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Dissertations / Theses on the topic 'Substrate binding amino acid'

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Published: 4 June 2021

Last updated: 1 February 2022

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1

Ghaddar, Kassem. "Structural analysis of yeast amino acid transporters: substrate binding and substrate-induced endocytosis." Doctoral thesis, Universite Libre de Bruxelles, 2014. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/209318.

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Plasma membrane transport proteins play a crucial role in all cells by conferring to the cell surface a selective permeability to a wide range of ions and small molecules. The activity of these transporters is often regulated by controlling their amount at the plasma membrane, via intracellular trafficking. The recent boom in the numbers of crystallized transporters shows that many of them that belong to different functional families with little sequence similarity adopt the same structural fold implying a conserved transport mechanism. These proteins belong to the APC (Amino acid-Polyamine-or

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2

Isogawa, Danya. "Studies on the active site of chitosanase from Paenibacillus fukuinensis and its functional modification for utilizing chitosan." Kyoto University, 2014. http://hdl.handle.net/2433/188769.

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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18331号<br>農博第2056号<br>新制||農||1022(附属図書館)<br>学位論文||H26||N4838(農学部図書室)<br>31189<br>京都大学大学院農学研究科応用生命科学専攻<br>(主査)教授植田充美, 教授三上文三, 教授小川順<br>学位規則第4条第1項該当

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3

Weiser, Armin. "Amino acid substitutions in protein binding." Doctoral thesis, Humboldt-Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät I, 2009. http://dx.doi.org/10.18452/15962.

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Die Modifizierung von Proteinsequenzen unter anderem durch den Austausch von Aminosäuren ist ein zentraler Aspekt in evolutionären Prozessen. Solche Prozesse ereignen sich nicht nur innerhalb großer Zeiträume und resultieren in der Vielfalt des Lebens, das uns umgibt, sondern sind auch täglich beobachtbar. Diese mikroevolutionären Prozesse bilden eine Grundlage zur Immunabwehr höherer Wirbeltiere und werden durch das humorale Immunsystem organisiert. Im Zuge einer Immunantwort werden Antikörper wiederholt der Diversifizierung durch somatische Hypermutation unterworfen. Ziele dieser Arbeit ware

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4

Hurley, Eldon Kenneth Jr. "Photolyase: Its Damaged DNA Substrate and Amino Acid Radical Formation During Photorepair." Thesis, Virginia Tech, 2005. http://hdl.handle.net/10919/31084.

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Ultraviolet light damages genomic material by inducing the formation of covalent bonds between adjacent pyrimidines. Cis-syn cyclobutane pyrimidine dimers (CPD)constitute the most abundant primary lesion in DNA. Photolyase, a light-activated enzyme, catalytically repairs these lesions. Although many steps in the photolyase-mediated repair process have been mapped, details of the mechanism remain cryptic. Difference FT-IR spectroscopy was employed to obtain new mechanistic information about photorepair. Purified oligonucleotides, containing a central diuracil, dithymidine, or cyclobutane thymid

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5

Li, Hong. "Azotobacter vinelandii Nitrogenase: Multiple Substrate-Reduction Sites and Effects of pH on Substrate Reduction and CO Inhibition." Diss., Virginia Tech, 2002. http://hdl.handle.net/10919/27608.

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Mo-nitrogenase consists of two component proteins, the Fe protein and the MoFe protein. The site of substrate binding and reduction within the Mo-nitrogenase is provided by a metallocluster, the FeMo cofactor, located in the a-subunit of the MoFe protein. The FeMo cofactorâ s polypeptide environment appears to be intimately involved in the delicate control of the MoFe proteinâ s interactions with its substrates and inhibitors (Fisher K et al., 2000c). In this work, the a-subunit 278-serine residue of the MoFe protein was targeted because (i) a serine residue at this position is conserved bot

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6

Mueller, Martin J. "Leukotriene A₄ hydrolase : identification of amino acid residues involved in catalyses and substrate-mediated inactivation /." Stockholm, 2001. http://diss.kib.ki.se/2001/91-628-4934-4/.

