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Martin TA, Fenton AW. Divalent cations in human liver pyruvate kinase exemplify the combined effects of complex-equilibrium and allosteric regulation. Sci Rep 2023; 13:10557. [PMID: 37386072 PMCID: PMC10310847 DOI: 10.1038/s41598-023-36943-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/13/2023] [Indexed: 07/01/2023] Open
Abstract
There is growing recognition that the functional outcome of binding of an allosteric regulator to a protein/enzyme is influenced by the presence of other ligands. Here, this complexity is exemplified in the allosteric regulation of human liver pyruvate kinase (hLPYK) that is influenced by the presence of a range of divalent cation types and concentrations. For this system, fructose-1,6-bisphosphate (activator) and alanine (inhibitor) both influence the protein's affinity for the substrate, phosphoenolpyruvate (PEP). Mg2+, Mn2+, Ni2+, and Co2+ were the primary divalent cations evaluated, although Zn2+, Cd2+, V2+, Pb2+, Fe2+, and Cu2+also supported activity. Allosteric coupling between Fru-1,6-BP and PEP and between Ala and PEP varied depending on divalent cation type and concentration. Due to complicating interactions among small molecules, we did not attempt the fitting of response trends and instead we discuss a range of potential mechanisms that may explain those observed trends. Specifically, observed "substrate inhibition" may result from substrate A in one active site acting as an allosteric regulator for the affinity for substrate B in a second active site of a multimer. We also discuss apparent changes in allosteric coupling that can result from a sub-saturating concentration of a third allosteric ligand.
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Affiliation(s)
- Tyler A Martin
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, MS 3030, 3901 Rainbow Boulevard, Kansas City, KS, 66160, USA
| | - Aron W Fenton
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, MS 3030, 3901 Rainbow Boulevard, Kansas City, KS, 66160, USA.
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Battisti UM, Gao C, Nilsson O, Akladios F, Lulla A, Bogucka A, Nain-Perez A, Håversen L, Kim W, Boren J, Hyvönen M, Uhlen M, Mardinoglu A, Grøtli M. Serendipitous Identification of a Covalent Activator of Liver Pyruvate Kinase. Chembiochem 2023; 24:e202200339. [PMID: 36250581 PMCID: PMC10099687 DOI: 10.1002/cbic.202200339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 10/14/2022] [Indexed: 01/05/2023]
Abstract
Enzymes are effective biological catalysts that accelerate almost all metabolic reactions in living organisms. Synthetic modulators of enzymes are useful tools for the study of enzymatic reactions and can provide starting points for the design of new drugs. Here, we report on the discovery of a class of biologically active compounds that covalently modifies lysine residues in human liver pyruvate kinase (PKL), leading to allosteric activation of the enzyme (EC50 =0.29 μM). Surprisingly, the allosteric activation control point resides on the lysine residue K282 present in the catalytic site of PKL. These findings were confirmed by structural data, MS/MS experiments, and molecular modelling studies. Altogether, our study provides a molecular basis for the activation mechanism and establishes a framework for further development of human liver pyruvate kinase covalent activators.
