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Ren C, Li X, Li J, Huang X, Bai Y, Schroyen M, Hou C, Wang Z, Zhang D. Acetylation and Phosphorylation Regulate the Role of Pyruvate Kinase as a Glycolytic Enzyme or a Protein Kinase in Lamb. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:11724-11732. [PMID: 38718268 DOI: 10.1021/acs.jafc.4c00082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Protein post-translational modifications (PTMs) play an essential role in meat quality development. However, the effect of specific PTM sites on meat proteins has not been investigated yet. The characteristics of pyruvate kinase M (PKM) were found to exhibit a close correlation with final meat quality, and thus, serine 99 (S99) and lysine 137 (K137) in PKM were mutated to study their effect on PKM function. The structural and functional properties of five lamb PKM variants, including wild-type PKM (wtPKM), PKM_S99D (S99 phosphorylation), PKM_S99A (PKM S99 dephosphorylation), PKM_K137Q (PKM K137 acetylation), and PKM_K137R (PKM K137 deacetylation), were evaluated. The results showed that the secondary structure, tertiary structure, and polymer formation were affected among different PKM variants. In addition, the glycolytic activity of PKM_K137Q was decreased because of its weakened binding with phosphoenolpyruvate. In the PKM_K137R variant, the actin phosphorylation level exhibited a decrease, suggesting a low kinase activity of PKM_K137R. The results of molecular simulation showed a 42% reduction in the interface area between PKM_K137R and actin, in contrast to wtPKM and actin. These findings are significant for revealing the mechanism of how PTMs regulate PKM function and provide a theoretical foundation for the development of precise meat quality preservation technology.
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Affiliation(s)
- Chi Ren
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-Products Quality & Safety in Harvest, Storage, Transportation, Management and Control, Ministry of Agriculture and Rural Affairs, Beijing 100193, P. R. China
- Precision Livestock and Nutrition Unit, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés 2, Gembloux 5030, Belgium
| | - Xin Li
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-Products Quality & Safety in Harvest, Storage, Transportation, Management and Control, Ministry of Agriculture and Rural Affairs, Beijing 100193, P. R. China
| | - Juan Li
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-Products Quality & Safety in Harvest, Storage, Transportation, Management and Control, Ministry of Agriculture and Rural Affairs, Beijing 100193, P. R. China
| | - Xiaolan Huang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-Products Quality & Safety in Harvest, Storage, Transportation, Management and Control, Ministry of Agriculture and Rural Affairs, Beijing 100193, P. R. China
| | - Yuqiang Bai
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-Products Quality & Safety in Harvest, Storage, Transportation, Management and Control, Ministry of Agriculture and Rural Affairs, Beijing 100193, P. R. China
| | - Martine Schroyen
- Precision Livestock and Nutrition Unit, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés 2, Gembloux 5030, Belgium
| | - Chengli Hou
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-Products Quality & Safety in Harvest, Storage, Transportation, Management and Control, Ministry of Agriculture and Rural Affairs, Beijing 100193, P. R. China
| | - Zhenyu Wang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-Products Quality & Safety in Harvest, Storage, Transportation, Management and Control, Ministry of Agriculture and Rural Affairs, Beijing 100193, P. R. China
| | - Dequan Zhang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-Products Quality & Safety in Harvest, Storage, Transportation, Management and Control, Ministry of Agriculture and Rural Affairs, Beijing 100193, P. R. China
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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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3
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Swint-Kruse L, Dougherty LL, Page B, Wu T, O’Neil PT, Prasannan CB, Timmons C, Tang Q, Parente DJ, Sreenivasan S, Holyoak T, Fenton AW. PYK-SubstitutionOME: an integrated database containing allosteric coupling, ligand affinity and mutational, structural, pathological, bioinformatic and computational information about pyruvate kinase isozymes. Database (Oxford) 2023; 2023:baad030. [PMID: 37171062 PMCID: PMC10176505 DOI: 10.1093/database/baad030] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/29/2023] [Accepted: 04/11/2023] [Indexed: 05/13/2023]
Abstract
Interpreting changes in patient genomes, understanding how viruses evolve and engineering novel protein function all depend on accurately predicting the functional outcomes that arise from amino acid substitutions. To that end, the development of first-generation prediction algorithms was guided by historic experimental datasets. However, these datasets were heavily biased toward substitutions at positions that have not changed much throughout evolution (i.e. conserved). Although newer datasets include substitutions at positions that span a range of evolutionary conservation scores, these data are largely derived from assays that agglomerate multiple aspects of function. To facilitate predictions from the foundational chemical properties of proteins, large substitution databases with biochemical characterizations of function are needed. We report here a database derived from mutational, biochemical, bioinformatic, structural, pathological and computational studies of a highly studied protein family-pyruvate kinase (PYK). A centerpiece of this database is the biochemical characterization-including quantitative evaluation of allosteric regulation-of the changes that accompany substitutions at positions that sample the full conservation range observed in the PYK family. We have used these data to facilitate critical advances in the foundational studies of allosteric regulation and protein evolution and as rigorous benchmarks for testing protein predictions. We trust that the collected dataset will be useful for the broader scientific community in the further development of prediction algorithms. Database URL https://github.com/djparente/PYK-DB.
