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Dissertations / Theses on the topic 'Amino acids - Structure'

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Published: 4 June 2021

Last updated: 13 February 2022

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1

Malešević, Miroslav. "[Beta]-amino [Beta-amino] acids as secondary structure inducers in peptides." [S.l. : s.n.], 2002. http://deposit.ddb.de/cgi-bin/dokserv?idn=966017811.

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2

Lin, Guoliang. "NOVEL METHANOPYRROLIDINE β– AMINO ACIDS". Diss., Temple University Libraries, 2010. http://cdm16002.contentdm.oclc.org/cdm/ref/collection/p245801coll10/id/92631.

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Chemistry<br>Ph.D.<br>Methanopyrrolidine-5-carboxylic acids (MetPyr-5-acids), or 5-syn-carboxy-2- azabicyclo[2.1.1]hexanes are building blocks for β-peptides that cannot form backbone hydrogen bonds. To introduce functionality to this ring system, 6-syn-benzyloxymethyl and 6-syn-phenyl substituted derivatives have been prepared by an efficient synthetic procedure. Addition of appropriately substituted allyl amines to 3-butynone, amide protection, and irradiation afford mainly 5-acetyl-2-azabicyclo[2.1.1]hexanes. Haloform oxidation leads to the desired 6-substituted MetPyr-5-acids. A 1-ethoxyca

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3

Li, Bing, and 李兵. "Aminoxy acids as building blocks for turns and helices." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2000. http://hub.hku.hk/bib/B31240549.

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4

Sweet, Miles J. "Applications of ÃŸ-amino acids in synthesis and structure." Thesis, University of Oxford, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.418131.

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5

吳飛虎 and Fei-fu Ng. "An unusual turn structure in peptides containing alpha-aminoxyacids." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 1998. http://hub.hku.hk/bib/B31219731.

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6

Ng, Fei-fu. "An unusual turn structure in peptides containing alpha-aminoxyacids /." Hong Kong : University of Hong Kong, 1998. http://sunzi.lib.hku.hk/hkuto/record.jsp?B19945747.

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7

Eastwood, Amy Lynn Gray Harry B. Dougherty Dennis A. "Investigating structure-function relationships in ion channels using unatural amino acids /." Diss., Pasadena, Calif. : California Institute of Technology, 2009. http://resolver.caltech.edu/CaltechETD:etd-01062009-133603.

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8

Halonski, John. "Utilization of Unnatural Amino Acids to Modulate Protein Structure and Function." W&M ScholarWorks, 2018. https://scholarworks.wm.edu/etd/1530192786.

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Proteins are capable of an astounding array of functions using only the 20 canonical amino acids; however, the ability to add new functional groups to the genetic code through the utilization of unnatural amino acids (UAAs) has greatly expanded our ability to study and manipulate proteins. By expanding the diversity of functional groups within proteins, a wide variety of applications in industry as well as in fields such as diagnostics, biochemistry, and materials science are now possible. These applications have further been expanded through the development and optimization of bioorthogonal r

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9

Baktula, Avinash M. "A Method Based on Conserved Multiple Amino Acid Properties to Predict Amino Acid Substitutions Which Maintain the Protein Structure." TopSCHOLAR®, 2004. http://digitalcommons.wku.edu/theses/1107.

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A METHOD BASED ON CONSERVED MULTIPLE AMINO ACID PROPERTIES TO PREDICT AMINO ACID SUBSTITUTIONS WHICH MAINTAIN THE PROTEIN STRUCTURE Avinash M. Baktula September 16, 2004 1-117 Directed by: Claire A. Rinehart, Doug McElroy and Sigrid Jacobshagen Department of Biology Western Kentucky University Proteins often contain several domains, each with a distinct structure. Such domains have evolved as units that, when combined in various arrangements, produce proteins of unique structure. This study was conducted to identify amino acid substitutions that don’t change structure. Amino acid properties wh

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10

Sutherland, Andrew. "The enantioselective synthesis of amino acids for the investigation of protein structure." Thesis, University of Bristol, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.388029.

