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Dissertations / Theses on the topic 'Allosteric binding'

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Published: 3 June 2025

Last updated: 31 July 2025

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1

Nandigrami, Prithviraj. "Cooperative allosteric ligand binding in calmodulin." Kent State University / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=kent1507302866723977.

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2

Devenish, Steven Oliver. "Identifying Allosteric Binding Sites of GABAA Receptors." Thesis, The University of Sydney, 2015. http://hdl.handle.net/2123/13627.

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Previously, we have shown that (2S,3R)-3-acetoxy-4’-methoxyflavan (Fa-131) is a subtype selective modulator of GABAA-receptors, exerting non-sedative anxiolytic effects in mice. In order to elucidate the flavanol binding site, photoaffinity labelling (PAL) experiments were undertaken in our laboratory. Three analogues of Fa-131 were prepared, bearing the photoreactive benzophenone moiety at distant points, with an alkyne tag for Cu(I)-catalysed-azide-alkyne-cycloaddition (CuAAC) mediated affinity purification. To utilise the tag, the highly functionalised Bio-SS-N3 was designed and synthesise

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3

Ivanisevic, Ljubica. "Neutrophin receptors: ligand-binding, activation sites and allosteric regulation." Thesis, McGill University, 2008. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=18758.

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The Trk family of tyrosine kinase receptors and the common p75NTR receptor are neurotrophin receptors. Nerve growth factor (NGF) binds TrkA, brain-derived neurotrophic factor (BDNF) binds TrkB, and neurotrophin-3 (NT-3) binds TrkC. The extracellular domain of the Trk receptor has five subdomains: a leucine-rich motif (D2), two cysteine-rich motifs (D1, D3) and immunoglobulin-like subdomains Ig-C1 (D4) and Ig-C2(D5). The Trk D4 subdomain regulates ligand-independent activation. The TrkA-D5 and TrkB-D5 subdomains regulate cognate ligand binding and Trk activation. However, the p75NTR receptor bi

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4

Rizzuto, Felix. "Allosteric interactions in coordination cages." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/278963.

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Biomolecular receptors can catalyse reactions, alter their geometry, and inhibit their activity in response to molecules binding around their periphery. Synthetic receptors that can mimic this allosteric binding behaviour extend the potential applications of host-guest chemistry to programmable molecular systems. Modulating the degree and magnitude of interaction between components within these systems enables the design of chemical behaviour akin to biological complexity. With a view to developing artificial guest-binding regulation systems, a series of metal-organic cages capable of both the

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5

Penny, R. A. "The applicability of allosteric models to oxygen binding by haemoglobin." Thesis, Oxford Brookes University, 1985. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.356455.

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6

Martinez, Jessica. "Monitoring Allosteric Effector Binding and Homotropic Cooperativity of Aspartate Transcarbamoylase." Thesis, Boston College, 2008. http://hdl.handle.net/2345/1359.

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Thesis advisor: Evan Kantrowitz<br>Aspartate transcarbamoylase (ATCase) catalyzes the reaction between carbamoyl phosphate (CP) and aspartate to form N-carbamoyl-L-aspartate (CA) and inorganic phosphate (Pi). In Escherichia coli, it catalyzes the committed step of pyrimidine nucleotide biosynthesis. It is heterotropically activated by ATP, and is inhibited by CTP and UTP. X-ray studies have revealed valuable information regarding the catalytic mechanism, as well as insights into the homotropic and heterotropic interactions. However, localized changes and changes under biological conditions are

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7

Al-Shar'i, Nizar Ali. "A computational method for identifying allosteric binding sites in kinases." Thesis, University of Strathclyde, 2013. http://oleg.lib.strath.ac.uk:80/R/?func=dbin-jump-full&object_id=18570.

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There are 518 protein kinases encoded within the human genome [1] that control cellular signal transduction and play a major role in almost all cellular events. Aberrant kinase activity is linked to pathological conditions including cancer, inflammation, diabetes and many others, making them a tractable target for drug discovery research [2-5]. To date, most of the current medicinal chemistry efforts target the ATP binding site, which is highly conserved amongst the kinase family, and many compounds suffer from cross-activity leading to undesirable side effects and toxicity. The ability to tar

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8

Dutta, Priyanka. "Computational Modeling of Allosteric Stimulation of Nipah Virus Host Binding Protein." Scholar Commons, 2016. http://scholarcommons.usf.edu/etd/6227.