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Affiliation(s)
- Liskin Swint-Kruse
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Larissa L Dougherty
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Braelyn Page
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Tiffany Wu
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Pierce T O’Neil
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Charulata B Prasannan
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Cody Timmons
- Chemistry Department, Southwestern Oklahoma State University, 100 Campus Dr., Weatherford, OK 73096, USA
| | - Qingling Tang
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Daniel J Parente
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
- Department of Family Medicine and Community Health, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Shwetha Sreenivasan
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Todd Holyoak
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
- Department of Biology, University of Waterloo, 200 University Ave. W, Waterloo, ON N2L 3G1, Canada
| | - Aron W Fenton
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
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Abdelhamid Y, Wang M, Parkhill SL, Brear P, Chee X, Rahman T, Welch M. Structure, Function and Regulation of a Second Pyruvate Kinase Isozyme in Pseudomonas aeruginosa. Front Microbiol 2021; 12:790742. [PMID: 34867929 PMCID: PMC8637920 DOI: 10.3389/fmicb.2021.790742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 10/26/2021] [Indexed: 11/21/2022] Open
Abstract
Pseudomonas aeruginosa (PA) depends on the Entner-Doudoroff pathway (EDP) for glycolysis. The main enzymatic regulator in the lower half of the EDP is pyruvate kinase. PA contains genes that encode two isoforms of pyruvate kinase, denoted PykAPA and PykFPA. In other well-characterized organisms containing two pyruvate kinase isoforms (such as Escherichia coli) each isozyme is differentially regulated. The structure, function and regulation of PykAPA has been previously characterized in detail, so in this work, we set out to assess the biochemical and structural properties of the PykFPA isozyme. We show that pykF PA expression is induced in the presence of the diureide, allantoin. In spite of their relatively low amino acid sequence identity, PykAPA and PykFPA display broadly comparable kinetic parameters, and are allosterically regulated by a very similar set of metabolites. However, the x-ray crystal structure of PykFPA revealed significant differences compared with PykAPA. Notably, although the main allosteric regulator binding-site of PykFPA was empty, the "ring loop" covering the site adopted a partially closed conformation. Site-directed mutation of the proline residues flanking the ring loop yielded apparent "locked on" and "locked off" allosteric activation phenotypes, depending on the residue mutated. Analysis of PykFPA inter-protomer interactions supports a model in which the conformational transition(s) accompanying allosteric activation involve re-orientation of the A and B domains of the enzyme and subsequent closure of the active site.
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Affiliation(s)
- Yassmin Abdelhamid
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Meng Wang
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | | | - Paul Brear
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Xavier Chee
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
| | - Taufiq Rahman
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
| | - Martin Welch
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
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5
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Swint-Kruse L, Martin TA, Page BM, Wu T, Gerhart PM, Dougherty LL, Tang Q, Parente DJ, Mosier BR, Bantis LE, Fenton AW. Rheostat functional outcomes occur when substitutions are introduced at nonconserved positions that diverge with speciation. Protein Sci 2021; 30:1833-1853. [PMID: 34076313 DOI: 10.1002/pro.4136] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 05/25/2021] [Accepted: 05/28/2021] [Indexed: 12/14/2022]
Abstract
When amino acids vary during evolution, the outcome can be functionally neutral or biologically-important. We previously found that substituting a subset of nonconserved positions, "rheostat" positions, can have surprising effects on protein function. Since changes at rheostat positions can facilitate functional evolution or cause disease, more examples are needed to understand their unique biophysical characteristics. Here, we explored whether "phylogenetic" patterns of change in multiple sequence alignments (such as positions with subfamily specific conservation) predict the locations of functional rheostat positions. To that end, we experimentally tested eight phylogenetic positions in human liver pyruvate kinase (hLPYK), using 10-15 substitutions per position and biochemical assays that yielded five functional parameters. Five positions were strongly rheostatic and three were non-neutral. To test the corollary that positions with low phylogenetic scores were not rheostat positions, we combined these phylogenetic positions with previously-identified hLPYK rheostat, "toggle" (most substitution abolished function), and "neutral" (all substitutions were like wild-type) positions. Despite representing 428 variants, this set of 33 positions was poorly statistically powered. Thus, we turned to the in vivo phenotypic dataset for E. coli lactose repressor protein (LacI), which comprised 12-13 substitutions at 329 positions and could be used to identify rheostat, toggle, and neutral positions. Combined hLPYK and LacI results show that positions with strong phylogenetic patterns of change are more likely to exhibit rheostat substitution outcomes than neutral or toggle outcomes. Furthermore, phylogenetic patterns were more successful at identifying rheostat positions than were co-evolutionary or eigenvector centrality measures of evolutionary change.
