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Dissertations / Theses on the topic 'Protein conformation'

Author: Grafiati

Published: 4 June 2021

Last updated: 25 July 2025

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1

Link, Justin J. "Ultrafast Protein Conformation Dynamics." The Ohio State University, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=osu1230584570.

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2

Wang, Chu. "Improved conformational sampling for protein-protein docking /." Thesis, Connect to this title online; UW restricted, 2007. http://hdl.handle.net/1773/9194.

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3

Billsten, Peter. "Studies on the conformation of adsorbed proteins." Lund : Göteborg University, 1997. http://catalog.hathitrust.org/api/volumes/oclc/39776983.html.

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4

Florane, H. "Exploring protein conformation with mass spectrometry." Thesis, University of Edinburgh, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.650980.

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The first part of this thesis describes the development and viability of a phase I screening system for obtaining a rank order of affinity of novel ligands against the immunophilin, Cyclophilin A (CypA). The naturally occurring inhibitor Cyclosporin A (CsA) was used as a positive control to validate a method for calculating the dissociation constant (K<sub>d</sub>). An HPLC autosampler and pumping system was used as a high throughput on-line electrospray ionisation (ESI)-MS sampling system. Optimised ESI conditions were then used to screen novel ligands from 3 combinatorial libraries and appro

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5

Nicholls, Robert Adam. "Conformation-independent comparison of protein structures." Thesis, University of York, 2011. http://etheses.whiterose.ac.uk/2120/.

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The comparative analysis of protein structures is often performed in order to identify and explore similarities/dissimilarities present between target structures. Whilst many tools are available for structural comparison, the development of new tools providing different information is desirable. The work presented here concerns the development of ProSMART (Procrustes Structural Matching Alignment and Restraints Tool), a tool to aid the comparative analysis of protein structures. Primarily, the software is used for conformation-independent pairwise structural alignment, allowing identification

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6

Watt, Stephen J. "Use of electrospray ionization mass spectrometry to study protein conformation and protein-protein interactions." Access electronically, 2005. http://www.library.uow.edu.au/adt-NWU/public/adt-NWU20060516.114814/index.html.

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Thesis (Ph.D.)--University of Wollongong, 2005.<br>Typescript. EMBARGOED-this thesis is subject to a six months embargo (07/09/06) and may only be viewed and copied with the permission of the author. For further information please Contact the Archivist. Includes bibliographical references: leaf 159-194.

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7

Rashid, Mahmood Abdur. "Heuristic Based Search for Protein Structure Prediction." Thesis, Griffith University, 2014. http://hdl.handle.net/10072/367134.

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Proteins that are essentially sequences of amino acids, adopt specific folded 3-dimensional (3D) structures to perform their specific tasks. However, misfolded proteins cause fatal diseases. Hence, protein structure prediction (PSP) has emerged as an important multi-disciplinary research problem. Given a protein sequence, the PSP problem is to find a 3D structure of the protein such that the total free energy amongst the amino acids in the sequence is minimised. In-vitro laboratory methods are time-consuming, expensive, and failure-prone. Conversely, computational methods are NP-hard even when

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8

Chivian, Dylan Casey. "Application of information from homologous proteins for the prediction of protein structure /." Thesis, Connect to this title online; UW restricted, 2005. http://hdl.handle.net/1773/9264.

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9

Hosia, Waltteri. "Molecular mechanisms in amyloid fibril formation /." Stockholm, 2004. http://diss.kib.ki.se/2004/91-7349-976-5.

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10

Sandin, Sara. "Cryo-electron tomography of individual protein molecules /." Stockholm, 2005. http://diss.kib.ki.se/2005/91-7140-462-7/.

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11

Giasuddin, Abul Bashar Mohammad. "Silane Modulation of Protein Conformation and Self-Assembly." DigitalCommons@USU, 2018. https://digitalcommons.usu.edu/etd/7029.