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Affiliation(s)
- Umberto Maria Battisti
- Department of Chemistry and Molecular Biology, University of Gothenburg, 412 96, Gothenburg, Sweden
| | - Chunxia Gao
- Department of Chemistry and Molecular Biology, University of Gothenburg, 412 96, Gothenburg, Sweden
| | - Oscar Nilsson
- Department of Chemistry and Molecular Biology, University of Gothenburg, 412 96, Gothenburg, Sweden
| | - Fady Akladios
- Department of Chemistry and Molecular Biology, University of Gothenburg, 412 96, Gothenburg, Sweden
| | - Aleksei Lulla
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Agnieszka Bogucka
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Amalyn Nain-Perez
- Department of Chemistry and Molecular Biology, University of Gothenburg, 412 96, Gothenburg, Sweden
| | - Liliana Håversen
- Department of Molecular and Clinical Medicine, University of Gothenburg and Sahlgrenska University Hospital, 413 45, Gothenburg, Sweden
| | - Woonghee Kim
- Science for Life Laboratory, KTH-Royal Institute of Technology, 171 21, Stockholm, Sweden
| | - Jan Boren
- Department of Molecular and Clinical Medicine, University of Gothenburg and Sahlgrenska University Hospital, 413 45, Gothenburg, Sweden
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Mathias Uhlen
- Science for Life Laboratory, KTH-Royal Institute of Technology, 171 21, Stockholm, Sweden
| | - Adil Mardinoglu
- Science for Life Laboratory, KTH-Royal Institute of Technology, 171 21, Stockholm, Sweden
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of Gothenburg, 412 96, Gothenburg, Sweden
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Deng J, Walther A. ATP-Responsive and ATP-Fueled Self-Assembling Systems and Materials. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e2002629. [PMID: 32881127 DOI: 10.1002/adma.202002629] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/21/2020] [Indexed: 06/11/2023]
Abstract
Adenosine triphosphate (ATP) is a central metabolite that plays an indispensable role in various cellular processes, from energy supply to cell-to-cell signaling. Nature has developed sophisticated strategies to use the energy stored in ATP for many metabolic and non-equilibrium processes, and to sense and bind ATP for biological signaling. The variations in the ATP concentrations from one organelle to another, from extracellular to intracellular environments, and from normal cells to cancer cells are one motivation for designing ATP-triggered and ATP-fueled systems and materials, because they show great potential for applications in biological systems by using ATP as a trigger or chemical fuel. Over the last decade, ATP has been emerging as an attractive co-assembling component for man-made stimuli-responsive as well as for fuel-driven active systems and materials. Herein, current advances and emerging concepts for ATP-triggered and ATP-fueled self-assemblies and materials are discussed, shedding light on applications and highlighting future developments. By bringing together concepts of different domains, that is from supramolecular chemistry to DNA nanoscience, from equilibrium to non-equilibrium self-assembly, and from fundamental sciences to applications, the aim is to cross-fertilize current approaches with the ultimate aim to bring synthetic ATP-dependent systems closer to living systems.
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Affiliation(s)
- Jie Deng
- A3BMS Lab - Active, Adaptive and Autonomous Bioinspired Materials, Institute for Macromolecular Chemistry, University of Freiburg, Stefan-Meier-Straße 31, Freiburg, 79104, Germany
- Freiburg Materials Research Center (FMF), University of Freiburg, Stefan-Meier-Str. 21, Freiburg, 79104, Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Georges-Köhler-Allee 105, Freiburg, 79110, Germany
| | - Andreas Walther
- A3BMS Lab - Active, Adaptive and Autonomous Bioinspired Materials, Institute for Macromolecular Chemistry, University of Freiburg, Stefan-Meier-Straße 31, Freiburg, 79104, Germany
- Freiburg Materials Research Center (FMF), University of Freiburg, Stefan-Meier-Str. 21, Freiburg, 79104, Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Georges-Köhler-Allee 105, Freiburg, 79110, Germany
- Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, Freiburg, D-79110, Germany
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Ueda S, Sakasegawa SI. Pyruvate kinase from Geobacillus stearothermophilus displays an unusual preference for Mn 2+ in a cycling reaction. Anal Biochem 2019; 570:27-31. [PMID: 30738758 DOI: 10.1016/j.ab.2019.02.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 02/06/2019] [Accepted: 02/06/2019] [Indexed: 10/27/2022]
Abstract
Previously, we developed a kinase cycling method using creatine kinase and pyruvate kinase (RMPK) both from rabbit muscle in the presence of an excess amount of ATP and IDP for the quantitative determination of substrate. To our surprise, the RMPK cycling reaction was 10-fold more efficient using Mn2+ rather than Mg2+. Here, we investigated PK from Geobacillus stearothermophilus (GSPK) as an alternative source of enzyme. Spectrophotometric real-time detection was accomplished by coupling the reaction to ADP-dependent glucokinase (ADP-GK) together with glucose-6-phosphate dehydrogenase (G6PD). The rate of increase in absorbance of NADH at 340 nm was monitored. GSPK displayed an even greater preference than RMPK for Mn2+ over Mg2+ in the cycling reaction with ATP and GDP or ATP and IDP. The much lower Km values for the substrate in the presence of Mn2+ rather than Mg2+ are consistent with the results of the cycling reaction observed in this study.