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7

Tolliver, Benjamin M., Devaiah P. Shivakumar, and Cecelia A. McIntosh. "Effects of Amino Acid Insertion on the Substrate and Regiospecificity of a Citrus paradisi Glucosyltransferase." Digital Commons @ East Tennessee State University, 2014. https://dc.etsu.edu/etsu-works/345.

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Glucosyltransferases, or GTs, are enzymes which perform glucosylation reactions. These glucosylation reactions involve attaching a UDP-activated glucose molecule to acceptor molecules specific to the enzyme. The products of these reactions are observed to have a myriad of effects on metabolic processes, including stabilization of structures, solubility modification, and regulation of compound bioavailability. The enzyme which our lab focuses its research on is a flavonol-specific 3-O-GT found in Citrus paradisi, or grapefruit. This enzyme is part of the class of enzymes known as flavonoid GTs,

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8

Tolliver, Benjamin M., Devaiah P. Shivakumar, and Cecelia A. McIntosh. "Effects of Amino Acid Sequence Insertion on the Substrate Preference of a Citrus Paradisi Glucosyltransferase." Digital Commons @ East Tennessee State University, 2013. https://dc.etsu.edu/etsu-works/347.

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Glucosyltransferases (GTs) are enzymes which perform glucosylation reactions, which involve attaching a UDP-activated glucose molecule to acceptor molecules specifi c to the enzyme. The enzyme which our lab focuses its research on is a fl avonol-specifi c 3-OGT found in Citrus paradisi, or grapefruit (Cp3GT). This enzyme is part of the class of enzymes known as fl avonoid GTs, which are responsible for, among other things, the formation of compounds which can affect the taste of citrus. Our lab focuses its research on performing site-directed mutagenesis on Cp3GT in an attempt to discover the

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9

Black, Donald Lee. "Modulation of the calcium binding properties of calmodulin via amino acid replacement and target interaction /." The Ohio State University, 2001. http://rave.ohiolink.edu/etdc/view?acc_num=osu1486397841221454.

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10

Pook, P. C. K. "Ligand binding and electrophysiological studies of excitatory amino acid receptors in the rat central nervous system." Thesis, University of Bristol, 1988. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.381675.

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11

Belk, Jonathan Philip. "A Characterization of Substrates and Factors Involved in Yeast Nonsense-Mediated mRNA Decay: A Dissertation." eScholarship@UMMS, 2002. https://escholarship.umassmed.edu/gsbs_diss/65.

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Many intricate and highly conserved mechanisms have evolved to safeguard organisms against errors in gene expression. The nonsense-mediated mRNA decay pathway (NMD) exemplifies one such mechanism, specifically by eliminating mRNAs containing premature translation termination codons within their protein coding regions, thereby limiting the synthesis of potentially deleterious truncated polypeptides. Studies in Saccharomyces Cerevisiae have found that the activity of at least three trans-acting factors, known as UPF1, UPF2/NMD2, and UPF3is necessary for the proper function of the NMD pathway. Fu

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12

Garza, John Anthony. "Structural and ligand-binding properties of a dual substrate specific enzymes from schizosaccharomyces pombe a dissertation /." San Antonio : UTHSC, 2009. http://learningobjects.library.uthscsa.edu/cdm4/item_viewer.php?CISOROOT=/theses&CISOPTR=45&CISOBOX=1&REC=17.

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13

Barcelona, Stephanie Suazo. "Investigation of the Mechanism of Substrate Transport by the Glutamate Transporter EAAC1." Scholarly Repository, 2007. http://scholarlyrepository.miami.edu/oa_theses/91.

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The activity of glutamate transporters is essential for the temporal and spatial regulation of the neurotransmitter concentration in the synaptic cleft which is critical for proper neuronal signaling. Because of their role in controlling extracellular glutamate concentrations, dysfunctional glutamate transporters have been implicated in several neurodegenerative diseases and psychiatric disorders. Therefore, investigating the mechanism of substrate transport by these transporters is essential in understanding their behavior when they malfunction. A bacterial glutamate transporter hom

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14

Henderson, Jeremy. "Investigation of Saccharomyces cerevisiae Trm10 tRNA methyltransferase (m1G9) activity substrate specificity and essential amino acid residues for catalysis /." Connect to resource, 2009. http://hdl.handle.net/1811/37269.

