1,822 results on '"Allosteric enzyme"'
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2. A novel polyamine allosteric site of SpeG from Vibrio cholerae is revealed by its dodecameric structure
- Author
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Anderson, Wayne [Northwestern Univ. School of Medicine, Chicago, IL (United States)]
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- 2015
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3. An overview of structure, function, and regulation of pyruvate kinases.
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Schormann, Norbert, Hayden, Katherine L., Lee, Paul, Banerjee, Surajit, and Chattopadhyay, Debasish
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In the last step of glycolysis Pyruvate kinase catalyzes the irreversible conversion of ADP and phosphoenolpyruvate to ATP and pyruvic acid, both crucial for cellular metabolism. Thus pyruvate kinase plays a key role in controlling the metabolic flux and ATP production. The hallmark of the activity of different pyruvate kinases is their tight modulation by a variety of mechanisms including the use of a large number of physiological allosteric effectors in addition to their homotropic regulation by phosphoenolpyruvate. Binding of effectors signals precise and orchestrated movements in selected areas of the protein structure that alter the catalytic action of these evolutionarily conserved enzymes with remarkably conserved architecture and sequences. While the diverse nature of the allosteric effectors has been discussed in the literature, the structural basis of their regulatory effects is still not well understood because of the lack of data representing conformations in various activation states. Results of recent studies on pyruvate kinases of different families suggest that members of evolutionarily related families follow somewhat conserved allosteric strategies but evolutionarily distant members adopt different strategies. Here we review the structure and allosteric properties of pyruvate kinases of different families for which structural data are available. [ABSTRACT FROM AUTHOR]
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- 2019
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4. The Secret of Protein Sophistication
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Yariv, Joseph and Yariv, Joseph
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- 2016
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5. Biochemical and Kinetic Analysis of Phosphofructokinase in the Eukaryotic Human Pathogen Entamoeba histolytica
- Author
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Cho, Jin
- Subjects
- Enzyme kinetics, Entamoeba histolytica, allosteric enzyme, Phosphofructokinase, Biochemistry, Molecular Biology
- Abstract
Entamoeba histolytica is a water- and food-borne intestinal parasite that causes amoebiasis and liver abscess in ~100 million people each year leading to ~100,000 deaths. This amitochondriate parasite lacks many metabolic pathways including the tricarboxylic acid cycle and oxidative phosphorylation, and cannot synthesize purines, pyrimidines, or most amino acids. As a result, E. histolytica is presumed to rely on its modified pyrophosphate (PPi)-dependent glycolytic pathway for ATP production during growth on glucose. This pathway relies on a PPi-dependent rather than ATP-dependent phosphofructokinase (PFK) and thus has a net production of three ATP per glucose. However, in addition to the one PPi-dependent PFK, the E. histolytica genome encodes three putative ATP-dependent PFKs, (designated as EhPFK1, EhPFK2, and EhPFK3). I have recombinantly produced and purified EhPFK2 and EhPFK3 to analyze their enzymatic activities and regulation. Both enzymes displayed cooperative kinetics instead of Michaelis-Menten kinetics with respect to the two substrates fructose 6-phosphate (F6P) and ATP. Kinetic analysis showed that EhPFK2 is the more efficient enzyme compared to EhPFK3. Various ligands such as AMP that have been shown to regulate PFKs in other organisms have been tested to analyze their effects on E. histolytica PFK activities. Specifically, I identified phosphoenolpyruvate (PEP), PPi, and citrate as inhibitors, with PEP being the most potent, and CoA is a potent activator, differentiating EhPFK2 and EhPFK3 from the canonical PFK. I have shown experimentally and through structural model predictions that PEP, PPi, and citrate each bind at different allosteric sites. In addition, these inhibitors had different effects with respect to F6P and ATP substrate binding. The gene encoding PPi-dependent PFK is highly expressed during standard trophozoite growth in E. histolytica as well as in the reptile pathogen Entamoeba invadens. RNAseq studies in E. invadens indicate that one of its two genes encoding putative ATP-dependent PFK is strongly upregulated during excystation. The differences in enzymatic activity and regulation suggest that the four PFKs play different metabolic roles.
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- 2023
6. Allosteric Enzymes
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Cohen, G. N. and Cohen, G. N.
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- 2014
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7. Allosteric Enzymes
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Cohen, G. N. and Cohen, G.N.
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- 2011
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8. Charge neutralization in the active site of the catalytic trimer of aspartate transcarbamoylase promotes diverse structural changes.
- Author
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Endrizzi, James A. and Beernink, Peter T.
- Abstract
A classical model for allosteric regulation of enzyme activity posits an equilibrium between inactive and active conformations. An alternative view is that allosteric activation is achieved by increasing the potential for conformational changes that are essential for catalysis. In the present study, substitution of a basic residue in the active site of the catalytic (C) trimer of aspartate transcarbamoylase with a non-polar residue results in large interdomain hinge changes in the three chains of the trimer. One conformation is more open than the chains in both the wild-type C trimer and the catalytic chains in the holoenzyme, the second is closed similar to the bisubstrate-analog bound conformation and the third hinge angle is intermediate to the other two. The active-site 240s loop conformation is very different between the most open and closed chains, and is disordered in the third chain, as in the holoenzyme. We hypothesize that binding of anionic substrates may promote similar structural changes. Further, the ability of the three catalytic chains in the trimer to access the open and closed active-site conformations simultaneously suggests a cyclic catalytic mechanism, in which at least one of the chains is in an open conformation suitable for substrate binding whereas another chain is closed for catalytic turnover. Based on the many conformations observed for the chains in the isolated catalytic trimer to date, we propose that allosteric activation of the holoenzyme occurs by release of quaternary constraint into an ensemble of active-site conformations. [ABSTRACT FROM AUTHOR]
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- 2017
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9. Mechanism of allosteric activation of SIRT6 revealed by the action of rationally designed activators
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Shaoyong Lu, Duan Ni, Xinheng He, Mingzhu Zhao, Jiacheng Wei, Jian Zhang, and Yingyi Chen
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Allosteric driver ,Stereochemistry ,Short Communication ,MST, microscale thermophoresis ,Allosteric regulation ,Protein dynamics ,RM1-950 ,ADPR, ADP-ribose ,EC50, Effective concentration ,Drug design ,Enzyme catalysis ,03 medical and health sciences ,NAM, nicotinamide ,0302 clinical medicine ,H3K56, histone 3 lysine 56 ,Myr-H3K9, myristoyl H3K9 ,RMSD, root-mean-square deviation ,General Pharmacology, Toxicology and Pharmaceutics ,Allosteric sites ,030304 developmental biology ,PCA, principal component analysis ,0303 health sciences ,biology ,Activator (genetics) ,Chemistry ,SIRT6, sirtuin 6 ,MD, molecular dynamics ,FDL, Fluor de Lys ,Allosteric enzyme ,Acetylation ,030220 oncology & carcinogenesis ,Allosteric mechanisms ,HPLC, high-performance liquid chromatography ,Sirtuin ,biology.protein ,NAD+ kinase ,Therapeutics. Pharmacology ,H3K9, histone 3 lysine 9 - Abstract
The recent discovery of activator compounds binding to an allosteric site on the NAD+-dependent protein lysine deacetylase, sirtuin 6 (SIRT6) has attracted interest and presents a pharmaceutical target for aging-related and cancer diseases. However, the mechanism underlying allosteric activation of SIRT6 by the activator MDL-801 remains largely elusive because no major conformational changes are observed upon activator binding. By combining molecular dynamics simulations with biochemical and kinetic analyses of wild-type SIRT6 and its variant M136A, we show that conformational rotation of 2-methyl-4-fluoro-5-bromo substituent on the right phenyl ring (R-ring) of MDL-801, which uncovers previously unseen hydrophobic interactions, contributes to increased activating deacetylation activity of SIRT6. This hypothesis is further supported by the two newly synthesized MDL-801 derivatives through the removal of the 5-Br atom on the R-ring (MDL-801-D1) or the restraint of the rotation of the R-ring (MDL-801-D2). We further propose that the 5-Br atom serves as an allosteric driver that controls the ligand allosteric efficacy. Our study highlights the effect of allosteric enzyme catalytic activity by activator binding and provides a rational approach for enhancing deacetylation activity., Graphical abstract Sirtuin 6 (SIRT6), a NAD+-dependent protein lysine deacetylase, has attracted interest and presents a pharmaceutical target for aging-related and cancer diseases. By combining molecular dynamics simulations, compound synthesis, and biochemical and kinetic analyses of wild-type SIRT6 and its variants, we elucidate the allosteric activation mechanism of SIRT6 by small-molecule compounds.Image 1
- Published
- 2021
10. Manipulation of a cation-π sandwich reveals conformational flexibility in phenylalanine hydroxylase
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Emilia C. Arturo, George Merkel, Deeanne Almeida, Kushol Gupta, Michael R. Hansen, Sophia Lisowski, and Eileen K. Jaffe
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Protein Conformation, alpha-Helical ,0301 basic medicine ,Conformational change ,Phenylalanine hydroxylase ,Stereochemistry ,Allosteric regulation ,Mutation, Missense ,Phenylalanine ,Biochemistry ,Article ,03 medical and health sciences ,Protein structure ,Tetramer ,Phenylketonurias ,Enzyme Stability ,polycyclic compounds ,Animals ,Humans ,Enzyme kinetics ,Protein Structure, Quaternary ,030102 biochemistry & molecular biology ,biology ,Chemistry ,Phenylalanine Hydroxylase ,General Medicine ,Rats ,030104 developmental biology ,Amino Acid Substitution ,Allosteric enzyme ,biology.protein ,Protein Multimerization ,Linker - Abstract
Phenylalanine hydroxylase (PAH) is an allosteric enzyme responsible for maintaining phenylalanine (Phe) below neurotoxic levels; its failure results in phenylketonuria. Wild type (WT) PAH equilibrates among resting-state (RS-PAH) and activated (A-PAH) conformations, whose equilibrium position depends upon allosteric Phe binding to the A-PAH conformation. The RS-PAH conformation of WT rat PAH (rPAH) contains a cation-π sandwich between Phe80, Arg123, and Arg420, which cannot exist in the A-PAH conformation. Phe80 variants F80A, F80D, F80L, and F80R were prepared; their conformational equilibrium was evaluated using native PAGE, size exclusion chromatography, ion exchange behavior, intrinsic protein fluorescence, enzyme kinetics, and limited proteolysis, each as a function of [Phe]. Like WT rPAH, F80A and F80D show allosteric activation by Phe while F80L and F80R are constitutively active. Maximal activity of all variants suggests relief of a rate-determining conformational change involving Phe80. Limited proteolysis of WT rPAH in the absence of Phe reveals facile cleavage within a C-terminal 4-helix bundle that is buried in the RS-PAH tetramer interface, reflecting dynamic dissociation of the RS-PAH conformation. This cleavage is not seen for the Phe80 variants, which all show proteolytic hypersensitivity in a linker that repositions during the RS-PAH to A-PAH conformational interchange. Hypersensitivity is corrected by addition of Phe such that all Phe80 variants become like WT rPAH and achieve the A-PAH conformation. Thus, manipulation of Phe80 perturbs the conformational space sampled by PAH, increasing the propensity to sample intermediates in the RS-PAH and A-PAH interchange, which are presumed on-pathway because they can readily achieve the A-PAH conformation by addition of Phe.
