (33%) than at the monomer-monomer interfaces (8%). The results from the interaction study indicated conformational changes upon interaction between the A. thaliana Med25 ACtivator Interaction Domain (ACID) and Dreb2a. Structural changes were probed to originate from unstructured Dreb2a and not from the Med25-ACID. Human Med25-ACID was also found to interact with the plant-specific Dreb2a, even though the ACIDs from human and A. thaliana share low sequence homology. Moreover, the human Med25-interacting transcription factor VP16 was found to interact with A. thaliana Med25. Finally, NMR, ITC and pull-down experiments showed that the unrelated transcription factors Dreb2a and VP16 interact with overlapping regions in the ACIDs of A. thaliana and human Med25. The results presented in this thesis contribute to previous reports in two different aspects. Firstly, they lend support to the findings that the intracellular environment affects the biophysical properties of proteins. It will therefore be important to continue comparing results between in vitro and cell-like conditions to measure the magnitude of such effects and to improve the understanding of protein folding and thereby misfolding of proteins in cells. Better knowledge of protein misfolding mechanisms is critical since they are associated to several neurodegenerative diseases such as Alzheimer’s and Parkinson's. Secondly, our results substantiate the notion that transcription factors are able to bind multiple targets and that they gain structure upon binding. They also show that subunits of the conserved Mediator complex, despite low sequence homologies, retain a conserved structure and function when comparing evolutionary diverged species.

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28

Altschuler, Gabriel Martin. "Protein folding studies on the actin-CCT chaperone system." Thesis, Institute of Cancer Research (University Of London), 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.440520.

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29

Dang, Zhijing. "Theoretical studies of protein folding and circular dichroism spectroscopy." Thesis, University of Nottingham, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.406982.

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30

Jenkins, David Christopher. "Equilibrium and kinetic folding studies of the prion protein." Thesis, University of Warwick, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.443621.

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31

Gladwin, Sharon T. "Studies on the kinetics and mechanism of protein folding." Thesis, University of Cambridge, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.388718.

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32

Tisi, Laurence Carlo. "Studies on the folding and packing of protein structures." Thesis, University of Cambridge, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.390040.

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33

Khan, Farid. "Folding and structural studies on the green fluorescent protein." Thesis, University of Cambridge, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.616097.

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34

Matthews, Jacqueline M. "Stability and folding studies of the #alpha#-helices in barnase." Thesis, University of Cambridge, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.319557.

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35

Evans, P. A. "NMR studies of the folding and unfolding of proteins." Thesis, University of Oxford, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.376891.

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36

Skorobogatiy, Maksim. "Theoretical studies of the thermodynamics and kinetics of proteins : application to protein folding." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1997. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp01/MQ44280.pdf.

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37

McCartney, Richard Graham. "Folding and assembly studies on the components of mammalian PDC and OGDC." Thesis, University of Glasgow, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.264145.

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38

Pan, Yinquan. "Biophysical studies of ubiquitin as a model for protein folding mechanisms." Diss., Georgia Institute of Technology, 1993. http://hdl.handle.net/1853/30261.

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39

Meiering, Elizabeth M. "Studies on the active site of barnase." Thesis, University of Cambridge, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.259633.

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40

Zhang, Wei. "Computational simulation of biological systems studies on protein folding and protein structure prediction /." Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file 2.84Mb, 184 p, 2005. http://wwwlib.umi.com/dissertations/fullcit/3181881.

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41

Sikor, Martin. "Single-molecule fluorescence studies of Protein Folding and Molecular Chaperones." Diss., lmu, 2011. http://nbn-resolving.de/urn:nbn:de:bvb:19-138521.

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42

Moparthi, Satish Babu. "Biophysical studies of protein folding upon interaction with molecular chaperones /." Linköping : Department of Physics, Chemistry and Biology, Linköping University, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-51604.

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43

Dittel, Agnes. "Protein folding and self-avoiding walks polyhedral studies and solutions /." Berlin : Logos-Verl, 2008. http://d-nb.info/990541827/04.

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44

Yano, Yoshiaki. "Fundamental studies on membrane protein folding using model transmembrane helices." 京都大学 (Kyoto University), 2005. http://hdl.handle.net/2433/145190.

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45

Kelly, Sharon Mary. "Studies on the unfolding and refolding of oligomeric proteins." Thesis, University of Stirling, 1994. http://hdl.handle.net/1893/21548.