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11

Prytz, Christopher. "Electronic Structure Calculations of Amino Acids Under the Influence of Electric Fields." Thesis, Uppsala universitet, Molekyl- och kondenserade materiens fysik, 2018. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-355141.

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By the use of highly intense X-ray pulses, with durations in the scale of tenths of fs, high resolutiondiffraction images of the structures of individual macro-molecules can be obtained. To generatea self-consistent 3D-image of the structures the diffraction images of thousands of copies of thesame molecules have to be compounded. The composition relies on advanced algorithms with longcomputational times and is not always successful or even possible. Simulations of proteins in electricfields have proven that pre-orientation of molecules could yield results otherwise unobtainable.When a molecul

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12

Mata, David Garcia. "Understanding Protein Structure And Function Using Rational Design And Unnatural Amino Acids." The Ohio State University, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=osu1338392020.

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13

Martari, Marco. "Structure-function relationships of bolaamphiphilic peptides and peptide hybrids." Thesis, Link to the online version, 2006. http://hdl.handle.net/10019/582.

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14

Sjöholm, Marcus. "Structure and function of the moth mushroom body /." Alnarp : Dept. of Crop Science, Swedish University of Agricultural Sciences, 2006. http://epsilon.slu.se/200638.pdf.

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15

Madden, David Christopher. "Chirality and surface structure : an experimental study of amino acids on Cu{311}." Thesis, University of Cambridge, 2014. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.648737.

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16

White, Christopher. "Stabilisation of peptide secondary structure by incorporation of side-chain linked amino acids." Thesis, University College London (University of London), 2008. http://discovery.ucl.ac.uk/1445181/.

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The aim of the project was to synthesise a novel small peptide containing an ether linkage between two side chains. Computer modelling had shown the structure was likely to form a stable p turn in solution and would therefore be a good candidate to study this class of protein secondary structure. To do this a differentially protected bis-amino acid containing the ether linkage was retrosynthesised to chiral pool synthons L-aspartic acid and L-methionine. Many attempts were then made to differentially protect and manipulate the respective acid and sulfide side chains into synthons that would pa

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17

Preuss, Monika Kathrin. "Recognition of secondary structure by the molecular chaperonin groEL." Thesis, Imperial College London, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.313410.

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18

Tian, Meilin. "Structure-function studies of membrane proteins by site-specific incorporation of unnatural amino acids." Thesis, Paris 6, 2017. http://www.theses.fr/2017PA066166.

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Les protéines membranaires comme les récepteurs, les canaux ioniques et les transporteurs possèdent des rôles cruciaux dans les processus biologiques tels que la signalisation physiologique et les fonctions cellulaires. La description dynamique et fonctionnelle des structures protéiques est fondamentale pour comprendre la plupart des processus concernant les macromolécules biologiques. L'incorporation, dans des protéines, d'acides aminés non naturels (Uaas) possédant des propriétés physiques ou chimiques spécifiques fournit un puissant outil pour définir la structure et la dynamique de protéin

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19

Cao, Haibo. "Protein Structure Recognition From Eigenvector Analysis to Structural Threading Method." Washington, D.C. : Oak Ridge, Tenn. : United States. Dept. of Energy. Office of Science ; distributed by the Office of Scientific and Technical Information, U.S. Dept. of Energy, 2003. http://www.osti.gov/servlets/purl/822060-2L2Xvm/native/.

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Thesis (Ph.D.); Submitted to Iowa State Univ., Ames, IA (US); 12 Dec 2003.<br>Published through the Information Bridge: DOE Scientific and Technical Information. "IS-T 2028" Haibo Cao. 12/12/2003. Report is also available in paper and microfiche from NTIS.

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20

Dayalan, Saravanan, and saravanan dayalan@rmit edu au. "On the Structure Differences of Short Fragments and Amino Acids in Proteins with and without Disulfide Bonds." RMIT University. Computer Science and Information Technology, 2008. http://adt.lib.rmit.edu.au/adt/public/adt-VIT20081128.122615.