- Published
- 2021
11. Molecular Dynamics-Based Allosteric Prediction Method to Design Key Residues in Threonine Dehydrogenase for Amino-Acid Production
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Sun Yu, Mingyu Wu, Meiru Zhu, Junhong Lü, Laiyu Zhu, and Feng Geng
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chemistry.chemical_classification ,Mutation ,biology ,Chemistry ,General Chemical Engineering ,Allosteric regulation ,In vitro toxicology ,General Chemistry ,medicine.disease_cause ,Article ,Amino acid ,Synthetic biology ,Molecular dynamics ,Allosteric enzyme ,Biochemistry ,biology.protein ,medicine ,Isoleucine ,QD1-999 - Abstract
Allosteric proteins are considered as one of the most critical targets to design cell factories via synthetic biology approaches. Here, we proposed a molecular dynamics-based allosteric prediction method (MBAP) to screen indirect-binding sites and potential mutations for protein re-engineering. Using this MBAP method, we have predicted new sites to relieve the allosteric regulation of threonine dehydrogenase (TD) by isoleucine. An obtained mutation P441L has been verified with the ability to significantly reduce the allosteric regulation of TD in vitro assays and with the fermentation application in vivo for amino-acid production. These findings have proved the MBAP method as an effective and efficient predicting tool to find new positions of the allosteric enzymes, thus opening a new path to constructing cell factories in synthetic biology.
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- 2021
12. Protein conformational switch discerned via network centrality properties
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Tongye Shen, Bill Pham, and David Foutch
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Closeness ,Biophysics ,Biomolecular structure ,Computational biology ,Biochemistry ,03 medical and health sciences ,0302 clinical medicine ,Protein structure ,Betweenness centrality ,Conformational switch ,Structural Biology ,Genetics ,Network centrality ,ComputingMethodologies_COMPUTERGRAPHICS ,030304 developmental biology ,0303 health sciences ,biology ,Chemistry ,Protein structure network ,Computer Science Applications ,Allosteric enzyme ,Structural biology ,030220 oncology & carcinogenesis ,biology.protein ,Network analysis ,Centrality ,TP248.13-248.65 ,Research Article ,Biotechnology - Abstract
Graphical abstract, Network analysis has emerged as a powerful tool for examining structural biology systems. The spatial organization of the components of a biomolecular structure has been rendered as a graph representation and analyses have been performed to deduce the biophysical and mechanistic properties of these components. For proteins, the analysis of protein structure networks (PSNs), especially via network centrality measurements and cluster coefficients, has led to identifying amino acid residues that play key functional roles and classifying amino acid residues in general. Whether these network properties examined in various studies are sensitive to subtle (yet biologically significant) conformational changes remained to be addressed. Here, we focused on four types of network centrality properties (betweenness, closeness, degree, and eigenvector centralities) for conformational changes upon ligand binding of a sensor protein (constitutive androstane receptor) and an allosteric enzyme (ribonucleotide reductase). We found that eigenvector centrality is sensitive and can distinguish salient structural features between protein conformational states while other centrality measures, especially closeness centrality, are less sensitive and rather generic with respect to the structural specificity. We also demonstrated that an ensemble-informed, modified PSN with static edges removed (which we term PSN*) has enhanced sensitivity at discerning structural changes.
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- 2021
13. Coherent Dynamics in Networks of Single Protein Molecules
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Lerch, Hans-Philipp, Stange, Pedro, Hess, Benno, Alt, Wolfgang, editor, Deutsch, Andreas, editor, Howard, Jonathon, editor, Falcke, Martin, editor, and Zimmermann, Walter, editor
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- 2004
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14. Aparición de oscilaciones autosostenidas en una ruta metabólica hipotética regulada por un bucle de retroalimentación positiva
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Pedro Martínez, Carlos José Boluda, María Ceballos, Daniela Hernández, Kiara Díaz, and Daniela Hidalgo
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Physics ,Amplitude ,Functional importance ,Kinetic model ,Allosteric enzyme ,biology ,Periodic oscillations ,biology.protein ,General Materials Science ,Mechanics ,Kinetic energy ,Instability ,Positive feedback - Abstract
Los comportamientos oscilatorios sostenidos pueden surgir tanto en sistemas químicos como biológicos, aunque con mayor frecuencia en estos últimos. En las vías metabólicas se han observado oscilaciones con períodos del orden de minutos a las que se atribuye importancia funcional. Esta ritmicidad bioquímica puede explicarse mediante la existencia de una enzima alostérica que es considerada el origen de la inestabilidad estructural del sistema, promoviendo su evolución hacia dinámicas no estacionarias como las oscilaciones sostenidas y el caos. Este artículo presenta un modelo cinético simple de una vía metabólica hipotética lineal de cuatro etapas y que consta de un bucle de retroalimentación positiva. El modelo permite la simulación de comportamientos periódicos con el objeto de poder analizar sus factores desencadenantes y mecanismos subyacentes. Las oscilaciones surgen debido a la retroalimentación positiva para un rango estrecho de valores del flujo de entrada. La amplitud de las oscilaciones en las concentraciones de metabolitos depende de la distancia al oscilador, el valor de las constantes cinéticas y el flujo de entrada. El sistema exhibe comportamientos más complejos cuando el flujo de entrada es oscilatorio.
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- 2020
15. Metabolic Control and Metabolons in the Millennium
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Srere, Paul A., Cornish-Bowden, Athel, editor, and Cárdenas, María Luz, editor
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- 2000
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16. Allosteric regulation of CRISPR-Cas9 for DNA-targeting and cleavage
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Zhicheng Zuo and Jin Liu
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Dna targeting ,Allosteric regulation ,Computational biology ,Protein Engineering ,Cleavage (embryo) ,Article ,03 medical and health sciences ,0302 clinical medicine ,Allosteric Regulation ,Dna cleavage ,Structural Biology ,CRISPR-Associated Protein 9 ,Humans ,CRISPR ,DNA Cleavage ,Molecular Biology ,030304 developmental biology ,0303 health sciences ,biology ,Chemistry ,Extramural ,Cas9 ,DNA ,Allosteric enzyme ,biology.protein ,CRISPR-Cas Systems ,030217 neurology & neurosurgery ,RNA, Guide, Kinetoplastida - Abstract
The CRISPR-Cas9 system from Streptococcus pyogenes has been exploited as a programmable RNA-guided DNA-targeting and DNA-editing platform. This evolutionary tool enables diverse genetic manipulations with unprecedented precision and ease. Cas9 is an allosteric enzyme, which is allosterically regulated in conformational activation, target recognition, and DNA cleavage. Here, we outline the underlying allosteric control over the Cas9 complex assembly and targeting specificity. We further review the strategies for mitigating intrinsic Cas9 off-target effects through allosteric modulations and the advances in engineering controllable Cas9 systems that are responsive to external allosteric signals. Future development of highly specific, tunable CRISPR-Cas9 systems through allosteric modulations would greatly benefit applications that require both conditional control and high precision.