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Nipah belongs to the family of paramyxoviruses that cause numerous fatal diseases in humans and farm animals. There are no FDA approved drugs for Nipah or any of the paramyxoviruses. Designing antiviral therapies that are more resistant to viral mutations require understanding of molecular details underlying infection. This dissertation focuses on obtaining molecular insights into the very first step of infection by Nipah. Such details, in fact, remain unknown for all paramyxoviruses. Infection begins with the allosteric stimulation of Nipah virus host binding protein by host cell receptors. U

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9

Vassileiou, Antony Dimitri. "A robust machine learning approach for the prediction of allosteric binding sites." Thesis, University of Strathclyde, 2016. http://digitool.lib.strath.ac.uk:80/R/?func=dbin-jump-full&object_id=27883.

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10

Vahdati, Nadia. "Application of simulation methods for the identification of allosteric binding site in human glucokinase." Thesis, University of Southampton, 2010. https://eprints.soton.ac.uk/171075/.

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Allosteric binding site, in generic terms, refers to a binding site distinct from the active site, where binding of an effector can enhance or decrease enzyme‟s activity. From a drug design point of view targeting allosteric binding sites can offer advantages in terms of selectivity, saturability, and the opportunity for discovering new chemotypes. Current known allosteric drugs have often been identified by chance with high-throughput screening. Although experimental methods can be successful in identifying such binding sites, owing to the cost and time associated with experiments, it would b

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11

Wen, Ya. "Identification and characterization of a novel allosteric glutamate binding site on the GABA-A receptor." Thesis, University of British Columbia, 2016. http://hdl.handle.net/2429/58835.

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12

Zhong, Yu. "Allosteric modulation of GABAâ†A receptors by steroids and related compounds : functional and binding studies." Thesis, University College London (University of London), 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.341894.

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13

Saponaro, A. C. "THE AUXILIARY SUBUNIT TRIP8B ANTAGONIZES THE BINDING OF CAMP TO HCN2 CHANNELS THROUGH AN ALLOSTERIC MECHANISM." Doctoral thesis, Università degli Studi di Milano, 2014. http://hdl.handle.net/2434/229903.

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In neurons, hyperpolarization-activated cyclic nucleotide-regulated (HCN1-4) channels are the molecular determinants of the Ih current, which controls several cognitive processes. Unique among the voltage-gated ion channel superfamily, HCN channels are modulated by the direct binding of cAMP to their cytoplasmic cyclic nucleotide binding domain (CNBD). Thus, cyclic nucleotide-dependent conformational changes of CNBD are determinant in the regulation of HCN channel opening. The rearrangements induced by cAMP in HCN CNBD are not yet elucidated, since for this protein is known only the cAMP-bound

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14

Luo, Yujia. "Analgesic Effect of Nicotine and Exploration of Binding Sites for α4β2 Nicotinic Acetylcholine Receptor Positive Allosteric Modulators". Thesis, The University of Sydney, 2023. https://hdl.handle.net/2123/30000.

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Pain is a leading cause of the global burden of disease and disability. Nicotinic acetylcholine receptors (nAChRs), especially the α4β2 subtype, are widely expressed throughout the central nervous system (CNS) and peripheral nervous system (PNS), making them critical analgesic targets for the development of novel drugs. In the early part of this thesis, the analgesic effects of nicotine were quantified through meta-analysis. Sixteen eligible articles, including five studies on pain tolerance (n = 210), five studies on pain threshold (n = 210), and 11 studies on pain scores (n = 1,148) were inc

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15

Leung, Daisy W. "Biochemical and biophysical characterization of the allosteric equilibrium of the Wiskott-Aldrich Syndrome protein." Access to abstract only; dissertation is embargoed until after 12/20/2006, 2005. http://www4.utsouthwestern.edu/library/ETD/etdDetails.cfm?etdID=131.