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This research focused on development of nanoparticle- based therapeutics against amyloid fibrils. Amyloid fibrils are associated with various diseases such as Parkinson’s, Huntington’s, mad cow disease, Alzheimer’s, and cataracts. Amyloid fibrils develop when proteins change their shape from a native form to a pathogenic “misfolded” form. The misfolded proteins have the ability to recruit more native proteins into the pathogenic forms, which self-assemble into amyloid fibrils that are hallmarks of the various protein-misfolding diseases listed above. Amyloid fibrils are highly resistant to deg

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12

Kim, Junghwa. "Roles of intermediate conformation and transient disulfide bonding on native folding of P22 tailspike protein." Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file 2.50 Mb., 176 p, 2006. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&res_dat=xri:pqdiss&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&rft_dat=xri:pqdiss:3220719.

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13

Pothier, Laura J. "Effects of amino acid substitutions on the conformation and stability of A[beta]₁₆₋₂₂ aggregates /." Connect to online version, 2007. http://ada.mtholyoke.edu/setr/websrc/pdfs/www/2007/213.pdf.

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14

Simons, Kim T. "Deciphering the protein folding code : ab initio prediction of protein structure /." Thesis, Connect to this title online; UW restricted, 1998. http://hdl.handle.net/1773/9234.

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15

Budi, Bunarta Hendra (Akin), and akin budi@rmit edu au. "On the effects of external stresses on protein conformation." RMIT University. School of Applied Sciences, 2006. http://adt.lib.rmit.edu.au/adt/public/adt-VIT20061116.123431.

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The use of electromagnetic devices such as microwave ovens and mobile phones has certainly brought convenience to our lives. At the same time, the proliferation of said devices has increased public awareness of the potential health hazards. It is generally assumed that there is little or no risk associated with the use of electromagnetic devices, based on the small amount of power associated with those devices. However, case studies on animals indicate that the risk cannot be entirely ruled out. It has long been known that proteins are sensitive to stress, arising from various sources suc

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16

Katayama, Derrick S. "Towards a mechanistic understanding of pharmaceutical protein stabilization in solution and the solid state /." Connect to full text via ProQuest. Limited to UCD Anschutz Medical Campus, 2006.

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Thesis (Ph.D. in Pharmaceutical Sciences) -- University of Colorado at Denver and Health Sciences Center, 2006.<br>Typescript. Includes bibliographical references (leaves 159-173). Free to UCDHSC affiliates. Online version available via ProQuest Digital Dissertations;

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17

Ngo, Jacky Chi Ki. "SR protein kinase 1 conformation, substrate recognition and catalysis /." Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2006. http://wwwlib.umi.com/cr/ucsd/fullcit?p3211379.

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Thesis (Ph. D.)--University of California, San Diego, 2006.<br>Title from first page of PDF file (viewed June 13, 2006). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references (p. 169-184).

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18

Marshall, R. Andrew. "Regulation of protein synthesis via changes in ribosome conformation /." May be available electronically:, 2008. http://proquest.umi.com/login?COPT=REJTPTU1MTUmSU5UPTAmVkVSPTI=&clientId=12498.

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19

Lundell, Sandra J. "Quantum Mechanical Studies of N-H···N Hydrogen Bonding in Acetamide Derivatives and Amino Acids." DigitalCommons@USU, 2018. https://digitalcommons.usu.edu/etd/7309.

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Proteins are made of vast chains of amino acids that twist and fold into intricate designs. These structures are held in place by networks of noncovalent interactions. One of these, the hydrogen bond, forms bridges between adjacent pieces of the protein chain and is one of the most important contributors to the shape and stability of proteins. Hydrogen bonds come in all shapes and sizes and a full understanding of these not only aids in our understanding of proteins in general but can bridge the gap to finding cures to many protein-related diseases, such as sickle-cell anemia. The primary aim

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20

Boussert, Stéphanie Van Dorsselaer Alain Giralt Ernest. "Structural studies of proteins and protein complexes by mass spectrometry and atomic force microscopy." Strasbourg : Université Louis Pasteur, 2008. http://eprints-scd-ulp.u-strasbg.fr:8080/977/01/BOUSSERT_Stephanie_2008.pdf.