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Affiliation(s)
- Liskin Swint-Kruse
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Tyler A Martin
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Braelyn M Page
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Tiffany Wu
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Paige M Gerhart
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Larissa L Dougherty
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA.,Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth College, Hanover, New Hampshire, USA
| | - Qingling Tang
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Daniel J Parente
- Department of Family Medicine and Community Health, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Brian R Mosier
- Department of Biostatistics and Data Science, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Leonidas E Bantis
- Department of Biostatistics and Data Science, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Aron W Fenton
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
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6
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McCabe JW, Mallis CS, Kocurek KI, Poltash ML, Shirzadeh M, Hebert MJ, Fan L, Walker TE, Zheng X, Jiang T, Dong S, Lin CW, Laganowsky A, Russell DH. First-Principles Collision Cross Section Measurements of Large Proteins and Protein Complexes. Anal Chem 2020; 92:11155-11163. [PMID: 32662991 PMCID: PMC7967297 DOI: 10.1021/acs.analchem.0c01285] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Rotationally averaged collision cross section (CCS) values for a series of proteins and protein complexes ranging in size from 8.6 to 810 kDa are reported. The CCSs were obtained using a native electrospray ionization drift tube ion mobility-Orbitrap mass spectrometer specifically designed to enhance sensitivity while having high-resolution ion mobility and mass capabilities. Periodic focusing (PF)-drift tube (DT)-ion mobility (IM) provides first-principles determination of the CCS of large biomolecules that can then be used as CCS calibrants. The experimental, first-principles CCS values are compared to previously reported experimentally determined and computationally calculated CCS using projected superposition approximation (PSA), the Ion Mobility Projection Approximation Calculation Tool (IMPACT), and Collidoscope. Experimental CCS values are generally in agreement with previously reported CCSs, with values falling within ∼5.5%. In addition, an ion mobility resolution (CCS centroid divided by CCS fwhm) of ∼60 is obtained for pyruvate kinase (MW ∼ 233 kDa); however, ion mobility resolution for bovine serum albumin (MW ∼ 68 kDa) is less than ∼20, which arises from sample impurities and underscores the importance of sample quality. The high resolution afforded by the ion mobility-Orbitrap mass analyzer provides new opportunities to understand the intricate details of protein complexes such as the impact of post-translational modifications (PTMs), stoichiometry, and conformational changes induced by ligand binding.
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Affiliation(s)
- Jacob W McCabe
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Christopher S Mallis
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Klaudia I Kocurek
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Michael L Poltash
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Mehdi Shirzadeh
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Michael J Hebert
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Liqi Fan
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Thomas E Walker
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Xueyun Zheng
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Ting Jiang
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Shiyu Dong
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Cheng-Wei Lin
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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Bianchi P, Fermo E, Glader B, Kanno H, Agarwal A, Barcellini W, Eber S, Hoyer JD, Kuter DJ, Maia TM, Mañu-Pereira MDM, Kalfa TA, Pissard S, Segovia JC, van Beers E, Gallagher PG, Rees DC, van Wijk R. Addressing the diagnostic gaps in pyruvate kinase deficiency: Consensus recommendations on the diagnosis of pyruvate kinase deficiency. Am J Hematol 2019; 94:149-161. [PMID: 30358897 DOI: 10.1002/ajh.25325] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 10/19/2018] [Accepted: 10/20/2018] [Indexed: 01/19/2023]
Abstract
Pyruvate kinase deficiency (PKD) is the most common enzyme defect of glycolysis and an important cause of hereditary, nonspherocytic hemolytic anemia. The disease has a worldwide geographical distribution but there are no verified data regarding its frequency. Difficulties in the diagnostic workflow and interpretation of PK enzyme assay likely play a role. By the creation of a global PKD International Working Group in 2016, involving 24 experts from 20 Centers of Expertise we studied the current gaps in the diagnosis of PKD in order to establish diagnostic guidelines. By means of a detailed survey and subsequent discussions, multiple aspects of the diagnosis of PKD were evaluated and discussed by members of Expert Centers from Europe, USA, and Asia directly involved in diagnosis. Broad consensus was reached among the Centers on many clinical and technical aspects of the diagnosis of PKD. The results of this study are here presented as recommendations for the diagnosis of PKD and used to prepare a diagnostic algorithm. This information might be helpful for other Centers to deliver timely and appropriate diagnosis and to increase awareness in PKD.