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16

Wohlever, Matthew L. "The role of the N domain in substrate binding, oligomerization, and allosteric regulation of the AAA+ Lon protease." Thesis, Massachusetts Institute of Technology, 2013. http://hdl.handle.net/1721.1/81034.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, June 2013.<br>"June 2013." Cataloged from PDF version of thesis.<br>Includes bibliographical references.<br>For cells and organisms to survive, they must maintain protein homeostasis in varied and often harsh environments. Cells utilize proteases and chaperones to maintain their proteomes. In bacteria, most cytosolic proteolysis is performed by self-compartmentalized AAA+ proteases, which convert the chemical energy of ATP binding and hydrolysis into mechanical work to unfold and translocate substrates into an internal d

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17

Tilborg, Marc van. "The glucocorticoid receptor DNA binding domain : structure and allosteric modulation = het DNA binded domein van de glucocorticoide receptor /." [S.l. : s.n.], 1998. http://www.gbv.de/dms/bs/toc/250860244.pdf.

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18

Ring, Joshua Roderick. "SYNTHETIC AROMATIC AGMATINE ANALOGS AS ALLOSTERIC MODULATORS OF THE N-METHYL-D-ASPARTATE (NMDA) RECEPTOR CHANNEL." UKnowledge, 2006. http://uknowledge.uky.edu/gradschool_diss/413.

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The N-methyl-D-aspartate (NMDA) receptors are highly regulated ligand-gated ion channels, which are affected by many substrates. Overactivation of the NMDA receptor can lead to hyperexcitability and a number of neurotoxic effects and neurological diseases. Agmatine has been demonstrated to act allosterically as an inhibitory modulator at the polyamine recognition sites of the NMDA receptor complex. The present study synthesized and evaluated a library of agmatine analogs for their ability to displace tritiated MK-801 from NMDARs in P2 membrane preparations from rat brains at ligand concentrati

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19

Gonzalez, Walter G. "Protein-Ligand Interactions and Allosteric Regulation of Activity in DREAM Protein." FIU Digital Commons, 2016. http://digitalcommons.fiu.edu/etd/2503.

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Downstream regulatory antagonist modulator (DREAM) is a calcium sensing protein that co-assembles with KV4 potassium channels to regulate ion currents as well as with DNA in the nucleus, where it regulates gene expression. The interaction of DREAM with A-type KV4 channels and DNA has been shown to regulate neuronal signaling, pain sensing, and memory retention. The role of DREAM in modulation of pain, onset of Alzheimer’s disease, and cardiac pacemaking has set this protein as a novel therapeutic target. Moreover, previous results have shown a Ca2+ dependent interaction between DREAM and KV4/D

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20

Hernández, Alvarez Lilian [UNESP]. "Identification and characterization of cruzain allosteric inhibitors: a computer-aided approach." Universidade Estadual Paulista (UNESP), 2017. http://hdl.handle.net/11449/151919.

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Submitted by LILIAN HERNÁNDEZ ALVAREZ null (lilianhern@gmail.com) on 2017-10-16T13:40:19Z No. of bitstreams: 1 Lilian_dissertacao_final.pdf: 8133270 bytes, checksum: ea7913c9f03bc3c89f0211896c01cc88 (MD5)<br>Approved for entry into archive by Monique Sasaki (sayumi_sasaki@hotmail.com) on 2017-10-18T17:58:56Z (GMT) No. of bitstreams: 1 hernandezalvarez_l_me_sjrp.pdf: 8133270 bytes, checksum: ea7913c9f03bc3c89f0211896c01cc88 (MD5)<br>Made available in DSpace on 2017-10-18T17:58:56Z (GMT). No. of bitstreams: 1 hernandezalvarez_l_me_sjrp.pdf: 8133270 bytes, checksum: ea7913c9f03bc3c89f0211896c

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21

Shimizu, Yuji. "Studies on the binding kinetics and signaling biases of drugs targeting seven-transmembrane receptors." Kyoto University, 2018. http://hdl.handle.net/2433/230981.