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21

Zang, Chen. "Ultrafast Spectroscopic Study of Protein Conformation Dynamics and Hydration Dynamics." The Ohio State University, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=osu1299481658.

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22

Nilsson, Johan. "Membrane protein topology : prediction, experimental mapping and genome-wide analysis /." Stockholm, 2004. http://diss.kib.ki.se/2004/91-7349-963-3/.

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23

Sapsaman, Temsiri. "An energy landscaping approach to the protein folding problem." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2009. http://hdl.handle.net/1853/31637.

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Thesis (Ph.D)--Mechanical Engineering, Georgia Institute of Technology, 2010.<br>Committee Chair: Harvey Lipkin; Committee Member: Joel S. Sokol; Committee Member: Michael J. Leamy; Committee Member: Nader Sadegh; Committee Member: Stephen C. Harvey. Part of the SMARTech Electronic Thesis and Dissertation Collection.

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24

Joseph, Agnel Praveen. "Comparison of protein folds based on similarities in local backbone conformation." Paris 7, 2011. http://www.theses.fr/2011PA077100.

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Une grande partie de mon travail de thèse porte sur le développement de méthodes efficaces pour l'alignement par paires et multiples protéines structurelles. Ceci est basé sur l'utilisation de la protéine Blocks qui est le plus largement utilisé alphabet structural [1, 2]. Une structure de la protéine complète peut être représenté par une séquence d'alphabets, où chaque alphabet correspond à un PB. L'alignement des séquences PB donne une comparaison de la structure des protéines. Basé sur des stratégies classiques d'alignement de séquences, un outil efficace pour l'alignement de séquences PB a

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25

Hatcher, Kristen-Louise. "Conformation Based Reagents for the Detection of Disease-Associated Prion Protein." Case Western Reserve University School of Graduate Studies / OhioLINK, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=case1232747817.

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26

Käll, Lukas. "Predicting transmembrane topology and signal peptides with hidden Markov models /." Stockholm, 2006. http://diss.kib.ki.se/2006/91-7140-719-7/.

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27

English, William R. "Effects of calcium on conformation and stability of porcine pancreatic phospholipase Aâ†2." Thesis, University of Kent, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.285981.

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28

Kallberg, Yvonne. "Bioinformatic methods in protein characterization /." Stockholm, 2002. http://diss.kib.ki.se/2002/91-7349-370-8/.

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29

Cao, Jin. "Single Molecular Spectroscopy and Atomic Force Manipulation of Protein Conformation and Dynamics." Bowling Green State University / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1416588612.

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30

Wang, Fei. "Biochemical Studies Of Interactions Between Prion Protein And Lipids." The Ohio State University, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=osu1227725062.

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31

Devlin, Glyn L. "The mechanisms of serpin misfolding and its inhibition." Monash University, Dept. of Biochemistry and Molecular Biology, 2003. http://arrow.monash.edu.au/hdl/1959.1/9469.

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32

Strickland, Dawn Michelle. "Maximum cliques with application to protein structure alignment." Diss., Georgia Institute of Technology, 2002. http://hdl.handle.net/1853/24081.

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33

Cassel, Marika. "Studies on the Conformation of Transmembrane Polypeptides in Membrane Proteins." Doctoral thesis, Stockholm : Deptartment of Biochemistry & Biophysics, Stockholm University, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-759.

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34

Larsericsdotter, Helén. "Macromolecules at interfaces /." Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-4661.

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35

Duan, Jianxin. "Protein folding, stability and recognition /." Stockholm, 2004. http://diss.kib.ki.se/2004/91-7140-098-2/.

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36

Masuda, Yuichi. "Identification of Toxic Conformation in the Aggregates of 42-residue Amyloid β-protein". Kyoto University, 2009. http://hdl.handle.net/2433/123973.