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Affiliation(s)
- Paola Bianchi
- UOC Ematologia, Fisiopatologia delle Anemie; Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico; Milan Italy
| | - Elisa Fermo
- UOC Ematologia, Fisiopatologia delle Anemie; Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico; Milan Italy
| | - Bertil Glader
- Lucile Packard Children's Hospital; Stanford University School of Medicine; Palo Alto California
| | - Hitoshi Kanno
- Department of Transfusion Medicine and Cell Processing; Faculty of Medicine, Tokyo Women's Medical University; Tokyo Japan
| | | | - Wilma Barcellini
- UOC Ematologia, Fisiopatologia delle Anemie; Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico; Milan Italy
| | - Stefan Eber
- Special Praxis for Pediatric Hematology and Childrens’ Hospital; Technical University; Munich Germany
| | - James D. Hoyer
- Department of Laboratory Medicine and Pathology; Mayo Clinic; Rochester Minnesota
| | - David J. Kuter
- Hematology Division; Massachusetts General Hospital; Boston Massachusetts
| | | | | | - Theodosia A. Kalfa
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center and Department of Pediatrics; University of Cincinnati, College of Medicine; Cincinnati Ohio
| | - Serge Pissard
- APHP-University Hospital Henri Mondor and Inserm IMRB U955eq2; Creteil France
| | - José-Carlos Segovia
- Differentiation and Cytometry Unit. Hematopoietic Innovative Therapies Division, Centro de Investigaciones Energéticas; Medioambientales y Tecnológicas (CIEMAT) - Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER); Madrid Spain
- Advance Therapies Mixed Unit; Instituto de Investigación Sanitaria-Fundación Jimenez Díaz (IIS-FJD); Madrid Spain
| | - Eduard van Beers
- Van Creveldkliniek, University Medical Center Utrecht; University of Utrecht; Utrecht The Netherlands
| | - Patrick G. Gallagher
- Departments of Pediatrics, Pathology and Genetics; Yale University School of Medicine; New Haven Connecticut
| | - David C. Rees
- Department of Paediatric Haematology; King's College Hospital; London United Kingdom
| | - Richard van Wijk
- Department of Clinical Chemistry and Haematology, Division Laboratories, Pharmacy and Biomedical Genetics; University Medical Center Utrecht, Utrecht University; Utrecht The Netherlands
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8
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Tang Q, Alontaga AY, Holyoak T, Fenton AW. Exploring the limits of the usefulness of mutagenesis in studies of allosteric mechanisms. Hum Mutat 2017; 38:1144-1154. [PMID: 28459139 DOI: 10.1002/humu.23239] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 04/24/2017] [Accepted: 04/26/2017] [Indexed: 11/12/2022]
Abstract
The outcome of structure-guided mutational analyses is often used in support of postulated mechanisms of protein allostery. However, the limits of how informative mutations can be in understanding allosteric mechanisms are not completely clear. Here, we report an exercise to evaluate whether mutational data can support a simplistic mechanistic model, developed with minimal data inputs. Due to the lack of a mechanism to explain how alanine allosterically modifies the affinity of human liver pyruvate kinase (approved symbol PKLR) for its substrate, phosphoenolpyruvate, we proposed a speculative allosteric mechanism for this system. Within the allosteric amino-acid-binding site (something in the effector site must, of necessity, contribute to the allosteric mechanism), we implemented multiple mutational strategies: (1) site-directed random mutagenesis at positions that contact bound alanine and (2) mutations to probe specific questions. Despite acknowledged inadequacies used to formulate the speculative mechanism, many mutations modified the allosteric coupling constant (Qax ) consistent with that mechanism. The observed support for this speculative mechanism leaves us to ponder the best use of mutational data in structure-function studies of allosteric mechanisms. The mutational databank derived from this exercise has an independent value for training and testing algorithms specific to allostery.