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Of the 20 standard amino acids, cysteines are the only amino acids that have a reactive sulphur atom, thus enabling two cysteines to form strong covalent bonds known as disulfide bonds. Even though almost all proteins have cysteines, not all of them have disulfide bonds. Disulfide bonds provide structural stability to proteins and hence are an important constraint in determining the structure of a protein. As a result, disulfide bonds are used to study various protein properties, one of them being protein folding. Protein structure prediction is the problem of predicting the three-dimensiona

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21

Peddie, Victoria. "β-Peptides: Influence of Fluorine on Structure, Conformation and Function". Thesis, University of Canterbury. Chemistry, 2010. http://hdl.handle.net/10092/4466.

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This thesis examines the synthesis of α-fluoro-β-amino acids, and the influence of the constituent fluorine on the conformation and biological properties of β-peptide derivatives. Chapter One discusses the unique properties of the C-F bond, and applications of fluorine substitution in organic and medicinal chemistry. This is followed by a review of fluorinated analogues of α-amino acids, and how their incorporation into α-peptides has resulted in profound modifications, such as enhanced thermal and chemical stability, increased affinity for lipid bilayers, stronger self-association and impro

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22

Cacan, Ercan. "Evolutionary synthetic biology: structure/function relationships within the protein translation system." Thesis, Georgia Institute of Technology, 2011. http://hdl.handle.net/1853/45838.

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Production of mutant biological molecules for understanding biological principles or as therapeutic agents has gained considerable interest recently. Synthetic genes are today being widely used for production of such molecules due to the substantial decrease in the costs associated with gene synthesis technology. Along one such line, we have engineered tRNA genes in order to dissect the effects of G:U base-pairs on the accuracy of the protein translation machinery. Our results provide greater detail into the thermodynamic interactions between tRNA molecules and an Elongation Factor protein (te

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23

Ma, Li. "Soil Organic Nitrogen - Investigation of Soil Amino Acids and Proteinaceous Compounds." Diss., Virginia Tech, 2015. http://hdl.handle.net/10919/51960.

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Soil carbon (C) and nitrogen (N) are predominantly in organic form. Proteins/ peptides, as an important organic form of N, constitute a substantial part of soil organic matter. On one hand, proteins/peptides are an important N source for plants and microorganisms, particularly in soils where inorganic N is limited. On the other hand, their stabilization in soils by forming organo-mineral associates or macromolecule complex reduces the C loss as CO2 into the atmosphere. Therefore, studies on the turnover, abundance, composition, and stability of proteins/peptides are of crucial importance to ag

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24

Smith, Mason Scott. "Measuring the Interaction and Cooperativity Between Ionic, Aromatic, and Nonpolar Amino Acids in Protein Structure." BYU ScholarsArchive, 2018. https://scholarsarchive.byu.edu/etd/7443.

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Protein folding studies have provided important insights about the key role of non-covalent interactions in protein structure and conformational stability. Some of these interactions include salt bridges, cation-π, and anion-Ï€ interactions. Understanding these interactions is crucial to developing methods for predicting protein secondary, tertiary, quaternary structure from primary sequence and understanding protein-protein interactions and protein-ligand interactions. Several studies have described how the interaction between two amino acid side chains have a substantial effect on protein s

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25

Kathuria, Sagar V. "Sequence Determinants of the Folding Free-Energy Landscape of beta alpha-Repeat Proteins: A Dissertation." eScholarship@UMMS, 2010. https://escholarship.umassmed.edu/gsbs_diss/480.

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The most common structural platform in biology, the βα-repeat classes of proteins, are represented by the (βα)8TIM barrel topology and the α/β/α sandwich, CheY-like topology. Previous studies on the folding mechanisms of several members of these proteins have suggested that the initial event during refolding involves the formation of a kinetically trapped species that at least partially unfolds before the native conformation can be accessed. The simple topologies of these proteins are thought to permit access to locally folded regions that may coalesce in non-native ways to form stable interac

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26

Seyedhosseini, Ensieh. "Piezoelectricity and ferroelectricity in amino acid glycine." Doctoral thesis, Universidade de Aveiro, 2015. http://hdl.handle.net/10773/15169.