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22

Jiménez-Avalos, Gabriel, A. Paula Vargas-Ruiz, Nicolás E. Delgado-Pease, et al. "Comprehensive virtual screening of 4.8 k flavonoids reveals novel insights into allosteric inhibition of SARS-CoV-2 M^PRO." Nature Research, 2021. http://hdl.handle.net/10757/657336.

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El texto completo de este trabajo no está disponible en el Repositorio Académico UPC por restricciones de la casa editorial donde ha sido publicado.<br>SARS-CoV-2 main protease is a common target for inhibition assays due to its high conservation among coronaviruses. Since flavonoids show antiviral activity, several in silico works have proposed them as potential SARS-CoV-2 main protease inhibitors. Nonetheless, there is reason to doubt certain results given the lack of consideration for flavonoid promiscuity or main protease plasticity, usage of short library sizes, absence of control molecul

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23

De, Zutter Julie Kelley. "Allosteric Regulation of Recombination Enzymes E. coli RecA and Human Rad51: A Dissertation." eScholarship@UMMS, 2000. https://escholarship.umassmed.edu/gsbs_diss/192.

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ATP plays a critical role in the regulation of many enzyme processes. In this work, I have focused on the ATP mediated regulation of the recombination processes catalyzed by the E. coliRecA and the human Rad51 proteins. The RecA protein is a multifunctional enzyme, which plays a central role in the processes of recombinational DNA repair, homologous genetic recombination and in the activation of the cellular SOS response to DNA damage. Each of these functions requires a common activating step, which is the formation of a RecA-ATP-ssDNA nucleoprotein filament. The binding of ATP results in the

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24

Vasquez, Colins. "Allosteric effects of the GTP-specific binding site and a benzimidazole-derivative non-nucleoside inhibitor on the hepatitis C virus RNA-dependent RNA polymerase." Thesis, McGill University, 2009. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=40750.

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The hepatitis C virus (HCV) is a positive-strand RNA virus that belongs to the Flaviviridae family. HCV expresses the non-structural protein, NS5B, an RNA-dependent RNA polymerase required for genome replication. Here, we describe the allosteric properties of both the GTP-specific binding site (G-site) of the HCV polymerase and VIR-1327, a benzimidazole-derivative non-nucleoside inhibitor (NNI). Using biochemical assays, we identified certain G-site residues that affect NS5B activity, including serine-29, proline-495 and valine-499. We also demonstrated that VIR-1327 is a potent inhibitor with

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25

Zoenen, Maxime. "Rôle de l'activité du récepteur sur la coopérativité de liaison dans les homomères de GPCRs." Doctoral thesis, Universite Libre de Bruxelles, 2011. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/209816.

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Dans l’étude des GPCRs, il a longtemps été considéré que ceux-ci étaient présents à la membrane sous forme de monomères et que chaque monomère pouvait être activé par un ligand et transmettre le signal grâce à une protéine G. Certains résultats comme des courbes de compétition ou d’activation à deux phases étaient difficilement explicables avec ce modèle 1 ligand, 1 récepteur, 1 protéine G.<p>Ces dernières années, il a été montré via différentes techniques que les GPCRs étaient présents à la membrane non pas sous forme de monomères mais plutôt de dimères, de rangées de dimères voire de multimè

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26

Laine, Jennifer M. "Protein Ligand Interactions Probed by NMR: A Dissertation." eScholarship@UMMS, 2012. https://escholarship.umassmed.edu/gsbs_diss/617.

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Molecular recognition, defined as the specific interactions between two or more molecules, is at the center of many biological processes including catalysis, signal transduction, gene regulation and allostery. Allosteric regulation is the modification of function caused by an intermolecular interaction. Allosteric proteins modify their activity in response to a biological signal that is often transmitted through the interaction with a small effector molecule. Therefore, determination of the origins of intermolecular interactions involved in molecular recognition and allostery are essential for

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27

Mullick, Abdul. "Engineering the cooperativity of Bacillus stearothermophilus pyruvate kinase." Thesis, University of Bristol, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.388329.