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15

Sathanantham, Preethi, Shiva K. Devaiah, and Cecelia A. McIntosh. "Structure-Function Analysis of Grapefruit Glucosyltransferase Protein – Identification of Key Amino Acid Residues for its Rigid Substrate Specificity." Digital Commons @ East Tennessee State University, 2015. https://dc.etsu.edu/etsu-works/352.

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Flavonoids are an important class of secondary metabolites widely distributed in plants. The majority of naturally occurring flavonoids are found in glucosylated form. Glucosyltransferases are enzymes that enable transfer of glucose from an activated donor (UDP-glucose) to the acceptor flavonoid substrates. A flavonol specific glucosyltransferase cloned from Citrus paradisi (Cp3OGT) has strict substrate and regiospecificity. In this study, amino acid residues that could potentially alter the rigidity observed in this enzyme were mutated to position equivalent residues of a putative anthocyanin

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16

Shafqat, Naeem. "Substrate specificities and functional properties of human short-chain dehydrogenases/reductases /." Stockholm, 2004. http://diss.kib.ki.se/2004/91-7349-829-7.

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17

Nygren, Patrik. "De Novo Design and Characterization of Surface Binding Peptides - Steps toward Functional Surfaces." Licentiate thesis, Linköping University, Linköping University, Sensor Science and Molecular Physics, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-8992.

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<p>The ability to create surfaces with well-defined chemical properties is a major research field. One possibility to do this is to design peptides that bind with a specific secondary structure to silica nanoparticles. The peptides discussed in this thesis are constructed to be random coil in solution, but are “forced” to become helical when adsorbed to the particles. The positively charged side-chains on the peptides strongly disfavor an ordered structure in solution due to electrostatic repulsion. When the peptides are introduced to the particles these charges will strongly favor the structu

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18

Chelliah, Vijayalakshmi. "Functional restraints on amino acid substitution patterns : application to definition of binding sites and sequence-structure homology recognition." Thesis, University of Cambridge, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.615170.

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19

Niemand, Jandeli. "A phage display study of interacting peptide binding partners of malarial S-Adenosylmethionine decarboxylase/Ornithine decarboxylase." Diss., University of Pretoria, 2007. http://hdl.handle.net/2263/24105.

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Due to the increasing resistance against the currently used antimalarial drugs, novel chemotherapeutic agents that target new metabolic pathways for the treatment of malarial infections are urgently needed. One approach to the drug discovery process is to use interaction analysis to find proteins that are involved in a specific metabolic pathway that has been identified as a drug target. Protein-protein interactions in such a pathway can be preferential targets since a) there is often greater structural variability in protein-protein interfaces, which can lead to more effective differentiation

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20

Tran, David. "Investigating the substrate specificity of 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAH7P) synthase." Thesis, University of Canterbury. Chemistry, 2011. http://hdl.handle.net/10092/6565.

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The shikimate pathway is a biosynthetic pathway that is responsible for producing a variety of organic compounds that are necessary for life in plants and microorganisms. The pathway consists of seven enzyme catalysed reactions beginning with the condensation reaction between D-erythrose 4-phosphate (E4P) and phosphoenolpyruvate (PEP) to give the seven-carbon sugar DAH7P. This thesis describes the design, synthesis and evaluation of a range of alternative non-natural four-carbon analogues of E4P (2- and 3-deoxyE4P, 3-methylE4P, phosphonate analogues of E4P) to probe the substrate specificity o

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21

St-Jacques, Antony D. "Engineering of Multi-Substrate Enzyme Specificity and Conformational Equilibrium Using Multistate Computational Protein Design." Thesis, Université d'Ottawa / University of Ottawa, 2018. http://hdl.handle.net/10393/38590.

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The creation of enzymes displaying desired substrate specificity is an important objective of enzyme engineering. To help achieve this goal, computational protein design (CPD) can be used to identify sequences that can fulfill interactions required to productively bind a desired substrate. Standard CPD protocols find optimal sequences in the context of a single state, for example an enzyme structure with a single substrate bound at its active site. However, many enzymes catalyze reactions requiring them to bind multiple substrates during successive steps of the catalytic cycle. The design of m

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22

Cherry, Melissa A. "Sequence dependence of the activity of amphipathic peptides." View electronic thesis, 2008. http://dl.uncw.edu/etd/2008-2/rp/cherrym/melissacherry.pdf.