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Doutoramento em Nanociências e Nanotecnologia<br>Bioorganic ferroelectrics and piezoelectrics are becoming increasingly important in view of their intrinsic compatibility with biological environment and biofunctionality combined with strong piezoelectric effect and switchable polarization at room temperature. Here we study piezoelectricity and ferroelectricity in the smallest amino acid glycine, representing a broad class of non-centrosymmetric amino acids. Glycine is one of the basic and important elements in biology, as it serves as a building block for proteins. Three polymorphic forms wit

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27

Paschal, Bryce M. "Structure and Function of Cytoplasmic Dynein: a Thesis." eScholarship@UMMS, 1992. https://escholarship.umassmed.edu/gsbs_diss/82.

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In previous work I described the purification and properties of the microtubule-based mechanochemical ATPase cytoplasmic dynein. Cytoplasmic dynein was found to produce force along microtubules in the direction corresponding to retrograde axonal transport. Cytoplasmic dynein has been identified in a variety of eukaryotes including yeast and human, and there is a growing body of evidence suggesting that this "molecular motor" is responsible for the transport of membranous organelles and mitotic chromosomes. The first part of this thesis investigates the molecular basis of microtubule-activation

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28

Shi, Zhengtao. "Structure-function studies of adenylate kinase by site-specific incorporation of both natural and unnatural amino acids /." The Ohio State University, 1994. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487854314871531.

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29

Wróblewska, Liliana. "Refinement of reduced protein models with all-atom force fields." Atlanta, Ga. : Georgia Institute of Technology, 2007. http://hdl.handle.net/1853/26606.

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Thesis (Ph.D)--Biology, Georgia Institute of Technology, 2008.<br>Committee Chair: Skolnick, Jeffrey; Committee Member: Fernandez, Facundo; Committee Member: Jordan, King; Committee Member: McDonald, John; Committee Member: Sherrill, David. Part of the SMARTech Electronic Thesis and Dissertation Collection.

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30

Tyagi, Rajiv. "Crystal structure determination and site-directed mutagenesis of active site residues in Escherichia coli ketol-acid reductoisomerase /." [St. Lucia, Qld.], 2005. http://www.library.uq.edu.au/pdfserve.php?image=thesisabs/absthe18926.pdf.

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31

Yu, Hongbin Yu Hongbin. "Part I, Nitrosation of amidines : structure and reactivity ; Part 2, Aldehyde mediated nitrosation of amino acids ; Part 3, Thermal decomposition of N-nitrosocarboxylic acids /." free to MU campus, to others for purchase, 2002. http://wwwlib.umi.com/cr/mo/fullcit?p3052235.

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32

Silva, Aparecido Rodrigues da. "Desenvolvimento e avaliação de modelos representativos para construção de aminoácidos e de estruturas de proteínas." Universidade de São Paulo, 2010. http://www.teses.usp.br/teses/disponiveis/76/76132/tde-16022011-091415/.

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Foi desenvolvido um conjunto de peças plásticas que permitem a montagem e representação dos aminoácidos mais comuns, bem como a construção de estruturas protéicas. Durante e após o desenvolvimento o material foi submetido a várias etapas de avaliação por professores (do ensino básico e universitário), alunos de pós-graduação e de graduação. A primeira etapa foi o desenvolvimento dos modelos em ambiente computacional, seguida da prototipagem das peças. Após discussão com a comunidade científica (apresentados na XXXVI Reunião Anual da SBBq em 2007) as sugestões foram implementadas nos modelos co

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33

Flanagan, Joan Frances. "The Yeast SWI/SNF Complex Structure and Function: A Dissertation." eScholarship@UMMS, 2001. https://escholarship.umassmed.edu/gsbs_diss/187.