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- 2020
17. Impact of the Protein Data Bank on antineoplastic approvals
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R. Soskind, John D. Westbrook, Stephen K. Burley, and Brian P. Hudson
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0301 basic medicine ,Protein Conformation ,Protein Data Bank (RCSB PDB) ,Druggability ,Antineoplastic Agents ,Computational biology ,Article ,03 medical and health sciences ,0302 clinical medicine ,Drug Discovery ,Animals ,Humans ,Databases, Protein ,Melanoma ,Protein Kinase Inhibitors ,Pharmacology ,biology ,computer.file_format ,Protein Data Bank ,Small molecule ,030104 developmental biology ,Allosteric enzyme ,030220 oncology & carcinogenesis ,biology.protein ,Molecular targets ,computer - Abstract
Open access to 3D structure information from the Protein Data Bank (PDB) facilitated discovery and development of >90% of the 79 new antineoplastic agents (54 small molecules, 25 biologics) with known molecular targets approved by the FDA 2010–2018. Analyses of PDB holdings, the scientific literature and related documents for each drug–target combination revealed that the impact of public-domain 3D structure data was broad and substantial, ranging from understanding target biology (~95% of all targets) to identifying a given target as probably druggable (~95% of all targets) to structure-guided lead optimization (>70% of all small-molecule drugs). In addition to aggregate impact assessments, illustrative case studies are presented for three protein kinase inhibitors, an allosteric enzyme inhibitor and seven advanced-stage melanoma therapeutics.
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- 2020
18. Biochemical and structural insights into how amino acids regulate pyruvate kinase muscle isoform 2
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Suparno Nandi and Mishtu Dey
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0301 basic medicine ,Thyroid Hormones ,Allosteric regulation ,PKM2 ,Biochemistry ,Serine ,03 medical and health sciences ,Allosteric Regulation ,Humans ,Enzyme kinetics ,Amino Acids ,Enzyme Inhibitors ,Molecular Biology ,chemistry.chemical_classification ,030102 biochemistry & molecular biology ,biology ,Chemistry ,Membrane Proteins ,Cell Biology ,Amino acid ,030104 developmental biology ,Allosteric enzyme ,biology.protein ,Protein Multimerization ,Carrier Proteins ,Molecular Biophysics ,Allosteric Site ,Pyruvate kinase ,Protein Binding ,Cysteine - Abstract
Pyruvate kinase muscle isoform 2 (PKM2) is a key glycolytic enzyme involved in ATP generation and critical for cancer metabolism. PKM2 is expressed in many human cancers and is regulated by complex mechanisms that promote tumor growth and proliferation. Therefore, it is considered an attractive therapeutic target for modulating tumor metabolism. Various stimuli allosterically regulate PKM2 by cycling it between highly active and less active states. Several small molecules activate PKM2 by binding to its intersubunit interface. Serine and cysteine serve as an activator and inhibitor of PKM2, respectively, by binding to its amino acid (AA)-binding pocket, which therefore represents a potential druggable site. Despite binding similarly to PKM2, how cysteine and serine differentially regulate this enzyme remains elusive. Using kinetic analyses, fluorescence binding, X-ray crystallography, and gel filtration experiments with asparagine, aspartate, and valine as PKM2 ligands, we examined whether the differences in the side-chain polarity of these AAs trigger distinct allosteric responses in PKM2. We found that Asn (polar) and Asp (charged) activate PKM2 and that Val (hydrophobic) inhibits it. The results also indicate that both Asn and Asp can restore the activity of Val-inhibited PKM2. AA-bound crystal structures of PKM2 displayed distinctive interactions within the binding pocket, causing unique allosteric effects in the enzyme. These structure-function analyses of AA-mediated PKM2 regulation shed light on the chemical requirements in the development of mechanism-based small-molecule modulators targeting the AA-binding pocket of PKM2 and provide broader insights into the regulatory mechanisms of complex allosteric enzymes.
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- 2020
19. Allosteric Regulation in the Catalytic Activity of Cyclodextrin Dimer as an Artificial Hydrolase
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Ikeda, H., Nishikawa, S., Ueno, A., Toda, F., and Coleman, A. W., editor
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- 1998
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20. Enzymes
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Chesworth, J. M., Stuchbury, T., Scaife, J. R., Chesworth, J. M., Stuchbury, T., and Scaife, J. R.
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- 1998
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21. Enzymes
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Stenesh, J. and Stenesh, J.
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- 1998
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22. Kinase Activation by Small Conformational Changes
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Lucas A. Defelipe, Juan Pablo Arcon, Marcelo A. Martí, Natalie G. Ahn, Elias Daniel Lopez, Osvaldo Burastero, and Adrian Turjanski
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Protein Conformation ,General Chemical Engineering ,Molecular Dynamics Simulation ,Library and Information Sciences ,01 natural sciences ,Article ,Conserved sequence ,purl.org/becyt/ford/1 [https] ,Enzyme activator ,Protein structure ,0103 physical sciences ,polycyclic compounds ,Disulfides ,Conformation ,Phosphorylation ,purl.org/becyt/ford/1.6 [https] ,Conserved Sequence ,Mitogen-Activated Protein Kinase 1 ,010304 chemical physics ,biology ,Chemistry ,Kinase ,bioinformatics ,General Chemistry ,0104 chemical sciences ,Computer Science Applications ,Cell biology ,Enzyme Activation ,010404 medicinal & biomolecular chemistry ,kinases ,Allosteric enzyme ,biology.protein ,Signal transduction - Abstract
Protein kinases (PKs) are allosteric enzymes that play an essential role in signal transduction by regulating a variety of key cellular processes. Most PKs suffer conformational rearrangements upon phosphorylation that strongly enhance the catalytic activity. Generally, it involves the movement of the phosphorylated loop toward the active site and the rotation of the whole C-terminal lobe. However, not all kinases undergo such a large configurational change: The MAPK extracellular signal-regulated protein kinases ERK1 and ERK2 achieve a 50»000 fold increase in kinase activity with only a small motion of the C-terminal region. In the present work, we used a combination of molecular simulation tools to characterize the conformational landscape of ERK2 in the active (phosphorylated) and inactive (unphosphorylated) states in solution in agreement with NMR experiments. We show that the chemical reaction barrier is strongly dependent on ATP conformation and that the "active" low-barrier configuration is subtly regulated by phosphorylation, which stabilizes a key salt bridge between the conserved Lys52 and Glu69 belonging to helix-C and promotes binding of a second Mg ion. Our study highlights that the on-off switch embedded in the kinase fold can be regulated by small, medium, and large conformational changes. Fil: Lopez, Elias Daniel. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Biológica; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Burastero, Osvaldo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina Fil: Arcon, Juan Pablo. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Biológica; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Defelipe, Lucas Alfredo. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Biológica; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Ahn, Natalie G.. University of Colorado; Estados Unidos Fil: Marti, Marcelo Adrian. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina Fil: Turjanski, Adrian. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina
- Published
- 2019
23. Modeling Catalysis in Allosteric Enzymes: Capturing Conformational Consequences
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Heidi Klem, Martin McCullagh, and Robert S. Paton
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chemistry.chemical_classification ,Quantum chemical ,biology ,Chemistry ,Allosteric regulation ,General Chemistry ,Glycerol phosphate ,Catalysis ,Article ,Enzyme catalysis ,Molecular dynamics ,Enzyme ,Allosteric enzyme ,Computational chemistry ,biology.protein - Abstract
Greater understanding of enzymatic mechanisms aids the discovery of new targets for biologics, the development of biocatalytic transformations, and de novo enzyme design. Methods using quantum mechanical (QM) potentials, such as Density Functional Theory (DFT), have enabled complex multistep enzymatic mechanisms to be studied, often in quantitative detail. Nevertheless, the dynamic interconversion of enzyme conformations between active and inactive catalytic forms, involving length- and timescales inaccessible to QM treatments, presents a formidable challenge for the development of computational models for allosterically modulated enzymes. We present an overview of the key concepts underlying multistate models of enzyme catalysis, enzyme allostery, and the challenge that large-scale conformational changes pose for methods using QM, QM/MM, and MM potentials. Structural clustering is highlighted as a valuable approach to bridge molecular dynamics conformational sampling of MM potentials and quantum chemical cluster models of catalysis. Particularly relevant to this discussion is structural allostery, which serves as the exemplar of conformational consequences. Here, a well-characterized allosteric enzyme, Imidazole Glycerol Phosphate Synthase (IGPS), is used to showcase the importance of multiple conformations and guide a new direction for qualitative understanding and quantitative modeling in enzyme catalysis.
