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Relevant bibliographies by topics / Allosteric binding

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Academic literature on the topic 'Allosteric binding'

Author: Grafiati

Published: 3 June 2025

Last updated: 31 July 2025

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Journal articles on the topic "Allosteric binding"

1

Guan, Xingyue, Cheng Tan, Wenfei Li, Wei Wang, and D. Thirumalai. "Role of water-bridged interactions in metal ion coupled protein allostery." PLOS Computational Biology 18, no. 6 (2022): e1010195. http://dx.doi.org/10.1371/journal.pcbi.1010195.

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Allosteric communication between distant parts of proteins controls many cellular functions, in which metal ions are widely utilized as effectors to trigger the allosteric cascade. Due to the involvement of strong coordination interactions, the energy landscape dictating the metal ion binding is intrinsically rugged. How metal ions achieve fast binding by overcoming the landscape ruggedness and thereby efficiently mediate protein allostery is elusive. By performing molecular dynamics simulations for the Ca2+ binding mediated allostery of the calmodulin (CaM) domains, each containing two Ca2+ b

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Kuznetsov, Aleksei, and Jaak Järv. "Ligand structure controlled allostery in cAMP-dependent protein kinase catalytic subunit." Open Life Sciences 4, no. 2 (2009): 131–41. http://dx.doi.org/10.2478/s11535-009-0012-6.

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AbstractProtein kinase A (cAMP dependent protein kinase catalytic subunit, EC 2.7.11.11) binds simultaneously ATP and a phosphorylatable peptide. These structurally dissimilar allosteric ligands influence the binding effectiveness of each other. The same situation is observed with substrate congeners, which reversibly inhibit the enzyme. In this review these allosteric effects are quantified using the interaction factor, which compares binding effectiveness of ligands with the free enzyme and the pre-loaded enzyme complex containing another ligand. This analysis revealed that the allosteric ef

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Xu, Yunyao, Dongyu Zhang, Rivkah Rogawski, Crina M. Nimigean, and Ann E. McDermott. "Identifying coupled clusters of allostery participants through chemical shift perturbations." Proceedings of the National Academy of Sciences 116, no. 6 (2019): 2078–85. http://dx.doi.org/10.1073/pnas.1811168116.

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Allosteric couplings underlie many cellular signaling processes and provide an exciting avenue for development of new diagnostics and therapeutics. A general method for identifying important residues in allosteric mechanisms would be very useful, but remains elusive due to the complexity of long-range phenomena. Here, we introduce an NMR method to identify residues involved in allosteric coupling between two ligand-binding sites in a protein, which we call chemical shift detection of allostery participants (CAP). Networks of functional groups responding to each ligand are defined through corre

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Ugbaja, Samuel C., Isiaka A. Lawal, Bahijjahtu H. Abubakar, Aganze G. Mushebenge, Monsurat M. Lawal, and Hezekiel M. Kumalo. "Allostery Inhibition of BACE1 by Psychotic and Meroterpenoid Drugs in Alzheimer’s Disease Therapy." Molecules 27, no. 14 (2022): 4372. http://dx.doi.org/10.3390/molecules27144372.

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In over a century since its discovery, Alzheimer’s disease (AD) has continued to be a global health concern due to its incurable nature and overwhelming increase among older people. In this paper, we give an overview of the efforts of researchers towards identifying potent BACE1 exosite-binding antibodies and allosteric inhibitors. Herein, we apply computer-aided drug design (CADD) methods to unravel the interactions of some proposed psychotic and meroterpenoid BACE1 allosteric site inhibitors. This study is aimed at validating the allosteric potentials of these selected compounds targeted at

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Balboni, Beatrice, Mirco Masi, Walter Rocchia, Stefania Girotto та Andrea Cavalli. "GSK-3β Allosteric Inhibition: A Dead End or a New Pharmacological Frontier?" International Journal of Molecular Sciences 24, № 8 (2023): 7541. http://dx.doi.org/10.3390/ijms24087541.

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Most kinase inhibitors are designed to bind to highly homologous ATP-binding sites, which leads to promiscuity and possible off-target effects. Allostery is an alternative approach to pursuing selectivity. However, allostery is difficult to exploit due to the wide variety of underlying mechanisms and the potential involvement of long-range conformational effects that are difficult to pinpoint. GSK-3β is involved in several pathologies. This critical target has an ATP-binding site that is highly homologous with the orthosteric sites of other kinases. Unsurprisingly, there is also great similari

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Abrusán, György, and Joseph A. Marsh. "Ligand-Binding-Site Structure Shapes Allosteric Signal Transduction and the Evolution of Allostery in Protein Complexes." Molecular Biology and Evolution 36, no. 8 (2019): 1711–27. http://dx.doi.org/10.1093/molbev/msz093.