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DNA is packaged within the cells' nucleus as a highly compact chromatin structure ranging between 100-400 nm fibers. The organization and alteration of this structure is mandatory in order to arbitrate DNA-mediated processes of the cell, including transcription, DNA replication, recombination and repair. Many different kinds of enzymes modify chromatin components and, in turn, regulate the accessibility of DNA. These multi-subunited enzymes have emerged as key regulators for several processes of the cell. Central to understanding how DNA-mediated processes are regulated is to comprehend the co

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34

Schiffrin, Agustin. "Self-assembly of amino acids on noble metal surfaces : morphological, chemical and electronic control of matter at the nanoscale." Thesis, University of British Columbia, 2008. http://hdl.handle.net/2429/798.

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Designing novel nanostructures which exploit the self-assembly capabilities of biomolecules yields a promising approach to control matter at the nanoscale. Here, the homochiral molecular self-assemblies of the methionine and tyrosine amino acids on the monocrystalline Ag(111) and Cu(111) surfaces are characterized by means of scanning tunneling microscopy (STM) and spectroscopy (STS), helium atom scattering (HAS), x-ray photoelectron spectroscopy (XPS) and near-edge x-ray absorption fine structure (NEXAFS) in ultrahigh vacuum (UHV). On Ag(111), methionine self-assembles into supramolecular cha

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35

Fahel, Jean. "Intercalation de dicarboxylates et d’acides aminés dans des hydroxydes doubles lamellaires : relation composition-structure." Thesis, Université de Lorraine, 2016. http://www.theses.fr/2016LORR0139/document.

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L’intercalation de molécules organiques dans les Hydroxydes Doubles Lamellaires conduit à la formation d’hybrides organo-minéraux lamellaires aux propriétés originales. La valorisation de ces matériaux pour des applications diverses nécessite d’une part, le développement d’une méthode de synthèse simple et efficace pour garantir la pureté des hybrides, et d’autre part, d’établir les relations composition-structure (feuillet cationique, anion et eau interfoliaire). C’est pour atteindre ces deux objectifs, que nous avons menés les travaux présentés dans ce mémoire. La stratégie de synthèse adopt

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36

Tonelli, Giovanni. "Systèmes organisés à base de molécules hybrides lipide-nucléotides pour la délivrance des acides nucléiques." Thesis, Bordeaux 2, 2013. http://www.theses.fr/2013BOR22097/document.

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La thérapie génique est une forme de médecine moléculaire qui a des potentialités majeures dans le traitement d'un grand nombre de maladies héréditaires ou de cancers. Les acides nucléiques doivent pénétrer à l'intérieur des cellules et interagir avec la machinerie génétique présente. Une des plus grandes limitations dans l'application de ce type de traitement est le développement d'un vecteur sûr et efficace pour transporter ces molécules dans les cellules. Les vecteurs sont classifiés traditionnellement en deux grandes catégories : viral et non-viral. Les vecteurs de type viral sont les plus

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37

Clairmont, Kevin B. "The Structure, Function, and Regulation of Insulin-like Growth factor II/Mannose 6-phosphate Receptor Forms: a Thesis." eScholarship@UMMS, 1990. https://escholarship.umassmed.edu/gsbs_diss/44.

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In mammals a single receptor protein binds both insulin-like growth factor II (IGF-II) and mannose 6-phosphate (Man 6-P) containing ligands, most notably lysosomal enzymes. However, in chick embryo fibroblasts IGF-II binds predominantly to a type 1 IGF receptor, and no IGF-II/Man 6-P receptor has been identified in this species. In order to determine if chickens possess an IGF-II/Man 6-P receptor, an affinity resin (pentamannosyl 6-phosphate (PMP) Sepharose) was used to purify receptors from chicken membrane extracts by their ability to bind mannose 6-phosphate. Then 125I-IGF-II was used to ev

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38

Storbeck, Karl-Heinz. "A structure/function investigation into baboon cytochrome P450 side-chain cleavage (CYP11A1)." Thesis, Stellenbosch : University of Stellenbosch, 2005. http://hdl.handle.net/10019.1/3113.