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28

Benabderrahmane, Mohammed. "Etude de la structure et la dynamique de Mcl-1 : application en cancérologie Binding mode of Pyridoclax to myeloid cell leukemia-1 (Mcl-1) revealed by nuclear magnetic resonance spectroscopy, docking and molecular dynamics approaches Insights into Mcl-1 Conformational States and Allosteric Inhibition Mechanism from Molecular Dynamics Simulations, Enhanced Sampling, and Pocket Crosstalk Analysis." Thesis, Normandie, 2020. http://www.theses.fr/2020NORMC426.

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Ce travail ayant pour objet l’étude de la structure et la dynamique de Mcl-1, une protéine anti-apoptotique d’intérêt en cancérologie, est scindé en trois parties.Une première étude concerne une caractérisation du mode d’interaction du Pyridoclax (un inhibiteur BH3-mimétique) avec Mcl-1 par des approches expérimentales (RMN) et théoriques (simulations de dynamique moléculaire). Une deuxième partie est consacrée à l’étude et à la caractérisation des espaces conformationnels de Mcl-1 et son mode d’inhibition allostérique. Le troisième volet de ce travail, traite d’une approche d’analyse, basée s

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He, Peng. "FREE ENERGY SIMULATIONS AND STRUCTURAL STUDIES OF PROTEIN-LIGAND BINDING AND ALLOSTERY." Diss., Temple University Libraries, 2018. http://cdm16002.contentdm.oclc.org/cdm/ref/collection/p245801coll10/id/531465.

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Chemistry<br>Ph.D.<br>Protein-ligand binding and protein allostery play a crucial role in cell signaling, cell regulation, and modern drug discovery. In recent years, experimental studies of protein structures including crystallography, NMR, and Cryo-EM are widely used to investigate the functional and inhibitory properties of a protein. On the one hand, structural classification and feature identification of the structures of protein kinases, HIV proteins, and other extensively studied proteins would have an increasingly important role in depicting the general figures of the conformational la

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30

Hultqvist, Greta. "Protein Folding, Binding and Evolution : PDZ domains and paralemmins as model systems." Doctoral thesis, Uppsala universitet, Institutionen för cell- och molekylärbiologi, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-185573.

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Proteins present at the synapse need to be multitasking in order to perform all vital functions in this limited space. In this thesis I have analyzed the function and evolution of such proteins, focusing on the PDZ domain and the paralemmin family. The PDZ domains bind to a wide variety of interaction partners. The affinity for each partner is regulated by residues at the binding site, but also through intradomain allostery. How this intradomain allostery is transferred to the binding site is not established. I here show that side chain interactions can explain all transfer of intradomain allo

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Mazzolari, A. "IN SILICO APPROACHES IN DRUG DESIGN AND DEVELOPMENT: APPLICATIONS TO RATIONAL LIGAND DESIGN AND METABOLISM PREDICTION." Doctoral thesis, Università degli Studi di Milano, 2015. http://hdl.handle.net/2434/347523.

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In the last decades, the applications of computational methods in medicinal chemistry have experienced significant changes which have incredibly expanded their approaches, and more importantly their objectives. The overall aim of the present research project is to explore the different fields of the modelling studies by using well-known computational methods as well as different and innovative techniques. Indeed, computational methods traditionally consisted in ligand-based and the structure-based approaches substantially aimed at optimizing the ligand structure in terms of affinity, potenc

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Subramaniam, Srisunder. "Studies of conformational changes and dynamics accompanying substrate recognition, allostery and catalysis in bacteriophage lambda integrase." The Ohio State University, 2005. http://rave.ohiolink.edu/etdc/view?acc_num=osu1111655332.

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33

Dinler, Gizem. "Mechanism of allosteric signaling in Hsp70 nucleotide binding domains." 2006. https://scholarworks.umass.edu/dissertations/AAI3206216.