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Affiliation(s)
- Qingling Tang
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas
| | - Aileen Y Alontaga
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas
| | - Todd Holyoak
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Aron W Fenton
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas
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9
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Jaouani M, Manco L, Kalai M, Chaouch L, Douzi K, Silva A, Macedo S, Darragi I, Boudriga I, Chaouachi D, Fitouri Z, Van Wijk R, Ribeiro ML, Abbes S. Molecular basis of pyruvate kinase deficiency among Tunisians: description of new mutations affecting coding and noncoding regions in the PKLR gene. Int J Lab Hematol 2017; 39:223-231. [PMID: 28133914 DOI: 10.1111/ijlh.12610] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 10/26/2016] [Indexed: 11/29/2022]
Abstract
INTRODUCTION Pyruvate kinase (PK) deficiency is one of the most common hereditary nonspherocytic hemolytic anemias worldwide with clinical manifestations ranging from mild to severe hemolysis. However, investigation of this enzymopathy is lacking in Tunisia. We report here a pioneer investigation of PK deficiency among Tunisian cases referred to our laboratory for biological analysis of unknown cause of hemolytic anemia. METHODS Two hundred and fifty-three patients with unknown cause of hemolytic anemia have been addressed to our laboratory in order to investigate for red blood cells genetic disorders. Red cell enzyme activities were measured by standard methods, and molecular analysis was performed by DNA sequencing. The interpretation of mutation effect and the molecular modeling were performed by using specific software. RESULTS Six different PKLR mutations were found (c.966-1G>T; c.965+1G>A; c.721G>T; c.1163C>A; c.1456C>T; c.1537T>A), among which four are described for the first time. Genotype-phenotype correlations for the novel missense mutations were investigated by three-dimensional structure analysis. CONCLUSION This study provides important data of PK deficiency among Tunisians. It might be followed by a large neonatal screening to determine the spectrum of PK mutations and identify potential deficient patients for an early medical follow-up.
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Affiliation(s)
- M Jaouani
- Laboratoire d'Hématologie Moléculaire et Cellulaire, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - L Manco
- Unidade de Hematlogia Molecular, Centro Hospitalar e Universitário de Coimbra (CHUC), Coimbra, Portugal.,Research Centre for Anthropology and Health (CIAS), Department of Life Sciences, Universidade de Coimbra, Coimbra, Portugal
| | - M Kalai
- Laboratoire d'Hématologie Moléculaire et Cellulaire, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - L Chaouch
- Laboratoire d'Hématologie Moléculaire et Cellulaire, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - K Douzi
- Laboratoire d'Hématologie Moléculaire et Cellulaire, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - A Silva
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - S Macedo
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - I Darragi
- Laboratoire d'Hématologie Moléculaire et Cellulaire, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - I Boudriga
- Laboratoire d'Hématologie Moléculaire et Cellulaire, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - D Chaouachi
- Laboratoire d'Hématologie Moléculaire et Cellulaire, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Z Fitouri
- Service de pédiatrie-urgences-consultations, Hôpital d'Enfants de Tunis, Tunis, Tunisia
| | - R Van Wijk
- Laboratory for Red Blood Cell Research, Department of Clinical Chemistry and Hematology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - M L Ribeiro
- Unidade de Hematlogia Molecular, Centro Hospitalar e Universitário de Coimbra (CHUC), Coimbra, Portugal
| | - S Abbes
- Laboratoire d'Hématologie Moléculaire et Cellulaire, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
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10
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Naithani A, Taylor P, Erman B, Walkinshaw MD. A Molecular Dynamics Study of Allosteric Transitions in Leishmania mexicana Pyruvate Kinase. Biophys J 2015. [PMID: 26210208 DOI: 10.1016/j.bpj.2015.05.040] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
A comparative molecular dynamics analysis of the pyruvate kinase from Leishmania mexicana is presented in the absence and presence of the allosteric effector fructose 2,6-bisphosphate. Comparisons of the simulations of the large 240 kDa apo and holo tetramers show that binding of fructose 2,6-bisphosphate cools the enzyme and reduces dynamic movement, particularly of the B-domain. The reduced dynamic movement of the holo form traps the pyruvate kinase tetramer in its enzymatically active state with the B-domain acting as a lid to cover the active site. The simulations are also consistent with a transition of the mobile active-site α6' helix, which would adopt a helical conformation in the active R-state and a less structured coil conformation in the inactive T-state. Analysis of the rigid body motions over the trajectory highlights the concerted anticorrelated rigid body rocking motion of the four protomers, which drives the T to R transition. The transitions predicted by these simulations are largely consistent with the Monod-Wyman-Changeux model for allosteric activation but also suggest that rigidification or cooling of the overall structure upon effector binding plays an additional role in enzyme activation.