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Kyoto University (京都大学)<br>0048<br>新制・課程博士<br>博士(農学)<br>甲第14661号<br>農博第1743号<br>新制||農||967(附属図書館)<br>学位論文||H21||N4434(農学部図書室)<br>UT51-2009-D373<br>京都大学大学院農学研究科食品生物科学専攻<br>(主査)教授入江一浩, 教授井上國世, 教授安達修二<br>学位規則第4条第1項該当

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37

Fears, Kenan Patrick. "Adsorption-induced changes in enzyme bioactivity correlated with adsorbed protein orientation and conformation." Connect to this title online, 2009. http://etd.lib.clemson.edu/documents/1246558493/.

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38

Mendez, Giraldez Raul. "Critical assessment of predicted interactions at atomic resolution." Doctoral thesis, Universite Libre de Bruxelles, 2007. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/210664.

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Molecular Biology has allowed the characterization and manipulation of the molecules of life in the wet lab. Also the structures of those macromolecules are being continuously elucidated. During the last decades of the past century, there was an increasing interest to study how the different genes are organized into different organisms (‘genomes’) and how those genes are expressed into proteins to achieve their functions. Currently the sequences for many genes over several genomes have been determined. In parallel, the efforts to have the structure of the proteins coded by those genes go on. H

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39

Bai, Shujun. "Understanding physicochemical stability of proteins in solution and development of new analytical methods for freeze-dried protein formulations /." Connect to full text via ProQuest. Limited to UCD Anschutz Medical Campus, 2008.

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Thesis (Ph.D. in Pharmaceutical Sciences) -- University of Colorado Denver, 2008.<br>Typescript. Includes bibliographical references (leaves 134-146). Free to UCD Anschutz Medical Campus. Online version available via ProQuest Digital Dissertations;

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40

Bruce, Neil John. "Investigating protein conformational change via molecular dynamics simulation." Thesis, University of Manchester, 2011. https://www.research.manchester.ac.uk/portal/en/theses/investigating-protein-conformational-change-via-molecular-dynamics-simulation(17145939-f643-4b23-bbb9-029cf5489c15).html.

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Accumulation and aggregation of the 42-residue amyloid-[beta] (A[beta]) protein fragment, which originates from the cleavage of amyloid precursor protein by beta and gamma secretase, correlates with the pathology of Alzheimer's disease (AD). Possible therapies for AD include peptides based on the A[beta] sequence, and recently identified small molecular weight compounds designed to mimic these, that interfere with the aggregation of A[beta] and prevent its toxic effects on neuronal cells in culture. Here, we use molecular dynamics simulations to compare the mode of interaction of an active (LP

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41

Phan, Jamie. "Investigating protein folding by the de novo design of an α-helix oligomer". Scholarly Commons, 2013. https://scholarlycommons.pacific.edu/uop_etds/859.

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Proteins are composed of a unique sequence of amino acids, whose order guides a protein to adopt its particular fold and perform a specific function. It has been shown that a protein's 3-dimensional structure is embedded within its primary sequence. The problem that remains elusive to biochemists is how a protein's primary sequence directs the folding to adopt such a specific conformation. In an attempt to gain a better understanding of protein folding, my research tests a novel model of protein packing using protein design. The model defines the knob-socket construct as the fundamental unit o

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42

Davidson, Patricia Marie L. "Langmuir films and nanoparticle applications of a spider silk protein analog." Thesis, McGill University, 2006. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=100794.

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A synthetic analog of a spider silk protein (M4) was studied. Langmuir films were made and an inflexion in the isotherm indicated conformational changes upon compression. Deposition onto solid substrates was most successful using a hydrophobic substrate and the Langmuir-Schaeffer method. AFM was used to image the surface, which was mesh like and did not show any indication of order.<br>Gold nanoparticles were produced in the presence of the protein and protein solutions were added to read made nanoparticles for the purpose of displacing the weak ligands present. CD measurements were performed

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43

Phan, Jamie. "Investigating protein folding by the de novo design of an α-helix oligomer : a thesis". Scholarly Commons, 2001. https://scholarlycommons.pacific.edu/uop_etds/859.