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Hsp70 molecular chaperones have key functions in the cell for folding, repair and degradation of proteins. Hsp70s are a conserved family of proteins that consist of an N-terminal ATPase domain (NBD) and a C-terminal substrate-binding domain. ATP binding leads to reduced substrate-binding affinity, and reciprocally, substrate binding activates their ATPase rate. This interdomain communication is essential for Hsp70 chaperone function. Previous work suggests a key role for a stretch of conserved hydrophobic residues, 389VLLL 392, in the interdomain linker of E. coli Hsp70, DnaK, in allosteric co

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Hall, Bradley 1977. "Computational prediction of allosteric nucleic acids." Thesis, 2008. http://hdl.handle.net/2152/3898.

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Selected nucleic acid binding species (aptamers) have been shown to undergo conformational changes in the presence of ligands, and have been adapted to function as biosensors. We were interested in whether the secondary structures of aptamers could be rationally engineered to undergo ligand dependent conformational changes. To this end, we used rational and computational design methods to generate a number of aptamer biosensors. First, we built upon previous work that showed that antisense oligonucleotides bearing reporter moieties could be used to denature aptamers. Upon addition of ligands,

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Nguyen, Hackley Doan Hanh. "Allosteric Inhibition of Zinc Finger Proteins by DNA Binding Polyamides." Thesis, 2002. https://thesis.library.caltech.edu/6979/1/Nguyen_dh_2002.pdf.

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Small molecules that can bind selectively to any predetermined DNA sequence in the human genome could potentially be powerful tools for molecular biology and human medicine. Polyamides containing N-methylimidazole (Im) and N-methylpyrrole (Py) are small molecules that bind DNA according to a set of "pairing rules" with affinities and specificities similar to many naturally occurring DNA binding proteins. The study of DNA binding polyamides is further expanded by the development of new monomer pairings and new synthetic methods which allow access to polyamides with varying truncated tails. A n

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Pektas, Serap. "Oxygen activation and allosteric Zinc(ii) binding on hif-prolyl hydroxylase-2 (phd2)." 2013. https://scholarworks.umass.edu/dissertations/AAI3603135.

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Oxygen homeostasis is essential to the life of aerobes, which is regulated in humans by Hypoxia Inducible Factor-1α (HIF-1α). Under hypoxic conditions, HIF-1α transactivates over a hundred genes related angiogenesis, erythropoiesis, etc. HIF-1α level and function is regulated by four HIF hydroxylase enzymes: three isoforms of prolyl hydroxylase domain (PHD1, PHD2 and PHD3) and factor inhibiting HIF-1α (FIH). PHD2 is the focus of this research. PHD2 is a non-heme Fe(II) 2-oxoglutarate dependent dioxygenase, which controls HIF-1α levels by hydroxylating two proline residues within the ODD domain

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Pektas, Serap. "O2 Activation and Allosteric Zn(Ii) Binding on Hif-Prolyl Hydroxylase-2 (Phd2)." 2013. https://scholarworks.umass.edu/open_access_dissertations/828.

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Oxygen homeostasis is essential to the life of aerobes, which is regulated in humans by Hypoxia Inducible Factor-1α (HIF-1α). Under hypoxic conditions, HIF-1α transactivates over a hundred genes related angiogenesis, erythropoiesis, etc. HIF-1α level and function is regulated by four HIF hydroxylase enzymes: three isoforms of prolyl hydroxylase domain (PHD1, PHD2 and PHD3) and factor inhibiting HIF-1α (FIH). PHD2 is the focus of this research. PHD2 is a non-heme Fe(II) 2-oxoglutarate dependent dioxygenase, which controls HIF-1α levels by hydroxylating two proline residues within the ODD domain

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Wang, Wei. "Allosteric Coupling, Nucleotide Binding and ATP Hydrolysis by Hsp70 Chaperones on a Structural Basis." Thesis, 2018. https://doi.org/10.7916/D8612H5F.

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Healthy cells continuously produce proteins to accomplish various functions, including immune responses, reaction catalyses, transmitting signals, structural supports and molecular transport. Protein needs to fold correctly into three-dimensional shape in order to function well, using the information stored in the amino acid sequence. Proteins may fold spontaneously in solution, but the situation in living cells can be complicated. Cells are filled with nucleic acids and proteins thus they are usually in a stressful environment. Under such circumstances, proteins can be unfolded or misfolded,

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Chen, Meng-Chun, and 陳孟君. "Creation of an allosteric site and a NAD+ binding site in cytosolic NADP+-dependent malic enzyme." Thesis, 2008. http://ndltd.ncl.edu.tw/handle/86838498621002700767.