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Affiliation(s)
- Ankita Naithani
- The Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Paul Taylor
- The Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Burak Erman
- Department of Chemical and Biological Engineering, Koҫ University, Istanbul, Turkey.
| | - Malcolm D Walkinshaw
- The Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom.
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11
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Canto AC, Suman SP, Nair MN, Li S, Rentfrow G, Beach CM, Silva TJ, Wheeler TL, Shackelford SD, Grayson A, McKeith RO, King DA. Differential abundance of sarcoplasmic proteome explains animal effect on beef Longissimus lumborum color stability. Meat Sci 2015; 102:90-8. [DOI: 10.1016/j.meatsci.2014.11.011] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 11/24/2014] [Accepted: 11/25/2014] [Indexed: 10/24/2022]
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12
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Zhong Y, Feng J, Ruotolo BT. Robotically assisted titration coupled to ion mobility-mass spectrometry reveals the interface structures and analysis parameters critical for multiprotein topology mapping. Anal Chem 2013; 85:11360-8. [PMID: 24164205 DOI: 10.1021/ac402276k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Multiprotein complexes have three-dimensional shapes and dynamic functions that impact almost every aspect of biochemistry. Despite this, our ability to rapidly assess the structures of such macromolecules lags significantly behind high-throughput efforts to identify their function, especially in the context of human disease. Here, we describe results obtained by coupling ion mobility-mass spectrometry with automated robotic sampling of different solvent compositions. This combination of technologies has allowed us to explore an extensive set of solution conditions for a group of eight protein homotetramers, representing a broad sample of protein structure and stability space. We find that altering solution ionic strength in concert with dimethylsulfoxide content is sufficient to disrupt the protein-protein interfaces of all of the complexes studied here. Ion mobility measurements captured for both intact assemblies and subcomplexes match expected values from available X-ray structures in all cases save two. For these exceptions, we find that distorted subcomplexes result from extreme disruption conditions, and are accompanied by small shifts in intact tetramers size, thus enabling the removal of distorted subcomplex data in downstream models. Furthermore, we find strong correlations between the relative intensities of disrupted protein tetramers and the relative number and type of interactions present at interfaces as a function of disrupting agent added. In most cases, this correlation appears strong enough to quantify various types of protein interfacial interactions within unknown proteins following appropriate calibration.
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Affiliation(s)
- Yueyang Zhong
- Department of Chemistry, University of Michigan , 930 North University Avenue, Ann Arbor, Michigan 48109, United States
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13
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14
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Zhong W, Morgan HP, McNae IW, Michels PAM, Fothergill-Gilmore LA, Walkinshaw MD. `In crystallo' substrate binding triggers major domain movements and reveals magnesium as a co-activator of Trypanosoma brucei pyruvate kinase. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1768-79. [PMID: 23999300 DOI: 10.1107/s0907444913013875] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 05/20/2013] [Indexed: 11/10/2022]
Abstract
The active site of pyruvate kinase (PYK) is located between the AC core of the enzyme and a mobile lid corresponding to domain B. Many PYK structures have already been determined, but the first `effector-only' structure and the first with PEP (the true natural substrate) are now reported for the enzyme from Trypanosoma brucei. PEP soaked into crystals of the enzyme with bound allosteric activator fructose 2,6-bisphosphate (F26BP) and Mg(2+) triggers a substantial 23° rotation of the B domain `in crystallo', resulting in a partially closed active site. The interplay of side chains with Mg(2+) and PEP may explain the mechanism of the domain movement. Furthermore, it is apparent that when F26BP is present but PEP is absent Mg(2+) occupies a position that is distinct from the two canonical Mg(2+)-binding sites at the active site. This third site is adjacent to the active site and involves the same amino-acid side chains as in canonical site 1 but in altered orientations. Site 3 acts to sequester Mg(2+) in a `priming' position such that the enzyme is maintained in its R-state conformation. In this way, Mg(2+) cooperates with F26BP to ensure that the enzyme is in a conformation that has a high affinity for the substrate.