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23

Trott, Amy Elizabeth. "Amino Acid Residues in LuxR Critical for its Mechanism of Transcriptional Activation during Quorum Sensing." Thesis, Virginia Tech, 2000. http://hdl.handle.net/10919/34070.

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<I>Vibrio fischeri</I>, a symbiotic bioluminescent bacterium, serves as one of the best understood model systems for a mechanism of cell-density dependent bacterial gene regulation known as quorum sensing. During quorum sensing in <I>V. fischeri</I>, an acylated homoserine chemical signal (autoinducer) is synthesized by the bacteria and used to sense their own species in a given environment. As the autoinducer levels rise, complexes form between the autoinducer and the N-terminal domain of a regulatory protein, LuxR. In response to autoinducer binding, LuxR is believed to undergo a conformatio

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24

Adepoju, Olusegun A., Devaiah K. Shiva, and Cecelia A. McIntosh. "Using Site-Directed Mutagenesis to Determine Impact of Amino Acid Substitution on Substrate and Regiospecificity of Grapefruit Flavonol 3-O-Glucosyltransferase." Digital Commons @ East Tennessee State University, 2014. https://dc.etsu.edu/etsu-works/346.

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Flavonoids are secondary metabolites that are important in plant defense, protection and human health. Most naturally-occurring flavonoids are found in glucosylated form. Glucosyltransferases (GTs) are enzymes that catalyze the transfer of glucose from a high energy sugar donor to an acceptor molecule. A flavonol-specific 3-O-GT enzyme has been identified and cloned from leaf tissues of grapefruit. The enzyme shows rigid substrate specificity and regiospecificity. F3-O-GTs from grape (Vitis vinifera) and grapefruit (Citrus paradisi) were modeled against F7-O-GTs from Crocus sativus and Scrutel

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25

Williams, Kyle Brandon. "The DamX cell division protein of Escherichia coli: identification of amino acid residues critical for septal localization and peptidoglycan binding." Diss., University of Iowa, 2010. https://ir.uiowa.edu/etd/625.

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In the bacterium Escherichia coli, cell division involves the concerted inward growth of all three layers of the cell envelope: the cytoplasmic membrane, the peptidoglycan (PG) cell wall, and the outer membrane. This is a complex, highly regulated process that involves over 20 proteins. Four of these proteins contain a domain of ~70 amino acids known as a SPOR domain (Pfam no. 05036). One of these SPOR domains (from a protein named FtsN) has been shown previously to bind PG. In this thesis we show that six additional SPOR domains, three from E. coli and three from other bacterial species, also

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Emami, Fatemesadat. "Thermodynamically Consistent Interatomic Potentials for Silica to Design Specifically Binding Peptides: Role of Surface Chemistry, PH, and Amino Acid Sequence." University of Akron / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=akron1366597654.

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27

Kobayashi, Takuya. "Amino acid residues conferring ligand binding properties of prostaglandin I and prostaglandin D receptorsに関する研究". Kyoto University, 2000. http://hdl.handle.net/2433/151431.

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28

Zhang, Deqiang Roberts Richard W. Goddard William A. "Structure-based design of mutant proteins : I. Molecular docking studies of amino acid binding to wild-type aminoacyl-tRNA synthetases. II. Structure-based design of mutant aminoacyl-tRNA synthetases for non-natural amino acid incorporation /." Diss., Pasadena, Calif. : California Institute of Technology, 2003. http://resolver.caltech.edu/CaltechETD:etd-12182002-190040.

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29

Papp, Laura V., and n/a. "Multiple Levels of Regulation of Human SECIS Binding Protein 2, SBP2." Griffith University. School of Biomolecular and Biomedical Science, 2006. http://www4.gu.edu.au:8080/adt-root/public/adt-QGU20070208.145623.

