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Dissertations / Theses on the topic 'Proteins crowding'

Author: Grafiati

Published: 10 March 2023

Last updated: 31 July 2025

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1

Malik, Ashima. "Proteins in crowding and confinement." Thesis, IIT Delhi, 2016. http://eprint.iitd.ac.in:80//handle/2074/8190.

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2

Candotti, Michela. "Environment matters : the impact of urea and macromolecular crowding on proteins." Doctoral thesis, Universitat de Barcelona, 2016. http://hdl.handle.net/10803/403839.

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This work aims to analytically understand the impact of two diametric opposite environments on protein structure and dynamics and compared them to the most common solvent on earth: water. The first environment is a popular denaturing solution (urea 8M), which has served for years in protein-science laboratories to investigate protein stability; still many open questions regarding its mechanism of action remained unclear. The second environment instead moves towards a more physiological representation of proteins. The cell interior, in fact, is a crowded solution highly populated prevalently b

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3

Toyooka, Tsuguyoshi. "Photoreaction Dynamics of Blue Light Sensor Proteins and Application to Crowding Environments." 京都大学 (Kyoto University), 2011. http://hdl.handle.net/2433/142398.

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4

Roos, Matthias [Verfasser], Kay [Akademischer Betreuer] Saalwächter, Wolfgang [Akademischer Betreuer] Paul, and Frank [Akademischer Betreuer] Schreiber. "Brownian dynamics of globular proteins under macromolecular crowding as studied by NMR : [kumulative Dissertation] / Matthias Roos ; Kay Saalwächter, Wolfgang Paul, Frank Schreiber." Halle, 2016. http://d-nb.info/1123998612/34.

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5

Ping, Guanghui Yuan Jian-Min. "Effects of confinement and macromolecular crowding on protein stability and protein folding dynamics /." Philadelphia, Pa. : Drexel University, 2005. http://dspace.library.drexel.edu/handle/1860/491.

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6

Li, X. F. "Investigation of protein-protein interactions : multibody docking, association/dissociation kinetics and macromolecular crowding." Thesis, University College London (University of London), 2011. http://discovery.ucl.ac.uk/1302277/.

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Protein-protein interactions are central to understanding how cells carry out their wide array of functions and metabolic procedures. Conventional studies on specific protein interactions focus either on details of one-to-one binding interfaces, or on large networks that require a priori knowledge of binding strengths. Moreover, specific protein interactions, occurring within a crowded macromolecular environment, which is precisely the case for interactions in a real cell, are often under-investigated. A macromolecular simulation package, called BioSimz, has been developed to perform Langevin

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7

Lu, Cheng [Verfasser], and Gerhard [Akademischer Betreuer] Stock. "Modeling protein dynamics in solution: effects of ligand binding and crowding." Freiburg : Universität, 2016. http://d-nb.info/1119452643/34.

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8

Cao, Yang. "Macromolecular crowding effects on the activity of the extracellular signal regulated kinase 2 /." View abstract or full-text, 2008. http://library.ust.hk/cgi/db/thesis.pl?CHEM%202008%20CAO.

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9

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

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10

Christiansen, Alexander. "Effects of Macromolecular Crowding on Protein Folding : - in-vitro equilibrium and kinetic studies on selected model systems." Doctoral thesis, Umeå universitet, Kemiska institutionen, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-82059.

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Protein folding is the process during which an extended and unstructured polypeptide converts to its compact folded structure that is most often the functional state. The process has been characterized extensively in dilute buffer in-vitro during the last decades but the actual biological place for this process is the inside of living cells. The cytoplasm of a cell is filled with a plethora of different macromolecules that together occupy up to 40% of the total volume. This large amount of macromolecules restricts the available space to each individual molecule, which has been termed macromole

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11

Köhn, Birgit Anna Luise [Verfasser]. "Characterizing the Effects of Macromolecular Crowding on Protein Stability, Dynamics and Function / Birgit Anna Luise Köhn." Konstanz : KOPS Universität Konstanz, 2020. http://d-nb.info/1233203436/34.

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12

Senske, Michael [Verfasser], Martina [Gutachter] Havenith, and Simon [Gutachter] Ebbinghaus. "Protein stability in crowding and confinement / Michael Senske ; Gutachter: Martina Havenith, Simon Ebbinghaus ; Fakultät für Chemie und Biochemie." Bochum : Ruhr-Universität Bochum, 2019. http://d-nb.info/117736431X/34.