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Affiliation(s)
- Wenhe Zhong
- Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JR, Scotland
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15
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Neves RPP, Sousa SF, Fernandes PA, Ramos MJ. Parameters for Molecular Dynamics Simulations of Manganese-Containing Metalloproteins. J Chem Theory Comput 2013; 9:2718-32. [DOI: 10.1021/ct400055v] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Rui P. P. Neves
- REQUIMTE,
Departamento de Química e Bioquímica,
Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Sérgio F. Sousa
- REQUIMTE,
Departamento de Química e Bioquímica,
Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Pedro A. Fernandes
- REQUIMTE,
Departamento de Química e Bioquímica,
Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Maria J. Ramos
- REQUIMTE,
Departamento de Química e Bioquímica,
Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
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16
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Prasannan CB, Villar MT, Artigues A, Fenton AW. Identification of regions of rabbit muscle pyruvate kinase important for allosteric regulation by phenylalanine, detected by H/D exchange mass spectrometry. Biochemistry 2013; 52:1998-2006. [PMID: 23418858 DOI: 10.1021/bi400117q] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Mass spectrometry has been used to determine the number of exchangeable backbone amide protons and the associated rate constants that are altered when rabbit muscle pyruvate kinase (rM1-PYK) binds either the allosteric inhibitor (phenylalanine) or a nonallosteric analogue of the inhibitor. Alanine is used as the nonallosteric analogue because it binds competitively with phenylalanine but elicits a negligible allosteric inhibition, i.e., a negligible reduction in the affinity of rM1-PYK for the substrate, phosphoenolpyruvate. This experimental design is expected to distinguish changes in the protein caused by effector binding (i.e., those changes common upon the addition of alanine vs phenylalanine) from changes associated with allosteric regulation (i.e., those elicited by the addition of phenylalanine binding, but not alanine binding). High-quality peptic fragments covering 98% of the protein were identified. Changes in both the number of exchangeable protons per peptide and in the rate constant associated with exchange highlight regions of the protein with allosteric roles. The set of allosterically relevant peptides identified by this technique includes residues previously identified by mutagenesis to have roles in allosteric regulation by phenylalanine.
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Affiliation(s)
- Charulata B Prasannan
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, MS 3030, 3901 Rainbow Boulevard, Kansas City, Kansas 66160, United States
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17
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Urness JM, Clapp KM, Timmons JC, Bai X, Chandrasoma N, Buszek KR, Fenton AW. Distinguishing the chemical moiety of phosphoenolpyruvate that contributes to allostery in muscle pyruvate kinase. Biochemistry 2012; 52:1-3. [PMID: 23256782 DOI: 10.1021/bi301628k] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A series of substrate analogues has been used to determine which chemical moieties of the substrate phosphoenolpyruvate (PEP) contribute to the allosteric inhibition of rabbit muscle pyruvate kinase by phenylalanine. Replacing the carboxyl group of the substrate with a methyl alcohol or removing the phosphate altogether greatly reduces substrate affinity. However, removal of the carboxyl group is the only modification tested that removes the ability to allosterically reduce the level of Phe binding. From this, it can be concluded that the carboxyl group of PEP is responsible for energetic coupling with Phe binding in the allosteric sites.
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Affiliation(s)
- James M Urness
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS 66160, USA
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18
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Chaneton B, Gottlieb E. Rocking cell metabolism: revised functions of the key glycolytic regulator PKM2 in cancer. Trends Biochem Sci 2012; 37:309-16. [PMID: 22626471 DOI: 10.1016/j.tibs.2012.04.003] [Citation(s) in RCA: 195] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Revised: 04/10/2012] [Accepted: 04/19/2012] [Indexed: 01/05/2023]
Abstract
Cancer cell metabolism is exemplified by high glucose consumption and lactate production. Pyruvate kinase (PK), which catalyzes the final step of glycolysis, has emerged as a potential regulator of this metabolic phenotype. The M2 isoform of PK (PKM2) is highly expressed in cancer cells. However, the mechanisms by which PKM2 coordinates high energy requirements with high anabolic activities to support cancer cell proliferation are still not completely understood. Current research has elucidated novel regulatory mechanisms for PKM2, contributing to its important role in cancer. This review summarizes the current understanding and explores future directions in the field, highlighting controversies regarding the activity and specificity of PKM2 in cancer. In light of this knowledge, the potential therapeutic implications and strategies are critically discussed.