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Selenium is an essential trace mineral of fundamental importance to human health. Its beneficial functions are largely attributed to its presence within a group of proteins named selenoproteins in the form of the amino acid selenocysteine (Sec). Recently, it was revealed that the human selenoproteome consists of 25 selenoproteins, and for many of them their function remains unknown. The most prominent known roles of selenoproteins are to maintain the intracellular redox homeostasis, redox regulation of intracellular signalling and thyroid hormone metabolism. Sec incorporation into selenoprotei

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30

Adepoju, Olusegun Adeboye. "Using Site-Directed Mutagenesis to Determine Impact of Amino Acid Substitution on Substrate and Regiospecificity of Grapefruit Flavonol Specific 3-O-Glucosyltransferase." Digital Commons @ East Tennessee State University, 2014. https://dc.etsu.edu/etd/2404.

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Flavonoids are secondary metabolites that are important in plant defense, protection, and human health. Most naturally-occurring flavonoids are found in glucosylated forms. Glucosyltransferases catalyze the transfer of glucose from high-energy sugar donors to an acceptor molecule. The grapefruit flavonol-specific 3-O-glucosyltransferase (F3-O-GT) is highly substrate and regio-specific. The goal of this research is to unravel the amino acid residues responsible for the grapefruit enzyme’s rigid specificity, while attempting to alter the regiospecific glucosylation pattern through site-directed

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31

Smith, Robert Peter. "Exploration of the active site of Staphylococcus aureus neuraminic acid lyase using non-canonical amino acids and their effects on substrate specificity." Thesis, University of Leeds, 2017. http://etheses.whiterose.ac.uk/20719/.

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The cost of chemical synthesis of pharmaceuticals contributes significantly to their final price and part of this cost is incurred due to use of extreme temperatures and pressures required by some traditional catalysts. The interest in catalysis using enzymes, or biocatalysis, from industry has been growing recently, due to enzymes’ ability to work at room temperature and pressure, and the reduction in toxic solvent waste produced from an enzyme reaction compared to a traditionally catalysed reaction. The specificity of enzymes, while useful in product formation, can make applying them to synt

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32

Gilbert, Michele. "Design of synthetic peptides that display cell binding and signaling sequences on calcium phosphate surfaces /." Thesis, Connect to this title online; UW restricted, 2001. http://hdl.handle.net/1773/8063.

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

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34

Bennett, Allison E. "Characterization of sortase and its effect on the virulence of Streptococcus pneumoniae." Thesis, Birmingham, Ala. : University of Alabama at Birmingham, 2008. https://www.mhsl.uab.edu/dt/2008d/bennet.pdf.

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35

Vichitphan, Kanit. "Azotobacter vinelandii Nitrogenase: Effect of Amino-Acid Substitutions at the Alpha Gln-191 Residue of the MoFe Protein on Substrate Reduction and CO Inhibition." Diss., Virginia Tech, 2001. http://hdl.handle.net/10919/11266.

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The FeMo cofactor is one of two types of prosthetic group found in the larger of the two nitrogenase component proteins, called the MoFe protein, and it is strongly implicated as the substrate binding and reduction site. The glutamine-191 residue in the Alpha-subunit of the MoFe protein of A. vinelandii nitrogenase was targeted for substitution because its side chain is involved in a hydrogen-bond network from one of the terminal carboxylates of the homocitrate component of FeMo cofactor through to the backbone NH of Alpha Gly-61, which is adjacent to Alpha Cys-62, which ligates to the P clus

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36

Pedersen, Sindre Andre. "Metal binding proteins and antifreeze proteins in the beetle Tenebrio molitor : a study on possible competition for the semi-essential amino acid cysteine." Doctoral thesis, Norwegian University of Science and Technology, Department of Biology, 2007. http://urn.kb.se/resolve?urn=urn:nbn:no:ntnu:diva-1504.