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Abstract The structure of ligand-binding sites has been shown to profoundly influence the evolution of function in homomeric protein complexes. Complexes with multichain binding sites (MBSs) have more conserved quaternary structure, more similar binding sites and ligands between homologs, and evolve new functions slower than homomers with single-chain binding sites (SBSs). Here, using in silico analyses of protein dynamics, we investigate whether ligand-binding-site structure shapes allosteric signal transduction pathways, and whether the structural similarity of binding sites influences the e

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Zhou, Tao, Huiling Zhang, Xiaoting Yu, et al. "Fc-Binding Cyclopeptide Induces Allostery from Fc to Fab: Revealed Through in Silico Structural Analysis to Anti-Phenobarbital Antibody." Foods 14, no. 8 (2025): 1360. https://doi.org/10.3390/foods14081360.

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Allostery is a fundamental biological phenomenon that occurs when a molecule binds to a protein’s allosteric site, triggering conformational changes that regulate the protein’s activity. However, allostery in antibodies remains largely unexplored, and only a few reports have focused on allostery from antigen-binding fragments (Fab) to crystallizable fragments (Fc). But this study, using anti-phenobarbital antibodies—which are widely applied for detecting the potential health food adulterant phenobarbital—as a model and employing multiple computational methods, is the first to identify a cyclop

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Patrick, John W., Christopher D. Boone, Wen Liu, et al. "Allostery revealed within lipid binding events to membrane proteins." Proceedings of the National Academy of Sciences 115, no. 12 (2018): 2976–81. http://dx.doi.org/10.1073/pnas.1719813115.

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Membrane proteins interact with a myriad of lipid species in the biological membrane, leading to a bewildering number of possible protein−lipid assemblies. Despite this inherent complexity, the identification of specific protein−lipid interactions and the crucial role of lipids in the folding, structure, and function of membrane proteins is emerging from an increasing number of reports. Fundamental questions remain, however, regarding the ability of specific lipid binding events to membrane proteins to alter remote binding sites for lipids of a different type, a property referred to as alloste

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Capdevila, Daiana A., Joseph J. Braymer, Katherine A. Edmonds, Hongwei Wu, and David P. Giedroc. "Entropy redistribution controls allostery in a metalloregulatory protein." Proceedings of the National Academy of Sciences 114, no. 17 (2017): 4424–29. http://dx.doi.org/10.1073/pnas.1620665114.

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Allosteric communication between two ligand-binding sites in a protein is a central aspect of biological regulation that remains mechanistically unclear. Here we show that perturbations in equilibrium picosecond–nanosecond motions impact zinc (Zn)-induced allosteric inhibition of DNA binding by the Zn efflux repressor CzrA (chromosomal zinc-regulated repressor). DNA binding leads to an unanticipated increase in methyl side-chain flexibility and thus stabilizes the complex entropically; Zn binding redistributes these motions, inhibiting formation of the DNA complex by restricting coupled fast m

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Thirumalai, D., and Changbong Hyeon. "Signalling networks and dynamics of allosteric transitions in bacterial chaperonin GroEL: implications for iterative annealing of misfolded proteins." Philosophical Transactions of the Royal Society B: Biological Sciences 373, no. 1749 (2018): 20170182. http://dx.doi.org/10.1098/rstb.2017.0182.

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Signal transmission at the molecular level in many biological complexes occurs through allosteric transitions. Allostery describes the responses of a complex to binding of ligands at sites that are spatially well separated from the binding region. We describe the structural perturbation method, based on phonon propagation in solids, which can be used to determine the signal-transmitting allostery wiring diagram (AWD) in large but finite-sized biological complexes. Application to the bacterial chaperonin GroEL–GroES complex shows that the AWD determined from structures also drives the allosteri

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Dissertations / Theses on the topic "Allosteric binding"

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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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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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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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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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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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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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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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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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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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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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Books on the topic "Allosteric binding"

1

Levitzki, Alexander. Quantitative Aspects of Allosteric Mechanisms. Springer, 2011.