- Published
- 2021
24. The active site region plays a critical role in Na+ binding to thrombin
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Sarah K. Koester, Cassandra R. Kukla, Leslie A. Pelc, Zhiwei Chen, and Enrico Di Cera
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Models, Molecular ,Stereochemistry ,Protein Conformation ,serine protease ,Allosteric regulation ,Biochemistry ,protein C ,Protein structure ,enzyme kinetics ,Catalytic Domain ,Cations ,Enzyme kinetics ,Binding site ,Molecular Biology ,Binding Sites ,biology ,Chemistry ,Sodium ,Thrombin ,Active site ,Cell Biology ,Cations, Monovalent ,Transduction (biophysics) ,A-site ,Kinetics ,Allosteric enzyme ,biology.protein ,Research Article - Abstract
The catalytic activity of thrombin and other enzymes of the blood coagulation and complement cascades is enhanced significantly by binding of Na+ to a site >15 A away from the catalytic residue S195, buried within the 180- and 220- loops that also contribute to the primary specificity of the enzyme. Rapid kinetics support a binding mechanism of conformational selection where the Na+ binding site is in equilibrium between open (N) and closed (N*) forms and the cation binds selectively to the N form. Allosteric transduction of this binding step produces enhanced catalytic activity. Molecular details on how Na+ gains access to this site and communicates allosterically with the active site remain poorly defined. In this study, we show that the rate of the N ∗ → N transition is strongly correlated with the analogous E ∗ → E transition that governs the interaction of synthetic and physiologic substrates with the active site. This correlation supports the active site as the likely point of entry for Na+ to its binding site. Mutagenesis and structural data rule out an alternative path through the pore defined by the 180- and 220- loops. We suggest that the active site communicates allosterically with the Na+ site through a network of H-bonded water molecules that embeds the primary specificity pocket. Perturbation of the mobility of S195 and its H-bonding capabilities alters interaction with this network and influences the kinetics of Na+ binding and allosteric transduction. These findings may have general mechanistic relevance for Na+-activated proteases and allosteric enzymes.
- Published
- 2021
25. Enzymes
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Cox, A. Chadwick, Chan, Wai-Yee, Briggs, Thomas, editor, and Chandler, Albert M., editor
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- 1995
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26. Development of an accurate kinetic model for the central carbon metabolism of Escherichia coli.
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Nusrat Jahan, Kazuhiro Maeda, Yu Matsuoka, Yurie Sugimoto, and Hiroyuki Kurata
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ESCHERICHIA coli DNA metabolism , *CARBON metabolism , *ENZYME kinetics - Abstract
Background: A kinetic model provides insights into the dynamic response of biological systems and predicts how their complex metabolic and gene regulatory networks generate particular functions. Of many biological systems, Escherichia coli metabolic pathways have been modeled extensively at the enzymatic and genetic levels, but existing models cannot accurately reproduce experimental behaviors in a batch culture, due to the inadequate estimation of a specific cell growth rate and a large number of unmeasured parameters. Results: In this study, we developed a detailed kinetic model for the central carbon metabolism of E. coli in a batch culture, which includes the glycolytic pathway, tricarboxylic acid cycle, pentose phosphate pathway, Entner-Doudoroff pathway, anaplerotic pathway, glyoxylate shunt, oxidative phosphorylation, phosphotransferase system (Pts), non-Pts and metabolic gene regulations by four protein transcription factors: cAMP receptor, catabolite repressor/activator, pyruvate dehydrogenase complex repressor and isocitrate lyase regulator. The kinetic parameters were estimated by a constrained optimization method on a supercomputer. The model estimated a specific growth rate based on reaction kinetics and accurately reproduced the dynamics of wild-type E. coli and multiple genetic mutants in a batch culture. Conclusions: This model overcame the intrinsic limitations of existing kinetic models in a batch culture, predicted the effects of multilayer regulations (allosteric effectors and gene expression) on central carbon metabolism and proposed rationally designed fast-growing cells based on understandings of molecular processes. [ABSTRACT FROM AUTHOR]
- Published
- 2016
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27. Enzymes
- Author
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Chan, Wai-Yee, Hyde, Richard M., editor, Briggs, Thomas, editor, and Chandler, Albert M., editor
- Published
- 1992
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28. Phosphorylation and the Frequency Encoding of Signal-Induced Calcium Oscillations
- Author
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Goldbeter, Albert, Dupont, Geneviève, and Heilmeyer, Ludwig M. G., Jr., editor
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- 1991
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29. Coupled Reactions and Channelling: their Role in the Control of Metabolism
- Author
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Keleti, Tamás, Cornish-Bowden, Athel, editor, and Cárdenas, María Luz, editor
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- 1990
- Full Text
- View/download PDF
30. An overview of structure, function, and regulation of pyruvate kinases
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Norbert Schormann, Debasish Chattopadhyay, Paul Lee, Surajit Banerjee, and Katherine L. Hayden
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0303 health sciences ,biology ,Protein Conformation ,Chemistry ,Kinase ,Pyruvate Kinase ,030302 biochemistry & molecular biology ,Allosteric regulation ,Reviews ,Biochemistry ,03 medical and health sciences ,Allosteric enzyme ,biology.protein ,Humans ,Transferase ,Glycolysis ,Phosphoenolpyruvate carboxykinase ,Molecular Biology ,Flux (metabolism) ,Pyruvate kinase ,030304 developmental biology - Abstract
In the last step of glycolysis Pyruvate kinase catalyzes the irreversible conversion of ADP and phosphoenolpyruvate to ATP and pyruvic acid, both crucial for cellular metabolism. Thus pyruvate kinase plays a key role in controlling the metabolic flux and ATP production. The hallmark of the activity of different pyruvate kinases is their tight modulation by a variety of mechanisms including the use of a large number of physiological allosteric effectors in addition to their homotropic regulation by phosphoenolpyruvate. Binding of effectors signals precise and orchestrated movements in selected areas of the protein structure that alter the catalytic action of these evolutionarily conserved enzymes with remarkably conserved architecture and sequences. While the diverse nature of the allosteric effectors has been discussed in the literature, the structural basis of their regulatory effects is still not well understood because of the lack of data representing conformations in various activation states. Results of recent studies on pyruvate kinases of different families suggest that members of evolutionarily related families follow somewhat conserved allosteric strategies but evolutionarily distant members adopt different strategies. Here we review the structure and allosteric properties of pyruvate kinases of different families for which structural data are available.
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- 2019
31. Deciphering the Allosterically Driven Conformational Ensemble in Tryptophan Synthase Evolution
- Author
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Javier Iglesias-Fernández, Miguel A. Maria-Solano, and Sílvia Osuna
- Subjects
Models, Molecular ,Protein Conformation ,Allosteric regulation ,Tryptophan synthase ,Crystallography, X-Ray ,010402 general chemistry ,01 natural sciences ,Biochemistry ,Catalysis ,chemistry.chemical_compound ,Colloid and Surface Chemistry ,Allosteric Regulation ,Biosynthesis ,Catalytic Domain ,Tryptophan Synthase ,Catalytic efficiency ,chemistry.chemical_classification ,biology ,Tryptophan ,General Chemistry ,biology.organism_classification ,0104 chemical sciences ,Pyrococcus furiosus ,Enzyme ,chemistry ,Allosteric enzyme ,biology.protein ,Biophysics ,Protein Multimerization ,Function (biology) - Abstract
Multimeric enzyme complexes are ubiquitous in nature and catalyze a broad range of useful biological transformations. They are often characterized by a tight allosteric coupling between subunits, making them highly inefficient when isolated. A good example is Tryptophan synthase (TrpS), an allosteric heterodimeric enzyme in the form of an αββα complex that catalyzes the biosynthesis of L-tryptophan. In this study, we decipher the allosteric regulation existing in TrpS from Pyrococcus furiosus (PfTrpS), and how the allosteric conformational ensemble is recovered in laboratory-evolved stand-alone β-subunit variants. We find that recovering the conformational ensemble of a subdomain of TrpS affecting the relative stabilities of open, partially closed, and closed conformations is a prerequisite for enhancing the catalytic efficiency of the β-subunit in the absence of its binding partner. The distal mutations resuscitate the allosterically driven conformational regulation and alter the populations and rates of exchange between these multiple conformational states, which are essential for the multistep reaction pathway of the enzyme. Interestingly, these distal mutations can be a priori predicted by careful analysis of the conformational ensemble of the TrpS enzyme through computational methods. Our study provides the enzyme design field with a rational approach for evolving allosteric enzymes toward improved stand-alone function for biosynthetic applications.