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<p>In their natural environment animals are confronted by both physical (eg. extreme temperatures, desiccation) and chemical stressors (e.g. pollutants). Stress may be defined as a condition that is evoked in an organism by one or more environmental factors that bring the organism near to or over the edges of its ecological niche (van Straalen 2003). Various defence systems exist to cope with different forms of stress and restore homeostasis. Often, production of various proteins or enzymes are involved in these defence systems (Korsloot et al. 2004). Since an organism’s resources may be consi

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Keyari, Charles Mambo. "Glycosylating Enkephalins: Design, Glycosylation Using Sugar Acetates in the Preparation of Glycosyl Amino Acids for Glycopeptide Syntheses, Binding at the Opioid Receptors and Analgesic Effects." Diss., The University of Arizona, 2007. http://hdl.handle.net/10150/193652.

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Improved procedures for the glycosylation of serine and threonine utilizing Schiff base activation are reported. The procedures are less expensive and more efficient alternatives to previously published methods. The Schiff bases exhibited ring-chain tautomerism in CDCl₃ as shown by ¹H NMR. Acting as glycosyl acceptors, the Schiff bases reacted at RT with simple sugar peracetate donors with BF₃•OEt₂ promotion to provide the corresponding protected amino acid glycosides in good yields. With microwave irradiation, the reactions were complete in 2-5 minutes. Glycosylation with the dipeptide Schiff

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Wang, Haihong. "Amino acid residues constituting the agonist binding site of the human P2X3 receptor and subunit stoichiometry of heteromeric P2X2/3 and P2X2/6 receptors." Doctoral thesis, Universitätsbibliothek Leipzig, 2013. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-112913.

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Homotrimeric P2X3 and heteromeric P2X2/3 receptors are present in sensory ganglia and participate in pain perception. In order to develop pharmacological antagonists for these receptors, it is important to clarify which amino acid (AA) residues constitute the agonist binding pouch as well as to learn the stoichiometry of the receptor subunits forming a heteromeric receptor. We expressed the homomeric human (h)P2X3 receptor or its mutants in HEK293 cells and measured the ATP-induced responses by the whole-cell patch-clamp method. For the binding-site mutants, all conserved and some non-conserve

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Ruhlman, Tracey. "Determinants of Chloroplast Gene Expression and Applications of Chloroplast Transformation in Lactuca Sativa and Nicotiana Tabacum." Doctoral diss., University of Central Florida, 2009. http://digital.library.ucf.edu/cdm/ref/collection/ETD/id/2854.

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Genetic modification of plastids in the model plant tobacco (Nicotiana tabacum) has demonstrated that numerous foreign gene products can accumulate to high levels in this setting. Plastid biotechnology is maturing to encompass the improvement of food and feed species and the production of biopharmaceutical proteins for oral delivery necessitating development of stable transplastomic edible plants. In the interest of establishing an edible platform we have investigated the use of native and foreign regulatory elements in relation to foreign gene expression in plastids. Multiple sequence alignme

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Li, Min. "Bayesian discovery of regulatory motifs using reversible jump Markov chain Monte Carlo /." Thesis, Connect to this title online; UW restricted, 2006. http://hdl.handle.net/1773/9529.

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Jiang, Ruisheng. "STUDIES OF THE PYRROLYSYL-TRNA SYNTHETASE." The Ohio State University, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=osu1365512882.

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Saliba, Elie. "A NOVEL TORC1 ACTIVATION PATHWAY STIMULATED BY THE PLASMA MEMBRANE H+-ATPASE UNRAVELED FROM THE STUDY OF SUBSTRATE-INDUCED ENDOCYTOSIS OF AMINO ACID TRANSPORTERS IN YEAST SACCHAROMYCES CEREVISIAE." Doctoral thesis, Universite Libre de Bruxelles, 2017. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/262158.

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Chez les eucaryotes, le complexe kinase TORC1 (Target Of Rapamycin Complex 1) joue un rôle central dans le contrôle de la croissance cellulaire. Il intègre de nombreux signaux et agit en modulant l’état de phosphorylation de différents effecteurs, principalement des protéines impliquées dans des processus anaboliques ou cataboliques. Parmi ces signaux, on distingue notamment les acides aminés. Ces derniers agissent sur TORC1 via l’action de protéines de la famille des GTPases Rag, elles-mêmes régulées par des facteurs GEF et GAP. Des études récentes sur des cellules mammifères ont mis en évide

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Clingman, Carina C. "A Feedback Loop Couples Musashi-1 Activity to Omega-9 Fatty Acid Biosynthesis: A Dissertation." eScholarship@UMMS, 2014. http://escholarship.umassmed.edu/gsbs_diss/718.