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13

Bokvist, Marcus. "Membrane mediated aggregation of amyloid-β protein : a potential key event in Alzheimer's disease". Doctoral thesis, Umeå universitet, Kemi, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-969.

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The pathogenesis of Alzheimer’s disease (AD), the most common senile dementia, is a complex process. A crucial event in AD is the aggregation of amyloid-β protein (Aβ), a cleavage product from the Amyloid Precursor Protein (APP). Aβ40, a common component in amyloid plaques found in patients, aggregates in vitro at concentrations, much higher than the one found in vivo. But in the presence of charged lipid membranes, aggregations occurs at much lower concentration in vitro compared to the membrane-free case. This can be understood due to the ability of Aβ to get electrostatically attracted to t

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14

Smith, Gregory Robert. "Unraveling the Role of Cellular Factors in Viral Capsid Formation." Research Showcase @ CMU, 2015. http://repository.cmu.edu/dissertations/475.

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Understanding the mechanisms of virus capsid assembly has been an important research objective over the past few decades. Determining critical points along the pathways by which virus capsids form could prove extremely beneficial in producing more stable DNA vectors or pinpointing targets for antiviral therapy. The inability of current experimental technology to address this objective has resulted in a need for alternative approaches. Theoretical and computational studies offer an unprecedented opportunity for detailed examination of capsid assembly. The Schwartz Lab has previously developed a

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15

Mikaelsson, Therese. "Electronic Energy Migration/Transfer as a Tool to Explore Biomacromolecular Structures." Doctoral thesis, Umeå universitet, Kemiska institutionen, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-86794.

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Fluorescence-based techniques are widely used in bioscience, offering a high sensitivity and versatility. In this work, fluorescence electronic energy migration/ transfer is applied to measure intramolecular distances in two types of systems and under various conditions. The main part of the thesis utilizes the process of donor-acceptor energy transfer to probe distances within the ribosomal protein S16. Proteins are essential to all organisms. Therefore, it is of great interest to study protein structure and function in order to understand and prevent protein malfunction. Moreover, it is also

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16

Miermont, Agnès. "Severe osmotic compression of the yeast Saccharomyces cerevisiae." Phd thesis, Université Paris-Diderot - Paris VII, 2013. http://tel.archives-ouvertes.fr/tel-00864602.

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Les cellules ont développé plusieurs voies de signalisation et de réponses transcriptionnelles pour réguler leur taille et coordonner leur croissance et leurs divisions cellulaires. L'intérieur des cellules est naturellement surchargé par des macromolécules. Cet encombrement macromoléculaire, appelé crowding, a été intensément étudié in vitro et est connu pour affecter la cinétique des réactions. Cependant, l'étude des effets d'encombrement in vivo est plus difficile en raison du haut niveau de complexité et d'hétérogénéité à l'intérieur d'une cellule. Au cours de cette thèse, nous nous sommes

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17

Ji, Sifan. "Analogues polypeptides intelligents de la protéine fluorescente verte." Electronic Thesis or Diss., Bordeaux, 2025. http://www.theses.fr/2025BORD0010.

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La protéine fluorescente verte (GFP) s'est imposée comme une sonde fluorescente unique qui trouve des applications dans le domaine des sciences de la vie. La découverte et le développement de la GFP ont été dûment récompensés par le prix Nobel de chimie en 2008. La protéine se compose d'un chromophore central, intégré dans une chaîne polypeptidique hélicoïdale et encapsulé dans une cage protéique. Ces dernières années, des fluorophores synthétiques analogues au chromophore de la GFP ont été développés dans le but d'imiter les propriétés de fluorescence de la protéine et de ses dérivés. Ces flu

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18

Medkour, Terkia. "Modélisation mathématique et simulation numérique de la polymérisation de l’hémoglobine drépanocytaire." Thesis, Paris Est, 2008. http://www.theses.fr/2008PEST0044/document.

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La drépanocytose, ou anémie falciforme, présente une variabilité interindividuelle considérable, conditionnée par de multiples facteurs, dynamiques et interactifs, depuis le niveau moléculaire jusqu’au niveau du patient. L’hémoglobine drépanocytaire, ou hémoglobine S (HbS, tétramère a2bS 2), est un mutant de l’hémoglobine A (a2b2) : elle possède à sa surface une valine (hydrophobe) substituant un acide glutamique natif (négativement chargé). Cette mutation entraîne l’agrégation de l’HbS désoxygénée en polymères, ainsi que l’altération des propriétés de l’érythrocyte -dont sa rhéologie et ses i

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19

Kundu, Jayanta. "Study of heme proteins in presence of macromolecular crowding agents." Thesis, 2017. http://localhost:8080/iit/handle/2074/7458.