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Proteins are composed of a unique sequence of amino acids, whose order guides a protein to adopt its particular fold and perform a specific function. It has been shown that a protein's 3-dimensional structure is embedded within its primary sequence. The problem that remains elusive to biochemists is how a protein's primary sequence directs the folding to adopt such a specific conformation. In an attempt to gain a better understanding of protein folding, my research tests a novel model of protein packing using protein design. The model defines the knob-socket construct as the fundamental unit o

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44

Estey, Tia Brie. "Protein instability associated with PLGA delivery systems and UV-induced protein oxidation /." Connect to full text via ProQuest. IP filtered, 2006.

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Thesis (Ph.D. in Pharmaceutical Sciences) -- University of Colorado, 2006.<br>Typescript. Includes bibliographical references (leaves 144-161). Free to UCDHSC affiliates. Online version available via ProQuest Digital Dissertations;

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45

Guan, Xiao, and 关晓. "NMR approaches to protein conformation and backbone dynamics: studies on hyperthermophilicacylphosphatase and neuropeptide secretoneurin." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2010. http://hub.hku.hk/bib/B44079230.

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46

Mermans, Daphne Maria Johanna. "Quality control of substrate conformation in the Escherichia coli twin arginine protein-targeting pathway." Thesis, University of Kent, 2018. https://kar.kent.ac.uk/69592/.

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In Escherichia coli, the twin arginine translocase (Tat) is one of the major protein translocation mechanisms. The Tat system has the ability to transport folded proteins across the inner membrane. Therefore, it has the ability to discriminate between folding states. However, it is not well understood how the Tat system senses the folding state of a substrate. In this study we probed the Tat proofreading mechanism and we investigated whether Tat substrates in E. coli are translocated by the Tat system due to their rapid folding kinetics. We demonstrate that the E. coli Tat machinery can proces

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47

Willis, William L. "YB-1 Stress-Response Protein Conformation Implicated in Post-transcriptional Control of Myofibroblast Differentiation." The Ohio State University, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=osu1376593223.

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48

Guo, Shenyuan. "Localization of protein segments affecting conformation of deoxyadenosine kinase from lactobacillus acidophilus r-26 /." The Ohio State University, 1998. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487949150070277.

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49

Brady, John Joseph. "VAPORIZATION OF BIOLOGICAL MACROMOLECULES USING INTENSE, ULTRAFAST LASERS: MECHANISM AND APPLICATION TO PROTEIN CONFORMATION." Diss., Temple University Libraries, 2011. http://cdm16002.contentdm.oclc.org/cdm/ref/collection/p245801coll10/id/211496.

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Chemistry<br>Ph.D.<br>This dissertation details the design and implementation of a state-of-the-art ambient trace analysis technique known as laser electrospray mass spectrometry. This novel technique utilizes an intense, nonresonant femtosecond laser pulse to transfer nonvolatile, fragile molecules into the gas phase from various substrates. The vaporized analyte is subsequently captured, solvated and ionized in an electrospray plume enabling mass analysis. Laser electrospray mass spectrometry is capable of analyzing samples in the liquid or solid states, mass spectral imaging of adsorbed mol

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50

Singh, Jaswinder. "Detection of Cis-Trans Conformation in Protein Structure using Deep Learning Neural Network Techniques." Thesis, Griffith University, 2019. http://hdl.handle.net/10072/384790.

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Proteins are important biological macromolecules that play critical roles in most biological processes. The functionality of protein depends on its three dimensional structure, which further depends on the protein's amino acid sequence. Direct prediction of 3D structure of protein from amino acid is challenging task. Therefore, prediction of three dimensional protein structure is divided into small sub-problems like one and two-dimensional properties of protein structure. The solution of these sub-problems can lead to successful three-dimensional structure prediction of protein. Accurate predi

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