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碩士<br>國立中興大學<br>生命科學系所<br>96<br>Cytosolic NADP+-dependent malic enzyme (c-NADP-ME) catalyzes a reversible oxidative decarboxylation converting L-malate into CO2 and pyruvate, concomitant with reduction of NADP+ to NADPH. Divalent metal ion (Mn2+ or Mg2+) is required for catalysis. According to the previous studies, mitochondrial malic enzyme (m-NAD-ME) is considered as an allosteric enzyme with fumarate as an activator and ATP as an inhibitor. In this study, we created a series of multiple mutations based on the sequence alignments to build a fumarate binding site for human c-NADP-ME. The opti

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Tilborg, Marcus Adrianus Antonius van. "The glucocorticoid receptor DNA binding domain : structure and allosteric modulation = Het DNA bindend domein van de glucocorticoide receptor structuur en allosterische modulatie /." 1998. http://www.gbv.de/dms/bs/toc/250860244.pdf.

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41

Hatley, Mark Edward. "Allosteric determinants of guanine nucleotide binding proteins and methods to crystallize the cytosolic domains of adenylyl cyclase." 2004. http://edissertations.library.swmed.edu/pdf/HatleyM050404/HatleyMark.pdf.

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42

Ferguson, Scarlett Blair. "Understanding Weak Binding for Phospho(enol)pyruvate to the Allosteric Site of Phosphofructokinase from Lactobacillus delbrueckii subspecies bulgaricus." Thesis, 2011. http://hdl.handle.net/1969.1/ETD-TAMU-2011-08-9696.

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Phosphofructokinase (PFK) from the lactic acid bacterium Lactobacillus delbrueckii subspecies bulgaricus (LbPFK) is a non-allosteric PFK with weak binding affinity for both the allosteric ligands phospho(enol)pyruvate (PEP) and magnesium adenosine diphosphate (MgADP). PEP and MgADP bind to the same allosteric binding site but exhibit opposite effects, PEP acting as an inhibitor and MgADP an activator. In 2005, Parichatttanakul, et al. solved the first crystal structure of LbPFK to 1.87 A resolution and allowed for a structural comparison of LbPFK to the allosteric forms of PFK from E. coli (

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Gallagher, Ryan. "Development of alkaloid derivatives to probe novel α4β2 nicotinic acetylcholine receptor (nAChR) binding sites". Phd thesis, 2015. http://hdl.handle.net/1885/104843.

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Nicotinic acetylcholine receptors (nAChRs) are a complex class of ligand gated ion channels consisting of multiple subtypes with different stoichiometries. Of these, the two most commonly found in the brain are the α7 and α4β2 nAChRs. The binding site of agonists and competitive antagonists at nAChRs is well established. However, the binding site of many allosteric modulators remains unknown. Additionally, despite their importance in brain function, the role of specific subtypes and stoichiometries is largely unknown. This thesis deals with the synt

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Hattendorf, Douglas Alan. "Multiple allosteric signaling events in the Hsp104 ATP hydrolysis cycle revealed by mutagenesis of conserved AAA active site residues /." 2001. 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:3034467.

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Shubina-McGresham, Maria. "Characterization of the Allosteric Properties of Thermus thermophilus Phosphofructokinase and the Sources of Strong Inhibitor Binding Affinity and Weak Inhibitory Response." Thesis, 2012. http://hdl.handle.net/1969.1/ETD-TAMU-2012-08-11750.

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Characterization of allosteric properties of phosphofructokinase from the extreme thermophile Thermus thermophilus (TtPFK) using thermodynamic linkage analysis revealed several peculiarities. Inhibition and activation of Fru-6-P binding by the allosteric effectors phosphoenolpyruvate (PEP) and MgADP are entropically-driven in TtPFK. It is also curious that PEP binding affinity is unusually strong in TtPFK when compared to PFKs from Escherichia coli, Bacillus stearothermophilus, and Lactobacillus delbrueckii, while the magnitude of the allosteric inhibition by PEP is much smaller in TtPFK. In a

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Chakrabarti, Kalyan Sundar. "Solution Structural Studies And Substrate Binding Properties Of The Amino-Terminal Domain Of E.coli Pantothenate Synthetase." Thesis, 2008. https://etd.iisc.ac.in/handle/2005/1103.