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All living creatures change their gene expression program in response to nutrient availability and metabolic demands. Nutrients and metabolites can directly control transcription and activate second-‐messenger systems. In bacteria, metabolites also affect post-‐transcriptional regulatory mechanisms, but there are only a few isolated examples of this regulation in eukaryotes. Here, I present evidence that RNA-‐binding by the stem cell translation regulator Musashi-‐1 (MSI1) is allosterically inhibited by 18-‐22 carbon ω-‐9 monounsaturated fatty acids. The fatty acid binds to the N-‐termi

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Keränen, Henrik. "Advances in Ligand Binding Predictions using Molecular Dynamics Simulations." Doctoral thesis, Uppsala universitet, Beräknings- och systembiologi, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-230777.

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Biochemical processes all involve associations and dissociations of chemical entities. Understanding these is of substantial importance for many modern pharmaceutical applications. In this thesis, longstanding problems with regard to ligand binding are treated with computational methods, applied to proteins of key pharmaceutical importance. Homology modeling, docking, molecular dynamics simulations and free-energy calculations are used here for quantitative characterization of ligand binding to proteins. By combining computational tools, valuable contributions have been made for pharmaceutical

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Kirov, Miroslav [Verfasser], Lutz [Akademischer Betreuer] Schmitt, and Ulrich [Akademischer Betreuer] Schulte. "The incorporation of an unnatural amino acid to study the nucleotide binding domain of the ABC transporter HlyB from Escherichia coli / Miroslav Kirov. Gutachter: Ulrich Schulte. Betreuer: Lutz Schmitt." Düsseldorf : Universitäts- und Landesbibliothek der Heinrich-Heine-Universität Düsseldorf, 2014. http://d-nb.info/1051076803/34.

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Huang, Charlie Chia Wei. "Regulation of Cat-1 gene transcription during physiological and pathological conditions." Case Western Reserve University School of Graduate Studies / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=case1270242874.

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Wang, Haihong [Verfasser], Peter [Akademischer Betreuer] Illes, Wolfgang [Gutachter] Nörenberg, and Andreas [Gutachter] Reichenbach. "Amino acid residues constituting the agonist binding site of the human P2X3 receptor and subunit stoichiometry of heteromeric P2X2/3 and P2X2/6 receptors / Haihong Wang ; Gutachter: Wolfgang Nörenberg, Andreas Reichenbach ; Betreuer: Peter Illes." Leipzig : Universitätsbibliothek Leipzig, 2013. http://d-nb.info/1238366546/34.

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Zhang, Wei. "Directed Evolution of Glutathione Transferases with Altered Substrate Selectivity Profiles : A Laboratory Evolution Study Shedding Light on the Multidimensional Nature of Epistasis." Doctoral thesis, Uppsala universitet, Biokemi, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-158400.

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Abstract:

Directed evolution is generally regarded as a useful approach in protein engineering. By subjecting members of a mutant library to the power of Darwinian evolution, desired protein properties are obtained. Numerous reports have appeared in the literature showing the success of tailoring proteins for various applications by this method. Is it a one-way track that protein practitioners can only learn from nature to enable more efficient protein engineering? A structure-and-mechanism-based approach, supplemented with the use of reduced amino acid alphabets, was proposed as a general means for sem

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Oswal, Dhawal P. "Peroxisome proliferator-activated receptor alpha: Insight into the structure, function and energy homeostasis." Wright State University / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=wright1401279322.

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Nordesjö, Olle. "Searching for novel protein-protein specificities using a combined approach of sequence co-evolution and local structural equilibration." Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-275040.

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Abstract:

Greater understanding of how we can use protein simulations and statistical characteristics of biomolecular interfaces as proxies for biological function will make manifest major advances in protein engineering. Here we show how to use calculated change in binding affinity and coevolutionary scores to predict the functional effect of mutations in the interface between a Histidine Kinase and a Response Regulator. These proteins participate in the Two-Component Regulatory system, a system for intracellular signalling found in bacteria. We find that both scores work as proxies for functional muta

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