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- 2019
32. An Allosteric Metal–Organic Framework That Exhibits Multiple Pore Configurations for the Optimization of Hydrocarbon Separation
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Yue-Biao Zhang, Zhao-Lin Shi, Beibei Zhou, Tengwu Zeng, Gen Zhang, and Satoshi Horike
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chemistry.chemical_classification ,biology ,010405 organic chemistry ,fungi ,Organic Chemistry ,Allosteric regulation ,General Chemistry ,010402 general chemistry ,01 natural sciences ,Biochemistry ,0104 chemical sciences ,Hydrocarbon ,Adsorption ,chemistry ,Allosteric enzyme ,Chemical engineering ,biology.protein ,Molecule ,Metal-organic framework ,Gas separation ,Solvent effects - Abstract
The function of allosteric enzymes can be activated or inhibited through binding of specific effector molecules. Herein, we describe how the skeletal deformation, pore configuration, and ultimately adsorptive behavior of a dynamic metal-organic framework (MOF), (Me2 NH2 )[In(atp)]2 (in which atp=2-aminoterephthalate), are controlled by the allocation and orientation of its counter ions triggered by the inclusion/removal of different guest molecules. The power of such allosteric control in MOFs is highlighted through the optimization of the hydrocarbon separation performance by achieving multiple pore configurations but without altering the chemical composition.
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- 2019
33. New views on an old enzyme: allosteric regulation and evolution of archaeal pyruvate kinases
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Fernando D. K. Tria, Giddy Landan, Andreas Reinhardt, Christopher Davies, Ulrike Johnsen, Jonathan M. Turner, and Peter Schönheit
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0301 basic medicine ,Archaeal Proteins ,Pyruvate Kinase ,Allosteric regulation ,Biochemistry ,Evolution, Molecular ,03 medical and health sciences ,0302 clinical medicine ,Allosteric Regulation ,Methanococcales ,Crenarchaeota ,polycyclic compounds ,Molecular Biology ,Phylogeny ,chemistry.chemical_classification ,Thermoproteus ,Sugar phosphates ,biology ,Chemistry ,Cell Biology ,biology.organism_classification ,Thermoproteales ,030104 developmental biology ,Allosteric enzyme ,030220 oncology & carcinogenesis ,biology.protein ,Allosteric Site ,Pyruvate kinase ,Archaea - Abstract
Pyruvate kinases (PKs) synthesize ATP as the final step of glycolysis in the three domains of life. PKs from most bacteria and eukarya are allosteric enzymes that are activated by sugar phosphates; for example, the feed-forward regulator fructose-1,6-bisphosphate, or AMP as a sensor of energy charge. Archaea utilize unusual glycolytic pathways, but the allosteric properties of PKs from these species are largely unknown. Here, we present an analysis of 24 PKs from most archaeal clades with respect to allosteric properties, together with phylogenetic analyses constructed using a novel mode of rooting protein trees. We find that PKs from many Thermoproteales, an order of crenarchaeota, are allosterically activated by 3-phosphoglycerate (3PG). We also identify five conserved amino acids that form the binding pocket for 3PG. 3PG is generated via an irreversible reaction in the modified glycolytic pathway of these archaea and therefore functions as a feed-forward regulator. We also show that PKs from hyperthermophilic Methanococcales, an order of euryarchaeota, are activated by AMP. Phylogenetic analyses indicate that 3PG-activated PKs form an evolutionary lineage that is distinct from that of sugar-phosphate activated PKs, and that sugar phosphate-activated PKs originated as AMP-regulated PKs in hyperthermophilic Methanococcales. Since the phospho group of sugar phosphates and 3PG overlap in the allosteric site, our data indicate that the allostery in PKs first started from a progenitor phosphate-binding site that evolved in two spatially distinct directions: one direction generated the canonical site that responds to sugar phosphates and the other gave rise to the 3PG site present in Thermoproteales. Overall, our data suggest an intimate connection between the allosteric properties and evolution of PKs.
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- 2019
34. Amperometric Detection of the Urinary Disease Biomarker p-HPA by Allosteric Modulation of a Redox Polymer-Embedded Bacterial Reductase
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Panida Khunkaewla, Somjai Teanphonkrang, Jeerus Sucharitakul, Adrian Ruff, Wipa Suginta, Wolfgang Schuhmann, Salome Janke, Pimchai Chaiyen, Andrzej Ernst, and Albert Schulte
- Subjects
Analyte ,Allosteric regulation ,Bioengineering ,Biosensing Techniques ,02 engineering and technology ,01 natural sciences ,Redox ,Enzyme activator ,Allosteric Regulation ,Electrochemistry ,Humans ,Instrumentation ,Phenylacetates ,Fluid Flow and Transfer Processes ,Bacteria ,biology ,Chemistry ,Process Chemistry and Technology ,010401 analytical chemistry ,Substrate (chemistry) ,Enzymes, Immobilized ,021001 nanoscience & nanotechnology ,Ascorbic acid ,Combinatorial chemistry ,0104 chemical sciences ,Allosteric enzyme ,biology.protein ,Oxidoreductases ,0210 nano-technology ,Oxidation-Reduction ,Biosensor ,Biomarkers - Abstract
We report an amperometric biosensor for the urinary disease biomarker para-hydroxyphenylacetate ( p-HPA) in which the allosteric reductase component of a bacterial hydroxylase, C1-hpah, is electrically wired to glassy carbon electrodes through incorporation into a low-potential Os-complex modified redox polymer. The proposed biosensing strategy depends on allosteric modulation of C1-hpah by the binding of the enzyme activator and analyte p-HPA, stimulating oxidation of the cofactor NADH. The pronounced concentration-dependence of allosteric C1-hpah modulation in the presence of a constant concentration of NADH allowed sensitive quantification of the target, p-HPA. The specific design of the immobilizing redox polymer with suitably low working potential allowed biosensor operation without the risk of co-oxidation of potentially interfering substances, such as uric acid or ascorbic acid. Optimized sensors were successfully applied for p-HPA determination in artificial urine, with good recovery rates and reproducibility and sub-micromolar detection limits. The proposed application of the allosteric enzyme C1-hpah for p-HPA trace electroanalysis is the first successful example of simple amperometric redox enzyme/redox polymer biosensing in which the analyte acts as an effector, modulating the activity of an immobilized biocatalyst. A general advantage of the concept of allosterically modulated biosensing is its ability to broaden the range of approachable analytes, through the move from substrate to effector detection.
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- 2019
35. CASBench: A Benchmarking Set of Proteins with Annotated Catalytic and Allosteric Sites in Their Structures
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V. К. Švedas, K. Е. Kopylov, Alexander Zlobin, and D. А. Suplatov
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web server ,Protein family ,Computer science ,Allosteric regulation ,Computational biology ,Biochemistry ,Set (abstract data type) ,protein function and regulation ,Protein structure ,ligand binding sites ,benchmarking set ,Molecular Biology ,biology ,bioinformatics ,computer.file_format ,catalytic site ,Protein Data Bank ,structure-function relationship ,Allosteric enzyme ,Benchmark (computing) ,biology.protein ,Molecular Medicine ,allosteric site ,computer ,Function (biology) ,Research Article ,Biotechnology - Abstract
In recent years, the phenomenon of allostery has witnessed growing attention driven by a fundamental interest in new ways to regulate the functional properties of proteins, as well as the prospects of using allosteric sites as targets to design novel drugs with lower toxicity due to a higher selectivity of binding and specificity of the mechanism of action. The currently available bioinformatic methods can sometimes correctly detect previously unknown ligand binding sites in protein structures. However, the development of universal and more efficient approaches requires a deeper understanding of the common and distinctive features of the structural organization of both functional (catalytic) and allosteric sites, the evolution of their amino acid sequences in respective protein families, and allosteric communication pathways. The CASBench benchmark set contains 91 entries related to enzymes with both catalytic and allosteric sites within their structures annotated based on the experimental information from the Allosteric Database, Catalytic Site Atlas, and Protein Data Bank. The obtained dataset can be used to benchmark the performance of existing computational approaches and develop/train perspective algorithms to search for new catalytic and regulatory sites, as well as to study the mechanisms of protein regulation on a large collection of allosteric enzymes. Establishing a relationship between the structure, function, and regulation is expected to improve our understanding of the mechanisms of action of enzymes and open up new prospects for discovering new drugs and designing more efficient biocatalysts. The CASBench can be operated offline on a local computer or online using built-in interactive tools at https://biokinet.belozersky.msu.ru/casbench.