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Allosteric Coupling, Nucleotide Binding and ATP Hydrolysis by Hsp70 Chaperones on a Structural Basis. [publisher not identified], 2018.

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Ren, Ke, and Ronald Dubner. The first crystal structure of an ionotropic glutamate receptor ligand-binding core. Edited by Paul Farquhar-Smith, Pierre Beaulieu, and Sian Jagger. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780198834359.003.0032.

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The known functional ionotropic glutamate receptors (iGluRs) are composed of three major subtypes: AMPA, NMDA, and kainate. In 1998, in the landmark paper discussed in this chapter, Armstrong et al. provided the first crystal structure of an iGluR-subunit ligand-binding core, the S1S2 region of the rat GluA2 ‘flop’ isoform. They solved its structure with X-ray crystallography from selenomethonine crystals. They also identified residues involved in kainate binding, analysed allosteric sites that regulate affinity and specificity of the agonist, and mapped potential subunit–subunit interaction s

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Hu, Guang, Pemra Doruker, Hongchun Li, and Ebru Demet Akten, eds. Understanding Protein Dynamics, Binding and Allostery for Drug Design. Frontiers Media SA, 2021. http://dx.doi.org/10.3389/978-2-88966-848-9.

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Book chapters on the topic "Allosteric binding"

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Song, Kun, and Jian Zhang. "Single Binding Pockets Versus Allosteric Binding." In Methods in Molecular Biology. Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-8639-2_9.

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Fasano, Mauro, Gabriella Fanali, Riccardo Fesce, and Paolo Ascenzi. "Human Serum Haeme-albumin: An Allosteric ‘Chronosteric’ Protein." In Dioxygen Binding and Sensing Proteins. Springer Milan, 2008. http://dx.doi.org/10.1007/978-88-470-0807-6_12.

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Ming, Dengming, and Michael E. Wall. "Predicting Binding Sites by Analyzing Allosteric Effects." In Methods in Molecular Biology. Springer New York, 2011. http://dx.doi.org/10.1007/978-1-61779-334-9_23.

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Kranz, James K., and José C. Clemente. "Binding Techniques to Study the Allosteric Energy Cycle." In Methods in Molecular Biology. Springer New York, 2011. http://dx.doi.org/10.1007/978-1-61779-334-9_1.

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Jakubík, Jan, and Esam E. El-Fakahany. "Allosteric Modulation of Ligand Binding to Muscarinic Receptors." In Neuromethods. Springer US, 2024. http://dx.doi.org/10.1007/978-1-0716-4015-9_4.

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Canagarajah, Bertram, William J. Smith, and James H. Hurley. "Structural Mechanisms of Allosteric Regulation by Membrane-binding Domains." In Protein-Lipid Interactions. Wiley-VCH Verlag GmbH & Co. KGaA, 2006. http://dx.doi.org/10.1002/3527606769.ch17.

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Ramirez, Ursula D., Faina Myachina, Linda Stith, and Eileen K. Jaffe. "Docking to Large Allosteric Binding Sites on Protein Surfaces." In Advances in Experimental Medicine and Biology. Springer New York, 2010. http://dx.doi.org/10.1007/978-1-4419-5913-3_54.

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Grossoehme, Nicholas E., and David P. Giedroc. "Allosteric Coupling Between Transition Metal-Binding Sites in Homooligomeric Metal Sensor Proteins." In Methods in Molecular Biology. Springer New York, 2011. http://dx.doi.org/10.1007/978-1-61779-334-9_3.

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Langmead, Christopher J. "Determining Allosteric Modulator Mechanism of Action: Integration of Radioligand Binding and Functional Assay Data." In Methods in Molecular Biology. Humana Press, 2011. http://dx.doi.org/10.1007/978-1-61779-126-0_10.

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Tovar-Méndez, A., H. Yampara-Iquise, C. Mújica-Jiménez, and R. A. Muñoz-Clares. "Binding of Ligands to the Glucose-6-Phosphate Allosteric Site in Maize-Leaf Phosphoenolpyruvate Carboxylase." In Photosynthesis: from Light to Biosphere. Springer Netherlands, 1995. http://dx.doi.org/10.1007/978-94-009-0173-5_951.

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Conference papers on the topic "Allosteric binding"

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Foley, Christopher E., Sana Al Azwari, Mark Dufton, and John N. Wilson. "Using microenvironments to identify allosteric binding sites." In 2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2012. http://dx.doi.org/10.1109/bibm.2012.6392711.