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20

Catalini, Sara. "Solvation water role in driving structural conformation and self-assembly of peptides and proteins." Doctoral thesis, 2021. http://hdl.handle.net/2158/1234476.

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“Solvation water role in driving structural conformation and self-assembly of peptides and proteins”, the title of the present thesis, summarizes the objective of my three years PhD course aimed to investigate the relationship existing between the structure of biomolecules in solution and their mutual influence with surrounding water molecules. The three year work has been mainly experimental and principally focused in analyzing the capability of vibrational spectroscopies and some non-linear spectroscopic techniques to disentangle various contributions to solvent-molecule interactions. Howeve

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21

Kumar, Manjeet. "The many faces of amyloid fibres: their detection and regulation by molecular chaperone proteins." Phd thesis, 2017. http://hdl.handle.net/1885/130970.

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Proteins are the molecular machines that control and regulate most of the vital cellular functions in living organisms, and account for about half of the total dry mass of the cell. For a protein to function properly, it must attain its correct conformation and location within the crowded milieu of the cell. A complex set of molecular chaperone proteins assist polypeptides to acquire their native functional fold within the relevant biological timescale. However, the intricacy and diverse nature of the protein folding process and various environmental fac

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22

Mondal, Somnath. "Structural and Dynamic Studies of Protein-Nanomaterial Interactions." Thesis, 2016. https://etd.iisc.ac.in/handle/2005/2823.

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My thesis is divided into five chapters, starting with a general introduction in first chapter and sample preparation and protein-NMR assignment techniques in second chapter. The remaining three chapters focus on three different areas/projects that I have worked on. Chapter 1: Introduction to nanomaterials and all the experimental techniques This chapter reviews different kinds of nanomaterials and their application utilized for protein-nanomaterial interaction in our study, along with the introduction to different spectroscopy and microscopy techniques used for the interaction studies. Sta

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23

Mondal, Somnath. "Structural and Dynamic Studies of Protein-Nanomaterial Interactions." Thesis, 2016. http://etd.iisc.ernet.in/handle/2005/2823.

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My thesis is divided into five chapters, starting with a general introduction in first chapter and sample preparation and protein-NMR assignment techniques in second chapter. The remaining three chapters focus on three different areas/projects that I have worked on. Chapter 1: Introduction to nanomaterials and all the experimental techniques This chapter reviews different kinds of nanomaterials and their application utilized for protein-nanomaterial interaction in our study, along with the introduction to different spectroscopy and microscopy techniques used for the interaction studies. Start

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24

Diniz, Ana Catarina Vitor Ferreira. "Mimicking cell environment: carbohydrate-protein interactions under macromolecular crowding." Master's thesis, 2016. http://hdl.handle.net/10362/18453.

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As molecular recognition players glycans mediate essential physiological events with high importance in Life. Galectin-3 (Gal-3) is a key regulator of the immune system and a potent effector in diverse cellular mechanisms inside the cell, at the cell surface and at extracellular matrix. Structurally Gal-3 FL is composed by a well-folded carbohydrate recognition domain (Gal-3 CRD) and a disorder tail. Gal-3 recognition events, including the dynamics and binding, are well characterized in diluted solutions. However, Gal-3 recognize galactose-unit in a complex biological medium that contains high

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25

Ganguly, Abantika. "Probing Macromolecular Reactions At Reduced Dimensionality : Mapping Of Sequence Specific And Non-Specific Protein-Ligand lnteractions." Thesis, 2012. https://etd.iisc.ac.in/handle/2005/2478.

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During the past decade the effects of macromolecular crowding on reaction pathways is gaining in prominence. The stress is to move out of the realms of ideal solution studies and make conceptual modifications that consider non-ideality as a variable in our calculations. In recent years it has been shown that molecular crowding exerts significant effects on all in vivo processes, from DNA conformational changes, protein folding to DNA-protein interactions, enzyme pathways and signalling pathways. Both thermodynamic as well as kinetic parameters vary by orders of magnitude in uncrowded buffer sy

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26

Ganguly, Abantika. "Probing Macromolecular Reactions At Reduced Dimensionality : Mapping Of Sequence Specific And Non-Specific Protein-Ligand lnteractions." Thesis, 2012. http://etd.iisc.ernet.in/handle/2005/2478.