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Affiliation(s)
- Shigeru Ueda
- R&D Group, Diagnostics Dept., Asahi Kasei Pharma Corporation, 632-1 Mifuku, Izunokuni-shi, Shizuoka, 410-2321, Japan.
| | - Shin-Ichi Sakasegawa
- R&D Group, Diagnostics Dept., Asahi Kasei Pharma Corporation, 632-1 Mifuku, Izunokuni-shi, Shizuoka, 410-2321, Japan
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de Souza RB, de Menezes JAS, de Souza RDFR, Dutra ED, de Morais MA. Mineral composition of the sugarcane juice and its influence on the ethanol fermentation. Appl Biochem Biotechnol 2014; 175:209-22. [PMID: 25248994 DOI: 10.1007/s12010-014-1258-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 09/11/2014] [Indexed: 10/24/2022]
Abstract
In the present work, we evaluated the mineral composition of three sugarcane varieties from different areas in northeast Brazil and their influence on the fermentation performance of Saccharomyces cerevisiae. The mineral composition was homogeneous in the different areas investigated. However, large variation coefficients were observed for concentrations of copper, magnesium, zinc and phosphorus. Regarding the fermentation performances, the sugarcane juices with the highest magnesium concentration showed the highest ethanol yield. Synthetic media supplemented with magnesium also showed the highest yield (0.45 g g(-1)) while the excess of copper led to the lowest yield (0.35 g g(-1)). According to our results, the magnesium is the principal responsible for the increase on the ethanol yield, and it also seems to be able to disguise the inhibitory effects of the toxic minerals present in the sugarcane juice.
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Affiliation(s)
- Rafael Barros de Souza
- Interdepartmental Research Group in Metabolic Engineering, Department of Genetics, Federal University of Pernambuco, Av. Prof. Moraes Rego, 1235, 50670-901, Recife, PE, Brazil
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Fenton AW, Williams R, Trewhella J. Changes in small-angle X-ray scattering parameters observed upon binding of ligand to rabbit muscle pyruvate kinase are not correlated with allosteric transitions. Biochemistry 2010; 49:7202-9. [PMID: 20712377 DOI: 10.1021/bi100147w] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein fluorescence and small-angle X-ray scattering (SAXS) have been used to monitor effector affinity and conformational changes previously associated with allosteric regulation in rabbit muscle pyruvate kinase (M(1)-PYK). In the absence of substrate [phosphoenolpyruvate (PEP)], SAXS-monitored conformational changes in M(1)-PYK elicited by the binding of phenylalanine (an allosteric inhibitor that reduces the affinity of M(1)-PYK for PEP) are similar to those observed upon binding of alanine or 2-aminobutyric acid. Under our assay conditions, these small amino acids bind to the protein but elicit a minimal change in the affinity of the protein for PEP. Therefore, if changes in scattering signatures represent cleft closure via domain rotation as previously interpreted, we can conclude that these motions are not sufficient to elicit allosteric inhibition. Additionally, although PEP has similar affinities for the free enzyme and the M(1)-PYK-small amino acid complexes (i.e., the small amino acids have minimal allosteric effects), PEP binding elicits different changes in the SAXS signature of the free enzyme versus the M(1)-PYK-small amino acid complexes.
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Affiliation(s)
- Aron W Fenton
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, MS 3030, 3901 Rainbow Boulevard, Kansas City, Kansas 66160, USA.
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Abstract
Progress curve analysis has been used sparingly in studies of enzyme-catalyzed reactions due largely to the complexity of the integrated rate expressions used in data analysis. Using an experimental design that simplifies the analysis, the advantages and limitations of progress curve experiments are explored in a study of four different enzyme-catalyzed reactions. The approach involves relatively simple protocols, requires 20-25% of the materials, and provides 10- to 20-fold signal enhancements compared to analogous initial rate studies. Product inhibition, which complicates integrated rate analysis, was circumvented using cloned, purified enzymes that remove the products and draw the reaction forward. The resulting progress curves can be transformed into the equivalent of thousands of initial rate and [S] measurements and, due to the absence of product inhibition, are plotted in the familiar, linear double-reciprocal format. Allowing product to accumulate during a reaction produces a continuously changing substrate/product ratio that can be used as the basis for obtaining product inhibition constants and to distinguish among the three classical inhibition mechanisms. Algebraic models describing the double-reciprocal patterns obtained from such inhibition studies are presented. The virtual continuum of substrate concentrations that occurs during a progress curve experiment provides a nearly errorless set of relative concentrations that results in remarkably precise data; kinetic constant standard deviations are on the order of 0.5%.