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Pantothenate synthetase (PS), which catalyzes the last step in the pantothenate (vitamin B5) biosynthesis, is a dimeric enzyme present in bacteria, fungi and plants. The enzymatic properties of PS from Escherichia Coli, Mycobacterium tuberculosi, Fusarium Oxysporum, Lotus japonicus, Oryza sativum, Brassica napus and Arabidopsis thaliana have been characterized. The chemical reaction and the proposed mechanism of reaction are identical for PS, irrespective of the source. However, from an enzyme mechanistic point of view, plant PS’s are dissimilar to their bacterial counterparts, in that they ex

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Chakrabarti, Kalyan Sundar. "Solution Structural Studies And Substrate Binding Properties Of The Amino-Terminal Domain Of E.coli Pantothenate Synthetase." Thesis, 2008. http://hdl.handle.net/2005/1103.

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Pantothenate synthetase (PS), which catalyzes the last step in the pantothenate (vitamin B5) biosynthesis, is a dimeric enzyme present in bacteria, fungi and plants. The enzymatic properties of PS from Escherichia Coli, Mycobacterium tuberculosi, Fusarium Oxysporum, Lotus japonicus, Oryza sativum, Brassica napus and Arabidopsis thaliana have been characterized. The chemical reaction and the proposed mechanism of reaction are identical for PS, irrespective of the source. However, from an enzyme mechanistic point of view, plant PS’s are dissimilar to their bacterial counterparts, in that they ex

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Daniels, Kyle Gabriel. "Kinetics of Coupled Binding and Conformational Change in Proteins and RNA." Diss., 2015. http://hdl.handle.net/10161/10532.

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<p>Ligand binding can modulate function of proteins and nucleic acids by changing both the populations of functionally distinct conformational states and the timescales on which they interconvert. For this reason, both thermodynamic and kinetic details of coupling can be important to proper function. How tightly does ligand bind to the different conformational states? What effect does ligand binding have on the conformational equilibrium and conformational kinetics? On what timescales and in what order do binding and conformational change occur? Using a combination of stopped-flow kinetics, is

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Tu, Jhe-Le, and 涂誌樂. "Unique GTP-Binding Pocket and Allostery of Uridylate Kinase from a Gram-Negative Phytopathogenic Bacterium." Thesis, 2010. http://ndltd.ncl.edu.tw/handle/51054245596663198244.

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博士<br>國立中興大學<br>生物化學研究所<br>98<br>Uridine 5’-monophosphate kinase (UMPK) catalyzes the reversible transfer of the γ-phosphoryl group from ATP to UMP to produce UDP. In general, UMPKs are stimulated by GTP and inhibited by UTP. In general, eukaryotic UMPKs exhibit dual specificity toward UMP or CMP, but the UMPKs of bacterial origin exhibit more dedicated UMP-specific activity and are essential for bacterial growth. Therefore, UMPKs are potential targets for developing antibacterial drug. To date, tertiary structures of a number of prokaryotic apo-form UMPKs and complexes with different nucleoti

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Momin, Mohamed. "Atomistic Insights into Binding Pocket Dynamics and Regulation in the Interleukin-2 T-Cell Kinase SH2 Domain." 2017. http://scholarworks.gsu.edu/chemistry_theses/102.

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Although the regulation of proteins functions by allosteric interactions has been identified in many subcellular processes, long-range conformational changes in proteins are also known to be induced by molecular switches. A molecular switch based on the cis-trans isomerization of a peptidyl-prolyl bond is capable of inducing a conformational change directly to the protein backbone, which is then propagated throughout the system. However, these switches are elusive and difficult to identify due to their intrinsic dynamics in the biomolecules where they are found. Herein, we explore the conforma

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