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The unfolding and refolding of a number of oligomeric enzymes have been studied. These were: fumarase from pig heart, the NAD+ -dependent isocitrate dehydrogenase from yeast, the citrate synthases from pig hean, Acinetobacter anitratum and Thermoplasma acidophilum and the chaperone protein GroEL from Escherichia coli. In each case the unfolding by guanidinium chloride (GdnHCI) was monitored by enzyme activity (to detect possible perturbations at the active site), protein fluorescence (to detect changes in tertiary structure) and far U.v. circular dichroism (to detect changes in protein secondary structure). In general the losses in secondary and tertiary structure were found to run broadly in parallel, whereas the enzyme activity was lost at much lower concentrations of GdnHCl. This sensitivity to mild, denaturing conditions may reflect the greater flexibility of the active site compared with the molecule as a whole. Interestingly) the bacterial citrate synthases were activated in the presence of low concentrations of GdnHCl. Following denaturation) refolding was initiated by lowering the concentration of GdnHCI by dilution or dialysis. Only the dimeric citrate synthases (from pig heart and Thermoplasma acidophilum) could be reactivated to a moderate extent using the dilution procedure; less than 5% reactivation was observed for the other enzymes. In the cases of fumarase, NAD+ -dependent isocitrate dehydrogenase and the dimeric citrate synthases the degrees of reactivation following dialysis were significantly greater (approximately 50-75% of the native enzymes) than those obtained following the dilution procedure. Factors such as protein concentration and the inclusion of dithiothreitol in the dialysis or dilution buffer were found to influence significantly the extent of reactivation. The greater yield of reactivation of unfolded protein using the dialysis procedure probably reflects the ability of the enzyme to make the correct structural adjustments between intermediates when the concentration of GdnHCI is lowered gradually. In the case of Thermoplasma acidophilum the recovery of citrate synthase activity was much greater at 20 ·C than at 55 ·C (the optimal temperature for growth of this organism). This has implications for the folding process in vivo under the extreme growth conditions of thermophiles and possibly other extremophiles. The hexameric citrate synthase from Acinetobacter anitratum and the tetradecameric chaperonin, GroEL could not be reactivated following denaturation. Far u.v. circular dichroism measurements on GroEL indicated that the native secondary structure of this protein was regained to a large extent. In vivo a number of the proteins studied (fumarase and citrate synthase from pig hean and yeast NAD+ -dependent isocitrate dehydrogenase)are translocated into mitochondria as precursors in a non-native state prior to processing, folding and assembly. The lack of complete refolding of the proteins studied in this work points to the existence of specialised mechanisms in vivo to promote efficient folding. Chaperone proteins have been implicated in the assistance of protein folding in vivo. Intriguingly. the studies on the inefficient refolding of the chaperonin GroEL support the proposal that this protein may fold in vivo by way of a "self chaperoning" mechanism.

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46

Briggs, Geoffrey Shaw. "Folding and stability studies on papain and the effect of recombinant papain pro fragment." Thesis, University of Kent, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.281755.

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47

Nordling, Erik. "Biocomputational studies on protein structures /." Stockholm, 2002.

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48

Pérez, González Daniel Cibrán. "Single-molecule studies of nucleic acid folding and nucleic acid-protein interactions." Thesis, University of St Andrews, 2017. http://hdl.handle.net/10023/12039.

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Nucleic acids and proteins, some of the building blocks of life, are not static structures but highly dynamic entities that need to interact with one another to meet cellular demands. The work presented in this thesis focuses on the application of highly sensitive fluorescence methods, both at ensemble and single-molecule level, to determine the dynamics and structure of specific biomolecular interactions with nanometer resolution and in temporal scales from nanoseconds to minutes, which includes most biologically relevant processes. The main aims of my PhD can be classified in three areas: i) exploring new fluorescent sensors with increased specificity for certain nucleic acid structures; ii) understanding how some of these nucleic acids sense the presence of small molecules in the cellular environment and trigger gene regulation by altering their structure; and iii) understanding how certain molecular machines, such as helicase proteins, are able to unwind the DNA double helix by using chemical energy in the form of ATP hydrolysis.

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49

Kemplen, Katherine Rosemary. "Biophysical studies of folding and misfolding in tandem repeat proteins." Thesis, University of Cambridge, 2015. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.709235.

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50

Mhaiskar, Vijay. "The expression and secretion of hPDI in the yeast Saccharomyces cerevisiae for site directed mutagenesis studies." Thesis, University of Kent, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.387018.

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