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Thesis (MSc (Biochemistry))--University of Stellenbosch, 2005.<br>This study describes: 1. The cloning of baboon cytochrome P450 side-chain cleavage (CYP11A1) cDNA by in vitro site-directed mutagenesis. 2. The identification and sequencing of three baboon CYP11A1 mutants: CYP11A1a, CYP11A1b and CYP11A1c. 3. The expression and characterisation of baboon and human CYP11A1 cDNA, CYP11A1a, CYP11A1b and CYP11A1c in nonsteroidogenic COS-1 cells. The Km and V-values for the metabolism of 25-hydroxycholesterol were determined. 4. The construction of the first homology model of CYP11A1, using b

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39

Zottola, Ralph J. "Molecular Determinants of GLUT1: Structure and Function: A Dissertation." eScholarship@UMMS, 1994. https://escholarship.umassmed.edu/gsbs_diss/170.

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Hebert and Carruthers (1992) showed that the human erythrocyte glucose transporter is an allosteric complex of four GLUT1 proteins whose structure and substrate binding properties are stabilized by reductant-sensitive noncovalent subunit interactions. The GLUT1 tetramer dissociates into dimers upon exposure to reductant but subunits are not associated via disulfide bridges. Each subunit of SDS-denatured tetrameric GLUT1 exposes only two thiols while reduced denatured GLUT1 exposes all six sulfhydryl groups. They hypothesized that glucose transporter oligomeric structure and cooperative catalyt

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40

Montecino, Martin A. "Chromatin Structure of the Rat Osteocalcin Gene Promoter in Bone-Derived Cells." eScholarship@UMMS, 1995. https://escholarship.umassmed.edu/gsbs_diss/33.

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Transcription of the osteocalcin gene, which encodes a bone-specific 10 kDa protein, is controlled by the coordinated utilization of modularly organized basal and hormone-responsive enhancer elements. Activation of these sequences involves the interaction of specific transcription factors to these promoter elements. It is becoming increasingly accepted that nuclear architecture provides a basis for support of tightly regulated modulation of cell growth and tissue-specific transcription which is required for the onset and progression of differentiation. Thus packaging of DNA as chromatin can fa

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41

Blodgett, David M. "Human Erythrocyte Glucose Transporter (GLUT1) Structure, Function, and Regulation: A Dissertation." eScholarship@UMMS, 2007. https://escholarship.umassmed.edu/gsbs_diss/326.

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The structure-function relationship explains how the human erythrocyte glucose transport protein (GLUT1) catalyzes sugar transport across the plasma membrane. This work investigates the glucose transport mechanism, the structural arrangement and dynamics of GLUT1 membrane-spanning α-helices, the molecular basis for glucose transport regulation by ATP, and how cysteine accessibility contributes to GLUT1 structure. A rapid kinetics approach was applied to examine the conformational changes GLUT1 undergoes during the transport cycle. To transition from a global to molecular focus, a novel mass sp

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42

Bell, Stacey. "Site-directed spin-labelling of proteins for EPR spectroscopy : application to protein complexes and development of new methods for cysteine rich proteins." Thesis, University of St Andrews, 2016. http://hdl.handle.net/10023/8237.

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The work described in this thesis is an experimental study into the application of Electron Paramagnetic Resonance (EPR) Spectroscopy for the study of biological systems. Using a variety of methods of site-directed spin-labelling (SDSL), this thesis aims to explore long range structure in an assortment of recombinant and native proteins, and complexes thereof. The work described in this thesis covers all aspects of the work, from experimental design, molecular biology and cloning, protein expression and purification, as well as functional characterisation, and finally EPR distance measurements

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43

Freudenberg, Jan Verfasser], Wolfgang H. [Gutachter] [Binder, and Helmut [Gutachter] Schlaad. "Multisegmented hybrid-polymers based on oligo-amino acids : synthesis and secondary structure in solution and the solid state / Jan Freudenberg ; Gutachter: Wolfgang H. Binder, Helmut Schlaad." Halle (Saale) : Universitäts- und Landesbibliothek Sachsen-Anhalt, 2020. http://d-nb.info/1224233263/34.