- Published
- 2019
36. Robust Determination of Protein Allosteric Signaling Pathways
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Yun Luo and Wesley M. Botello-Smith
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Protein Conformation ,Computer science ,Dimer ,Allosteric regulation ,Saccharomyces cerevisiae ,Molecular Dynamics Simulation ,Ligands ,Topology ,Network topology ,01 natural sciences ,law.invention ,chemistry.chemical_compound ,Molecular dynamics ,Protein structure ,Allosteric Regulation ,Betweenness centrality ,Aminohydrolases ,law ,0103 physical sciences ,Thermotoga maritima ,Physical and Theoretical Chemistry ,chemistry.chemical_classification ,Quantitative Biology::Biomolecules ,010304 chemical physics ,biology ,Protein dynamics ,Ligand (biochemistry) ,Amino acid ,Weighting ,Computer Science Applications ,chemistry ,Allosteric enzyme ,Electrical network ,biology.protein ,Signal transduction ,Biological system ,Protein Binding ,Signal Transduction - Abstract
To understand how protein function changes upon an allosteric perturbation, such as ligand binding and mutation, significant progress in characterizing allosteric network from molecular dynamics (MD) simulations has been made. However, determining which amino acid(s) play an essential role in the propagation of signals may prove challenging, even when the location of the source and sink is known for a protein or protein complex. This challenge is mainly due to the large fluctuations in protein dynamics that cause instability of the network topology within a single trajectory or between multiple replicas. To solve this problem, we introduce the current-flow betweenness scheme, originated from electrical network theory, to protein dynamical network analysis. To demonstrate the benefit of this new method, we chose a prototypic allosteric enzyme (IGPS or HisH-HisF dimer) as our benchmark system. Using multiple replicas of simulations and multiple network topology comparison metrics (edge ranking, path length, and node frequency), we show that the current-flow betweenness provides a significant improvement in the convergence of the allosteric networks. The improved stability of the network topology allows us to generate a delta-network between the apo and holo forms of the protein. We illustrated that the delta-network is a more rigorous way to capture the subtle changes in the networks that would otherwise be neglected by comparing node usage frequencies alone. We have also investigated the use of a linear smoothing function to improve the stability of the contact map. The methodology presented here is general and may be applied to other topology and weighting schemes. We thus conclude that, for determining protein signaling pathways between the pair(s) of source and sink, multiple MD simulation replicas are necessary and the current-flow betweenness scheme introduced here provides a more robust approach than the geodesic scheme based on correlation edge weighting.For Table of Contents Only
- Published
- 2019
37. Biochemical, structural and dynamical studies reveal strong differences in the thermal-dependent allosteric behavior of two extremophilic lactate dehydrogenases
- Author
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Dominique Madern, Sylvain Engilberge, Eric Girard, Fabio Sterpone, Antonio Iorio, Nicolas Coquelle, Jennifer Roche, Laboratoire de biochimie théorique [Paris] (LBT (UPR_9080)), Institut de biologie physico-chimique (IBPC (FR_550)), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Institut de biologie structurale (IBS - UMR 5075), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)-Institut de biologie physico-chimique (IBPC (FR_550)), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), and ANR-16-CE11-0011,AlloAnc,Allostérie Ancestrale(2016)
- Subjects
Allosteric regulation ,Molecular dynamics ,010402 general chemistry ,Hyperthermophilic ,01 natural sciences ,03 medical and health sciences ,chemistry.chemical_compound ,Extremophiles ,Allosteric Regulation ,Structural Biology ,Lactate dehydrogenase ,Quaternary structure ,Lactate Dehydrogenases ,ComputingMilieux_MISCELLANEOUS ,030304 developmental biology ,chemistry.chemical_classification ,0303 health sciences ,biology ,[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM] ,L-Lactate Dehydrogenase ,Chemistry ,Thermophile ,Thermus thermophilus ,biology.organism_classification ,0104 chemical sciences ,Enzyme ,Allosteric enzyme ,Biophysics ,biology.protein ,Conformational landscape ,Protein quaternary structure - Abstract
International audience; In this work, we combined biochemical and structural investigations with molecular dynamics (MD) simulations to analyze the very different thermal-dependent allosteric behavior of two lactate dehydrogenases (LDH) from thermophilic bacteria. We found that the enzyme from Petrotoga mobilis (P. mob) necessitates an absolute requirement of the allosteric effector (fructose 1, 6-bisphosphate) to ensure functionality. In contrast, even without allosteric effector, the LDH from Thermus thermophilus (T. the) is functional when the temperature is raised. We report the crystal structure of P. mob LDH in the Apo state solved at 1.9 Å resolution. We used this structure and the one from T. the, obtained previously, as a starting point for MD simulations at various temperatures. We found clear differences between the thermal dynamics, which accounts for the behavior of the two enzymes. Our work demonstrates that, within an allosteric enzyme, some areas act as local gatekeepers of signal transmission, allowing the enzyme to populate either the T-inactive or the R-active states with different degrees of stringency.
- Published
- 2021
38. Community Network Analysis of Allosteric Proteins
- Author
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Ivan Rivalta, Victor S. Batista, Rivalta I., and Batista V.S.
- Subjects
chemistry.chemical_classification ,0303 health sciences ,biology ,Community network ,Computer science ,030302 biochemistry & molecular biology ,Allosteric regulation ,Protein graph ,Computational biology ,Mutual information ,Complex network ,Allosteric enzyme ,Amino acid ,Community network analysi ,Allosteric pathway ,03 medical and health sciences ,Molecular dynamics ,chemistry ,biology.protein ,Protein correlated motion ,Amino acid residue ,030304 developmental biology - Abstract
Community network analysis (CNA) of correlated protein motions allows modeling of signals propagation in allosteric proteic systems. From standard classical molecular dynamics (MD) simulations, protein motions can be analysed by means of mutual information between pairs of amino acid residues, providing dynamical weighted networks that contains fundamental information of the communication among amino acids. The CNA method has been successfully applied to a variety of allosteric systems including an enzyme, a nuclear receptor and a bacterial adaptive immune system, providing characterization of the allosteric pathways. This method is complementary to network analyses based on different metrics and it is particularly powerful for studying large proteic systems, as it provides a coarse-grained view of the communication flows within large and complex networks.
- Published
- 2021
39. BIOJUTIKLIO SU ALOSTERINIO FERMENTO SLUOKSNIU KOMPIUTERINIS MODELIAVIMAS.
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Ričkus, Liutauras and Baronas, Romas
- Abstract
Copyright of Information Sciences / Informacijos Mokslai is the property of Vilnius University and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
- Published
- 2015
40. Nucleotide-dependent structural fluctuations and regulation of microtubule-binding affinity of KIF1A.
- Author
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Kanada, Ryo, Takagi, Fumiko, and Kikuchi, Macoto
- Abstract
ABSTRACT Molecular motors such as kinesin regulate affinity to a rail protein during the ATP hydrolysis cycle. The regulation mechanism, however, is yet to be determined. To understand this mechanism, we investigated the structural fluctuations of the motor head of the single-headed kinesin called KIF1A in different nucleotide states using molecular dynamics simulations of a Gō-like model. We found that the helix [ABSTRACT FROM AUTHOR]
- Published
- 2015
- Full Text
- View/download PDF
41. A Novel Polyamine Allosteric Site of SpeG from Vibrio cholerae Is Revealed by Its Dodecameric Structure.
- Author
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Filippova, Ekaterina V., Kuhn, Misty L., Osipiuk, Jerzy, Kiryukhina, Olga, Joachimiak, Andrzej, Ballicora, Miguel A., and Anderson, Wayne F.
- Subjects
- *
POLYAMINES , *ALLOSTERIC regulation , *VIBRIO cholerae , *SPERMIDINE , *SPERMIDINE acetyltransferase , *BACTERIAL enzymes , *PHYSIOLOGICAL stress - Abstract
Spermidine N -acetyltransferase, encoded by the gene speG , catalyzes the initial step in the degradation of polyamines and is a critical enzyme for determining the polyamine concentrations in bacteria. In Escherichia coli , studies have shown that SpeG is the enzyme responsible for acetylating spermidine under stress conditions and for preventing spermidine toxicity. Not all bacteria contain speG , and many bacterial pathogens have developed strategies to either acquire or silence it for pathogenesis. Here, we present thorough kinetic analyses combined with structural characterization of the VCA0947 SpeG enzyme from the important human pathogen Vibrio cholerae . Our studies revealed the unexpected presence of a previously unknown allosteric site and an unusual dodecameric structure for a member of the Gcn5-related N -acetyltransferase superfamily. We show that SpeG forms dodecamers in solution and in crystals and describe its three-dimensional structure in several ligand-free and liganded structures. Importantly, these structural data define the first view of a polyamine bound in an allosteric site of an N -acetyltransferase. Kinetic characterization of SpeG from V . cholerae showed that it acetylates spermidine and spermine. The behavior of this enzyme is complex and exhibits sigmoidal curves and substrate inhibition. We performed a detailed non-linear regression kinetic analysis to simultaneously fit families of substrate saturation curves to uncover a simple kinetic mechanism that explains the apparent complexity of this enzyme. Our results provide a fundamental understanding of the bacterial SpeG enzyme, which will be key toward understanding the regulation of polyamine levels in bacteria during pathogenesis. [ABSTRACT FROM AUTHOR]
- Published
- 2015
- Full Text
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42. Comparison of Plant-Type Phosphoenolpyruvate Carboxylases from Rice: Identification of Two Plant-Specific Regulatory Regions of the Allosteric Enzyme.