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Wall, Michael E. "Ligand Binding, Protein Fluctuations, And Allosteric Free Energy." In FROM PHYSICS TO BIOLOGY: The Interface between Experiment and Computation - BIFI 2006 II International Congress. AIP, 2006. http://dx.doi.org/10.1063/1.2345620.

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Planesas, Jesús M., Violeta I. Pérez-Nueno, José I. Borrell, and Jordi Teixidó. "Polypharmacology within CXCR4: Multiple binding sites and allosteric behavior." In INTERNATIONAL CONFERENCE OF COMPUTATIONAL METHODS IN SCIENCES AND ENGINEERING 2014 (ICCMSE 2014). AIP Publishing LLC, 2014. http://dx.doi.org/10.1063/1.4898789.

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Nechipurenko, Y. D., A. S. Buchelnikov, and I. A. Lavrinenko. "COOPERATIVE EFFECTS IN BINDING OF LIGANDS TO BIOPOLYMERS." In NOVEL TECHNOLOGIES IN MEDICINE, BIOLOGY, PHARMACOLOGY AND ECOLOGY. Institute of information technology, 2022. http://dx.doi.org/10.47501/978-5-6044060-2-1.257-261.

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Models and methods of statistical thermodynamics and physical adsorption theory allow us to quantitate cooperative interactions between ligand molecules adsorbed on a macromol-ecule, in particular allosteric effects described in detail in oxygen binding to hemoglobin. We show how the Hill equation can be modified and how the Hill coefficient can be interpreted. On the other hand, the entropy of the adsorption system allows us to visualize cooperative binding processes. Cooperative interactions lead to a decrease in the entropy of the system and an increase in the information it contains.

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Dolzhikova, O. A., O. A. Semikolenova, M. I. Meschaninova, and D. S. Novopashina. "ALLOSTERIC REGULATION OF CRISPR/CAS9 SYSTEM ON THE RNA LEVEL." In X Международная конференция молодых ученых: биоинформатиков, биотехнологов, биофизиков, вирусологов и молекулярных биологов — 2023. Novosibirsk State University, 2023. http://dx.doi.org/10.25205/978-5-4437-1526-1-71.

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CRISPR/Cas9 systems are commonly used for the introduction of double-strand break at the targeted point of DNA. A possible way to improve its specificity is allosteric regulation. Here, we designed guide RNA containing theophylline-binding or Mango aptamer and investigated their functional activity by the example of the model DNA cleavage either in absence or in presence of theophylline or thiazole orange respectively.

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Qi, Wei, Kehao Zhao, Justin Gu, et al. "Abstract LB-288: An allosteric PRC2 inhibitor targeting the H3K27me3 binding pocket of EED." In Proceedings: AACR Annual Meeting 2017; April 1-5, 2017; Washington, DC. American Association for Cancer Research, 2017. http://dx.doi.org/10.1158/1538-7445.am2017-lb-288.

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Varga, Balazs R., Sarah M. Bernhard, Amal El Daibani, et al. "Efficacy modulation by targeting the sodium binding allosteric site in the delta opioid receptor." In ASPET 2024 Annual Meeting Abstract. American Society for Pharmacology and Experimental Therapeutics, 2024. http://dx.doi.org/10.1124/jpet.286.100583.

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Gosens, Reinoud, Loes Kistemaker, Carolina Elzinga, et al. "Secondary allosteric M3 receptor binding for tiotropium: implications for bronchoprotection and functional interactions with LABAs." In ERS International Congress 2017 abstracts. European Respiratory Society, 2017. http://dx.doi.org/10.1183/1393003.congress-2017.oa4408.

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Hanson, John N., Ashley N. Nilson, Eve Cohen, et al. "Characterization of the Binding Pocket for a Novel Positive Allosteric Modulator of the D1 Dopamine Receptor." In ASPET 2024 Annual Meeting Abstract. American Society for Pharmacology and Experimental Therapeutics, 2024. http://dx.doi.org/10.1124/jpet.344.909500.

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Wang, Duen-Shian, Hamed S. Hayatshahi, Vindi M. Jayasinghe-Arachchige, and Jin Liu. "Allosteric Modulation of Small Molecule Drugs on ACE2 Conformational Change upon Binding to SARS-CoV-2 Spike Protein." In 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2021. http://dx.doi.org/10.1109/bibm52615.2021.9669438.

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