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Affiliation(s)
- Qingxiu Tang
- The Department of Microbiology and Immunology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, New York 10461-1926, USA
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Chen P, Li J. Sequence-based identification of interface residues by an integrative profile combining hydrophobic and evolutionary information. BMC Bioinformatics 2010; 11:402. [PMID: 20667087 PMCID: PMC2921408 DOI: 10.1186/1471-2105-11-402] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Accepted: 07/28/2010] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Protein-protein interactions play essential roles in protein function determination and drug design. Numerous methods have been proposed to recognize their interaction sites, however, only a small proportion of protein complexes have been successfully resolved due to the high cost. Therefore, it is important to improve the performance for predicting protein interaction sites based on primary sequence alone. RESULTS We propose a new idea to construct an integrative profile for each residue in a protein by combining its hydrophobic and evolutionary information. A support vector machine (SVM) ensemble is then developed, where SVMs train on different pairs of positive (interface sites) and negative (non-interface sites) subsets. The subsets having roughly the same sizes are grouped in the order of accessible surface area change before and after complexation. A self-organizing map (SOM) technique is applied to group similar input vectors to make more accurate the identification of interface residues. An ensemble of ten-SVMs achieves an MCC improvement by around 8% and F1 improvement by around 9% over that of three-SVMs. As expected, SVM ensembles constantly perform better than individual SVMs. In addition, the model by the integrative profiles outperforms that based on the sequence profile or the hydropathy scale alone. As our method uses a small number of features to encode the input vectors, our model is simpler, faster and more accurate than the existing methods. CONCLUSIONS The integrative profile by combining hydrophobic and evolutionary information contributes most to the protein-protein interaction prediction. Results show that evolutionary context of residue with respect to hydrophobicity makes better the identification of protein interface residues. In addition, the ensemble of SVM classifiers improves the prediction performance. AVAILABILITY Datasets and software are available at http://mail.ustc.edu.cn/~bigeagle/BMCBioinfo2010/index.htm.
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Affiliation(s)
- Peng Chen
- Bioinformatics Research Center, School of Computer Engineering, Nanyang Technological University, 639798 Singapore
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Abstract
Experimental designs used to monitor the magnitude of an allosteric response can greatly influence observed values. We report here the impact of buffer, monovalent cation, divalent cation, and anion on the magnitude of the allosteric regulation of the affinity of human liver pyruvate kinase (hL-PYK) for substrate, phosphoenolpyruvate (PEP). The magnitudes of the allosteric activation by fructose-1,6-bisphosphate (Fru-1,6-BP) and the allosteric inhibition by alanine are independent of most, but not all buffers tested. However, these magnitudes are dependent on whether Mg(2+) or Mn(2+) is included as the divalent cation. In the presence of Mn(2+), any change in K(app-PEP) caused by Fru-1,6-BP is minimal. hL-PYK activity does not appear to require monovalent cation. Monovalent cation binding in the active site impacts PEP affinity with minimum influence on the magnitude of allosteric coupling. However, Na(+) and Li(+) reduce the magnitude of the allosteric response to Fru-1,6-BP, likely due to mechanisms outside of the active site. Which anion is used to maintain a constant monovalent cation concentration also influences the magnitude of the allosteric response. The value of determining the impact of ions on allosteric function can be appreciated by considering that representative structures used in comparative studies have often been determined using protein crystals grown in diverse buffer and salt conditions.
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Current awareness on yeast. Yeast 2002; 19:285-92. [PMID: 11816036 DOI: 10.1002/yea.821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
In order to keep subscribers up-to-date with the latest developments in their field, this current awareness service is provided by John Wiley & Sons and contains newly-published material on yeasts. Each bibliography is divided into 10 sections. 1 Books, Reviews & Symposia; 2 General; 3 Biochemistry; 4 Biotechnology; 5 Cell Biology; 6 Gene Expression; 7 Genetics; 8 Physiology; 9 Medical Mycology; 10 Recombinant DNA Technology. Within each section, articles are listed in alphabetical order with respect to author. If, in the preceding period, no publications are located relevant to any one of these headings, that section will be omitted. (3 weeks journals - search completed 5th. Dec. 2001)
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