- Author
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Masayuki Muramatsu, Rintaro Suzuki, Toshimasa Yamazaki, and Mitsue Miyao
- Subjects
- *
CARBOXYLASES , *ALLOSTERIC enzymes , *RICE , *VASCULAR plants , *PLANT metabolism , *ALLOSTERIC regulation , *CHLOROPLASTS , *PHYSIOLOGY - Abstract
Phosphoenolpyruvate carboxylase (PEPC) is a key enzyme of primary metabolism in bacteria, algae and vascular plants, and it undergoes allosteric regulation by various metabolic effectors. Rice (Oryza sativa) has five plant-type PEPCs, four cytosolic and one chloroplastic. We investigated their kinetic properties using recombinant proteins and found that, like most plant-type PEPCs, rice cytosolic isozymes were activated by glucose 6-phosphate and by alkaline pH. In contrast, no such activation was observed for the chloroplastic isozyme, Osppc4. In addition, Osppc4 showed low affinity for the substrate phosphoenolpyruvate (PEP) and very low sensitivities to allosteric inhibitors aspartate and glutamate. By comparing the isozyme amino acid sequences and three-dimensional structures simulated on the basis of the reported crystal structures, we identified two regions where Osppc4 has unique features that can be expected to affect its kinetic properties. One is the N-terminal extension; replacement of the extension of Osppc2a (cytosolic) with that from Osppc4 reduced the aspartate and glutamate sensitivities to about one-tenth of the wild-type values but left the PEP affinity unaffected. The other is the N-terminal loop, in which a conserved lysine at the N-terminal end is replaced with a glutamate-alanine pair in Osppc4. Replacement of the lysine of Osppc2a with glutamate- alanine lowered the PEP affinity to a quarter of the wildtype level (down to the Osppc4 level), without affecting inhibitor sensitivity. Both the N-terminal extension and the N-terminal loop are specific to plant-type PEPCs, suggesting that plant-type isozymes acquired these regions so that their activity could be regulated properly at the sites where they function. [ABSTRACT FROM AUTHOR]
- Published
- 2015
- Full Text
- View/download PDF
43. Biosensors Utilizing Non-Michaelis–Menten Kinetics
- Author
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Juozas Kulys, Feliksas Ivanauskas, and Romas Baronas
- Subjects
biology ,Chemistry ,Diffusion ,Substrate (chemistry) ,Thermodynamics ,Michaelis–Menten kinetics ,Diffusion layer ,symbols.namesake ,Allosteric enzyme ,biology.protein ,symbols ,Nernst equation ,Enzyme kinetics ,Steady state (chemistry) - Abstract
The action of biosensors utilizing non-Michaelis–Menten kinetics is modeled at mixed enzyme kinetics and diffusion limitation in the cases of substrate and reaction product inhibition as well as of allostery at steady state and transient conditions. Computational modeling of the substrate inhibition at steady state shows multi-steady state concentrations of the substrate at the surface of the enzyme layer (membrane) when the diffusion module is much larger than one and the substrate bulk concentration is much higher than Michaelis–Menten constant. The multi-steady state concentration generates multi-response of the biosensor. At transient conditions, analytical systems are modeled by a two-compartment model comprising a mono-enzyme layer and an external Nernst diffusion layer. The complex enzyme kinetics produces different calibration curves for the response at the transition and the steady state. The cooperative phenomena of allosteric enzymes are modeled by applying the substrate uptake and the Hill equations. The positive cooperativity leads to a steady state current less than that when the biosensor action obeys the Michaelis–Menten kinetics, while negative cooperativity leads to increasing the biosensor response. The substrate concentration, at which the saturation curves of allosteric biosensors intersect, increases with increasing the external diffusion limitation.
- Published
- 2020
44. MnSOD functions as a thermoreceptor activated by low temperature.
- Author
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Zhang, Xu, Zhang, Depei, Xiang, Li, and Wang, Qiying
- Subjects
- *
LOW temperatures , *ALLOSTERIC enzymes , *SUPEROXIDE dismutase , *MANGANESE , *HIGH temperatures , *PHYSIOLOGICAL effects of cold temperatures - Abstract
A conservative characteristic of manganese superoxide dismutase is the rapid formation of product inhibition at high temperatures. At lower temperatures, the enzyme is less inhibited and undergoes more catalytic fast cycles before being product-inhibited. The temperature-dependent kinetics could be rationalized by the temperature-dependent coordination in the conserved center of manganese superoxide dismutase. As temperature decreases, a water molecule (WAT2) approaches or even coordinates Mn as the sixth ligand to interfere with O 2 •--Mn coordination and reduce product inhibition, so the dismutation should mainly proceed in the fast outer-sphere pathway at low temperatures. Cold-activation is an adaptive response to low temperature rather than a passive adaptation to excess superoxide levels since the cold-activated dismutase activity significantly exceeds the amount of superoxide in the cell or mitochondria. Physiologically speaking, cold activation of manganese superoxide dismutase mediates cold stress signaling and transduces temperature (physical signal) degree into H 2 O 2 fluxes (chemical signal), which in turn may act as a second messenger to induce a series of physiological responses such as cold shock. Manganese superoxide dismutase acts as a cold-activated allosteric enzyme. Lower temperatures induce the equilibrium to predominately WAT2-adduct six-coordination center, which is logically an activated conformation of the enzyme since there is no open position on Mn for O 2 •− to coordinate and form product inhibition. [Display omitted] • Low-temperature induce manganese superoxide dismutase into the fast cycle pathway to catalyze superoxide dismutation. • Low-temperature induces a water molecule coordinating Mn ion at the enzyme center to keep the enzyme in its active conformation. • Manganese superoxide dismutase is activated by cold which is an adaptive response to cold and leads to more H 2 O 2 production. • Manganese superoxide dismutase regulates the O 2 •−/H 2 O 2 homeostasis which unbalance will induce cellular heat or cold shock. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
45. Engineering the allosteric properties of archaeal non-phosphorylating glyceraldehyde-3-phosphate dehydrogenases.
- Author
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Ito, Fumiaki, Miyake, Masayuki, Fushinobu, Shinya, Nakamura, Shugo, Shimizu, Kentaro, and Wakagi, Takayoshi
- Subjects
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GLYCERALDEHYDEPHOSPHATE dehydrogenase , *ALLOSTERIC regulation , *PHOSPHORYLATION , *SULFOLOBUS solfataricus , *CHIMERISM , *BIOCHEMICAL substrates , *TETRAMERS (Oligomers) - Abstract
Abstract: The archaeal non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN, EC 1.2.1.9) is a highly allosteric enzyme activated by glucose 1-phosphate (Glc1P). Recent kinetic analyses of two GAPN homologs from Sulfolobales show different allosteric behaviors toward the substrate glyceraldehyde-3-phosphate (GAP) and the allosteric effector Glc1P. In GAPN from Sulfolobus tokodaii (Sto-GAPN), Glc1P-induced activation follows an increase in affinity for GAP rather than an increase in maximum velocity, whereas in GAPN from Sulfolobus solfataricus (Sso-GAPN), Glc1P-induced activation follows an increase in maximum velocity rather than in affinity for GAP. To explore the molecular basis of this difference between Sto-GAPN and Sso-GAPN, we generated 14 mutants and 2 chimeras. The analyses of chimeric GAPNs generated from regions of Sto-GAPN and Sso-GAPN indicated that a 57-residue module located in the subunit interface was clearly involved in their allosteric behavior. Among the point mutations in this modular region, the Y139R variant of Sto-GAPN no longer displayed a sigmoidal K-type-like allostery, but instead had apparent V-type allostery similar to that of Sso-GAPN, suggesting that the residue located in the center of the homotetramer critically contributes to the allosteric behavior. [Copyright &y& Elsevier]
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- 2014
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46. Remarkable Improvement of Methylglyoxal Synthase Thermostability by His-His Interaction.