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During the past decade the effects of macromolecular crowding on reaction pathways is gaining in prominence. The stress is to move out of the realms of ideal solution studies and make conceptual modifications that consider non-ideality as a variable in our calculations. In recent years it has been shown that molecular crowding exerts significant effects on all in vivo processes, from DNA conformational changes, protein folding to DNA-protein interactions, enzyme pathways and signalling pathways. Both thermodynamic as well as kinetic parameters vary by orders of magnitude in uncrowded buffer sy

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27

Chung, Tse-Yu, and 鍾澤裕. "The Effects of Macromolecular Crowding on the Conformation and Stability of Protein." Thesis, 2007. http://ndltd.ncl.edu.tw/handle/25w38z.

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碩士<br>國立東華大學<br>化學系<br>95<br>Physiological fluid media contain macromolecules occupying a significant fraction (typically 20-30%) of the total volume. Biological macromolecules have evolved to function inside such crowded environments. It has been shown the natural and synthetic macromolecules can be used to mimic the crowding environments in cells. In this study, we applied NMR and other biophysical techniques to investigate the effect of crowding on the stability and conformation of ubiquitin and its mutants. Ubiquitin (Ub), a small protein with 76 residues, contained 5-stranded b-sheet

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28

Dong, Guangqiang. "Modelling and Experimental Results on Stochastic Model Reduction, Protein Maturation, Macromolecular Crowding, and Time-varying Gene Expression." Thesis, 2009. http://hdl.handle.net/1807/19264.

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Gene expression, which connects genomic information to functional units in living cells, has received substantial attention since the completion of The Human Genome Project. Quantitative characterization of gene expression will provide valuable information for understanding the behavior of living cells, and possibilities of building synthetic gene circuits to control or modify the behavior of naturally occurring cells. Many aspects of quantitative gene expression have been studied, including gene expression dynamics and noise in E. coli. The gene expression process itself is stochastic, and mo

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29

"Ultralow background substrate for protein microarray technology and on-chip study of macromolecular crowding effect on FRET." 2015. http://repository.lib.cuhk.edu.hk/en/item/cuhk-1292119.

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Feng, Hui.<br>Thesis Ph.D. Chinese University of Hong Kong 2015.<br>Includes bibliographical references (leaves 91-102).<br>Abstracts also in Chinese.<br>Title from PDF title page (viewed on 05, January, 2017).

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30

Tsai, Chia Jung, and 蔡佳容. "ESR Approaches to Reveal Protein Dynamics and Activity under Conditions of Nano-confinement, Allosteric Transition, and Molecular Crowding." Thesis, 2015. http://ndltd.ncl.edu.tw/handle/83407107144832112896.

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博士<br>國立清華大學<br>化學系<br>103<br>Spin-label electron spin resonance (ESR) spectroscopy has been extensively developed in the latest decade for studying problems in the fields of biology, physics, and chemistry. With the site-directed spin-labeling techniques, ESR can be employed to resolve the complexity of molecular dynamics, probing local environments of various molecular complexes such as protein, membrane, and macromolecular assemblies. In particular, continuous wave (cw) ESR and double electron-electron resonance (DEER) are among the most powerful ESR techniques. This dissertation demonstr

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31

Silva, Micael Simões. "Design of bio-inspired ionic liquids for protein stabilisation." Master's thesis, 2015. http://hdl.handle.net/10362/17071.

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Ionic Liquids (ILs) consist in organic salts that are liquid at/or near room temperature. Since ILs are entirely composed of ions, the formation of ion pairs is expected to be one essential feature for describing solvation in ILs. In recent years, protein - ionic liquid (P-IL) interactions have been the subject of intensive studies mainly because of their capability to promote folding/unfolding of proteins. However, the ion pairs and their lifetimes in ILs in P-IL thematic is dismissed, since the action of ILs is therefore the result of a subtle equilibrium between anion-cation interaction, i

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32

Afonso, Cláudia Filipa Martins. "Development of in-cell NMR methodologies." Master's thesis, 2017. http://hdl.handle.net/10362/27626.

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The characterization of molecules within a biologically relevant environment distinguishes nuclear magnetic resonance (NMR) spectroscopy from other molecular-based biophysical techniques, such as X-ray crystallography and cryo-electron microscopy. Due to its exceptional stability and reduced ability to interact in a specific manner with other cellular components, the GB1 protein represents the quintessential probe to investigate the physiochemical effects imposed by the crowded environment on the structure and dynamics of proteins, without simultaneously compromising the ability to obtain in-c

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