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44

Wróblewska, Liliana. "Refinement of reduced protein models with all-atom force fields." Diss., Georgia Institute of Technology, 2007. http://hdl.handle.net/1853/26606.

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The goal of the following thesis research was to develop a systematic approach for the refinement of low-resolution protein models, as a part of the protein structure prediction procedure. Significant progress has been made in the field of protein structure prediction and the contemporary methods are able to assemble correct topology for a large fraction of protein domains. But such approximate models are often not detailed enough for some important applications, including studies of reaction mechanisms, functional annotation, drug design or virtual ligand screening. The development of a metho

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45

Zhao, Zhong. "Part I. Structure-function studies of adenylate kinase with unnatural amino acids. Part II. Structure-function studies of phosphatidylinositol-specific phospholipase C: Kinetic analysis and the roles of His-32 and Asp-274 /." The Ohio State University, 1996. http://rave.ohiolink.edu/etdc/view?acc_num=osu148794273980584.

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46

Chotikasemsri, Pongsathorn. "Computational Prediction of the Agregated Structure of Denatured Lysozyme." TopSCHOLAR®, 2009. http://digitalcommons.wku.edu/theses/120.

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Mis-folded proteins and their associated aggregates are a contributing factor in some human diseases. In this study we used the protein lysozyme as a model to define aggregation structures under denaturing conditions. Sasahara et al. (2007), Frare et al. (2009, 2006), and Rubin et al. (2008) observed conditions where heat denatured lysozyme formed fibril structures that were observed to be 8-17 nanometers in diameter under the electron microscope. Even though the crystal structure of lysozyme is known, the denatured form of this protein is still unknown. Therefore, we used Rosetta++ protein fo

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47

Ahmed, Mostafa H. "Hydropathic Interactions and Protein Structure: Utilizing the HINT Force Field in Structure Prediction and Protein‐Protein Docking." VCU Scholars Compass, 2014. http://scholarscompass.vcu.edu/etd/3581.

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Protein structure predication is a field of computational molecular modeling with an enormous potential for improvement. Side-chain geometry prediction is a critical component of this process that is crucial for computational protein structure predication as well as crystallographers in refining experimentally determined protein crystal structures. The cornerstone of side-chain geometry prediction are side-chain rotamer libraries, usually obtained through exhaustive statistical analysis of existing protein structures. Little is known, however, about the driving forces leading to the preference

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Odgren, Paul R. "Molecular Characterization of Mitofilin, a Novel, Mitochondrial, Coiled Coil Protein, and the Relationship Between Organism Complexity and Coiled Coil Protein-Mediated Structure: A Dissertation." eScholarship@UMMS, 1995. https://escholarship.umassmed.edu/gsbs_diss/28.

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In the course of experiments designed to identify and characterize structural proteins of the nuclear matrix, one antibody was generated which recognized an extraction-resistant cytoplasmic protein. This antibody was used as the starting point in the cloning and molecular characterization of a novel protein of the inter-membrane space of the mitochondrion which has been named mitofilin. Mitofilin is expressed in all human cell types, and murine homologues also exist. Mitofilin associates only with mitochondria and not with other membrane-bounded organelles such as Golgi or endoplasmic reticulu

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Robichaud, Trista K. "GLUT1 Structure Function; Context, Ligand Cooperativity, and Mutagenesis Studies: A Dissertation." eScholarship@UMMS, 2008. https://escholarship.umassmed.edu/gsbs_diss/393.

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Carrier mediated nutrient import is vital for cell and tissue homeostasis. Structural insights of carrier mediated transport, particularly the human glucose transporter GLUT1, are essential for understanding the mechanisms of human metabolic disease, and provide model systems for cellular processes as a whole. GLUT1 function and expression is characterized by a complexity unexplained by the current hypotheses for carrier-mediated sugar transport (9). It is possible that the operational properties of GLUT1 are determined by host cell environment. A glucose transport-null strain of Saccharomyces

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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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