- Author
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Mohammadi, Malihe, Kashi, Mona, Zareian, Shekufeh, Mirshahi, Manoochehr, and Khajeh, Khosro
- Abstract
Lately it has been proposed that interaction between two positively charged side chains can stabilize the folded state of proteins. To further explore this point, we studied the effect of histidine-histidine interactions on thermostability of methylglyoxal synthase from Thermus sp. GH5 (TMGS). The crystal structure of TMGS revealed that His23, Arg22, and Phe19 are in close distance and form a surface loop. Here, two modified enzymes were produced by site-directed mutagenesis (SDM); one of them, one histidine (TMGS-HH), and another two histidines (TMGS-HHH) were inserted between Arg22 and His23 (H). In comparison with the wild type, TMGS-HH thermostability increased remarkably, whereas TMGS-HHH was very unstable. To explore the role of His23 in the observed phenomenon, the original His23 in TMGS-HHH was replaced with Ala (TMGS-HHA). Our data showed that the half-life of TMGS-HHA decreased in relation to the wild type. However, its half-life increased in comparison with TMGS-HHH. These results demonstrated that histidine-histidine interactions at position 23 in TMGS-HH probably have the main role in TMGS thermostability. [ABSTRACT FROM AUTHOR]
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- 2014
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47. Control of allosteric electrochemical protein switch using magnetic signals
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Evgeny Katz, Selvakumar Edwardraja, Paolo Bollella, Zhong Guo, and Kirill Alexandrov
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Oxidoreductases Acting on CH-CH Group Donors ,Bioelectric Energy Sources ,Recombinant Fusion Proteins ,Cell ,Allosteric regulation ,Glucose Dehydrogenases ,Peptide ,02 engineering and technology ,010402 general chemistry ,7. Clean energy ,01 natural sciences ,Signal ,Catalysis ,Allosteric Regulation ,Calmodulin ,Glucose dehydrogenase ,Materials Chemistry ,medicine ,Magnetite Nanoparticles ,Electrodes ,chemistry.chemical_classification ,biology ,Chemistry ,Nanotubes, Carbon ,Metals and Alloys ,Alanine Transaminase ,General Chemistry ,Electrochemical Techniques ,021001 nanoscience & nanotechnology ,Ligand (biochemistry) ,Enzymes, Immobilized ,0104 chemical sciences ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials ,medicine.anatomical_structure ,Glucose ,Magnetic Fields ,Allosteric enzyme ,Cascade ,Ceramics and Composites ,biology.protein ,Biophysics ,Calmodulin-Binding Proteins ,Amino Acid Oxidoreductases ,0210 nano-technology - Abstract
We report a novel approach for magneto-controlled activation of an artificial electro-enzymatic cascade. The input signal triggers release of a caged ligand peptide, its proteolytic processing and activation of an artificial allosteric enzyme based on PQQ-dependent glucose dehydrogenase. The developed cascade was used to assemble a magneto-controlled biofuel cell.
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- 2020
48. A shared alarmone-GTP switch underlies triggered and spontaneous persistence
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Jue D. Wang, Jessica T Barra, Jeremy W. Schroeder, David Ying, and Danny Ka Chun Fung
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biology ,GTP' ,Chemistry ,Cell ,Wild type ,biology.organism_classification ,Cell biology ,Cell wall ,medicine.anatomical_structure ,Allosteric enzyme ,biology.protein ,medicine ,Pathogen ,Bacteria ,Alarmone - Abstract
SummaryPhenotypically-switched, antibiotic-refractory persisters may prevent pathogen eradication. Although how triggered persistence via starvation-induced (p)ppGpp is well characterized, generation of persisters without starvation are poorly understood. Here we visualized the formation of spontaneous persisters in a small fraction of cells from growing wild type bacteria, revealing a striking single cell rapid switch from growth to dormancy. This switch-like entrance is triggered by GTP dropping beneath a threshold due to stochastic production and self-amplification of (p)ppGpp via allosteric enzyme activation. In addition, persisters are induced by lethal and sublethal concentrations of cell wall antibiotics by inducing (p)ppGpp via cell wall stress response. Thus spontaneous, triggered and antibiotic-induced persisters can all stem from a common metabolic switch: GTP depletion by (p)ppGpp induction, and each pathway of persister formation is activated by different (p)ppGpp synthetases. These persistence pathways are likely conserved in pathogens which may be exploited to potentiate antibiotic efficacy.
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- 2020
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49. A Peptidomimetic Fluorescent Probe to Detect the Trypsin β2 Subunit of the Human 20S Proteasome
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Natalia Gruba, Magdalena Wysocka, Adam Lesner, Artur Giełdoń, Anita Romanowska, and Michalina Michalska
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0301 basic medicine ,Models, Molecular ,Proteasome Endopeptidase Complex ,Peptidomimetic ,Chemical synthesis ,Catalysis ,Article ,Substrate Specificity ,lcsh:Chemistry ,Inorganic Chemistry ,03 medical and health sciences ,0302 clinical medicine ,fluorogenic substrates ,libraries ,medicine ,Humans ,Nuclear Receptor Co-Repressor 1 ,Trypsin ,ortho-Aminobenzoates ,Enzyme kinetics ,Physical and Theoretical Chemistry ,lcsh:QH301-705.5 ,Molecular Biology ,Spectroscopy ,Fluorescent Dyes ,chemistry.chemical_classification ,biology ,Organic Chemistry ,Substrate (chemistry) ,General Medicine ,Computer Science Applications ,Kinetics ,030104 developmental biology ,Enzyme ,proteasome ,lcsh:Biology (General) ,lcsh:QD1-999 ,Allosteric enzyme ,chemistry ,Biochemistry ,Proteasome ,Urinary Bladder Neoplasms ,030220 oncology & carcinogenesis ,peptidomimetics ,biology.protein ,bladder cancer ,medicine.drug - Abstract
This work describes the chemical synthesis, combinatorial selection, and enzymatic evaluation of peptidomimetic fluorescent substrates specific for the trypsin-like (&beta, 2) subunit of the 20S human proteasome. After deconvolution of a library comprising nearly 6000 compounds composed of peg substituted diaminopropionic acid DAPEG building blocks, the sequence ABZ&ndash, Dap(O2(Cbz))&ndash, Dap(GO1)&ndash, Arg&ndash, ANB&ndash, NH2, where ABZ is 2-aminobenzoic acid, and ANB- 5 amino 2- nitro benzoic acid was selected. Its cleavage followed sigmoidal kinetics, characteristic for allosteric enzymes, with Km = 3.22 ±, 0.02 &mu, M, kcat = 245 s&minus, 1, and kcat/Km = 7.61 ×, 107 M&minus, 1 s&minus, 1. This process was practically halted when a selective inhibitor of the &beta, 2 subunit of the 20S human proteasome was supplemented to the reaction system. Titration of the substrate resulting in decreased amounts of proteasome 20S produced a linear signal up to 10&minus, 11 M. Using this substrate, we detected human proteasome 20S in human urine samples taken from the bladders of cancer patients. This observation could be useful for the noninvasive diagnosis of this severe disease.
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- 2020
50. The endocannabinoid hydrolase FAAH is an allosteric enzyme
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Beatrice Dufrusine, Sergio Oddi, Gianni De Fabritiis, Filomena Fezza, Mauro Maccarrone, Monica Simonetti, Annalaura Sabatucci, Clotilde B. Angelucci, Enrico Dainese, and Alice Ballone
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Allosteric regulation ,Mutant ,lcsh:Medicine ,Article ,03 medical and health sciences ,0302 clinical medicine ,Fatty acid amide hydrolase ,Hydrolase ,Settore BIO/10 ,lcsh:Science ,030304 developmental biology ,chemistry.chemical_classification ,0303 health sciences ,Multidisciplinary ,biology ,Chemistry ,lcsh:R ,Biological activity ,Endocannabinoid system ,Enzymes ,Enzyme ,Biochemistry ,Allosteric enzyme ,nervous system ,Enzyme mechanisms ,biology.protein ,lcsh:Q ,lipids (amino acids, peptides, and proteins) ,030217 neurology & neurosurgery ,psychological phenomena and processes - Abstract
Fatty acid amide hydrolase (FAAH) is a membrane-bound homodimeric enzyme that in vivo controls content and biological activity of N-arachidonoylethanolamine (AEA) and other relevant bioactive lipids termed endocannabinoids. Parallel orientation of FAAH monomers likely allows both subunits to simultaneously recruit and cleave substrates. Here, we show full inhibition of human and rat FAAH by means of enzyme inhibitors used at a homodimer:inhibitor stoichiometric ratio of 1:1, implying that occupation of only one of the two active sites of FAAH is enough to fully block catalysis. Single W445Y substitution in rat FAAH displayed the same activity as the wild-type, but failed to show full inhibition at the homodimer:inhibitor 1:1 ratio. Instead, F432A mutant exhibited reduced specific activity but was fully inhibited at the homodimer:inhibitor 1:1 ratio. Kinetic analysis of AEA hydrolysis by rat FAAH and its F432A mutant demonstrated a Hill coefficient of ~1.6, that instead was ~1.0 in the W445Y mutant. Of note, also human FAAH catalysed an allosteric hydrolysis of AEA, showing a Hill coefficient of ~1.9. Taken together, this study demonstrates an unprecedented allosterism of FAAH, and represents a case of communication between two enzyme subunits seemingly controlled by a single amino acid (W445) at the dimer interface. In the light of extensive attempts and subsequent failures over the last decade to develop effective drugs for human therapy, these findings pave the way to the rationale design of new molecules that, by acting as positive or negative heterotropic effectors of FAAH, may control more efficiently its activity. This work was supported by the BioStruct X-BAG project “A new player in the modulation of protein function: the biological membranes” under the EU Framework Programme grant agreement n. 283570) to E.D. and M.M., by the Italian Ministry of Health (IZS LT 14/11 RC project) to E.D., and by the Italian Ministry of Education, University and Research (competitive PRIN 2015 project) to M.M. and S.O.
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- 2020
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