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Affiliation(s)
- Barbara Chaneton
- Cancer Research UK, The Beatson Institute for Cancer Research, Switchback Road, Glasgow, UK
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19
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Jiang K, He B, Lai L, Chen Q, Liu Y, Guo Q, Wang Q. Cyclosporine A inhibits breast cancer cell growth by downregulating the expression of pyruvate kinase subtype M2. Int J Mol Med 2012; 30:302-8. [PMID: 22580449 DOI: 10.3892/ijmm.2012.989] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Accepted: 04/09/2012] [Indexed: 01/12/2023] Open
Abstract
The high proliferative rate of tumor cells leads to metabolic needs distinct from those of their normal counterparts. An embryonic- and tumor-specific isoform of the enzyme pyruvate kinase M2 (PKM2) is overexpressed in cancer cells to increase the use of glycolytic intermediates for macromolecular biosynthesis and tumor growth. We report that Cyclosporin A (CsA) can regulate the expression and activity of PKM2 in breast cancer cell lines MCF-7, MDA-MB-435 and MDA-MB-231. PKM2 was found to be highly expressed in the three breast cancer cell lines compared to normal primary breast cells. Treatment with CsA inhibited the viability of breast cancer cells in a time- and dose-dependent manner. CsA significantly downregulated the expression of PKM2 in breast cancer cells and decreased adenosine triphosphate (ATP) synthesis, which induced cancer cells to undergo necrosis. Furthermore, the growth suppression effect of CsA was impaired in MCF-7 cells when they were transfected with the PKM2 overexpression plasmid, suggesting that CsA was an effective inhibitor of PKM2-dependent proliferation of breast cancer cells. These results may provide new insights into the mechanism of CsA in cancer therapy.
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Affiliation(s)
- Kai Jiang
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, P.R. China
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20
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Gas-phase protein assemblies: Unfolding landscapes and preserving native-like structures using noncovalent adducts. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2011.11.014] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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21
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Kumar S, Barth A. The allosteric effect of fructose bisphosphate on muscle pyruvate kinase studied by infrared spectroscopy. J Phys Chem B 2011; 115:11501-5. [PMID: 21870844 DOI: 10.1021/jp206272x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Pyruvate kinase exhibits allosteric properties. The allosteric effect of fructose 1,6-bisphosphate (FBP) on phosphoenolpyruvate (PEP) binding to rabbit muscle pyruvate kinase (PK) in the presence of various ions (Mg(2+), Mn(2+), K(+), Na(+)) was studied by attenuated total reflection infrared spectroscopy in combination with a dialysis accessory. The experiments indicated that FBP binding causes conformational changes of PK that are of the same order of magnitude as those of PEP binding. The conformational change of PEP binding to PK/Mg(2+)/K(+) in the presence of FBP was about twice as large as in its absence, which is tentatively ascribed to a higher occupancy of the closed state. The affinity for PEP increased in the presence of Mg(2+) and K(+). No such effects were observed with the other ion combinations Mn(2+)/K(+) and Mg(2+)/Na(+) or in D(2)O (with Mg(2+)/K(+)), and therefore we did not detect an allosteric effect on PEP binding under these conditions.
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Affiliation(s)
- Saroj Kumar
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden.
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22
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Abstract
The understanding of the molecular mechanisms of allostery in rabbit muscle pyruvate kinase (RMPK) is still in its infancy. Although, there is a paucity of knowledge on the ground rules on how its functions are regulated, RMPK is an ideal system to address basic questions regarding the fundamental chemical principles governing the regulatory mechanisms about this enzyme which has a TIM (α/β)(8) barrel structural motif [Copley, R. R., and Bork, P. (2000). Homology among (βα)8 barrels: Implications for the evolution of metabolic pathways. J. Mol. Biol.303, 627-640; Farber, G. K., and Petsko, G. A. (1990). The evolution of α/ß barrel enzymes. Trends Biochem.15, 228-234; Gerlt, J. A., and Babbitt, P. C. (2001). Divergent evolution of enzymatic function: Mechanistically diverse superfamilies and functionally distinct superfamilies. Annu. Rev. Biochem.70, 209-246; Heggi, H., and Gerstein, M. (1999). The relationship between protein structure and function: A comprehensive survey with application to the yeast genome. J. Mol. Biol.288, 147-164; Wierenga, R. K. (2001). The TIM-barrel fold: A versatile framework for efficient enzymes. FEB Lett.492, 193-198]. RMPK is a homotetramer. Each subunit consists of 530 amino acids and multiple domains. The active site resides between the A and B domains. Besides the basic TIM-barrel motif, RMPK also exhibits looped-out regions in the α/β barrel of each monomer forming the B- and C-domains. The two isozymes of PK, namely, the kidney and muscle isozymes, exhibit very different allosteric behaviors under the same experimental condition. The only amino acid sequence differences between the mammalian kidney and muscle PK isozymes are located in the C-domain and are involved in intersubunit interactions. Thus, embedded in these two isozymes of PK are the rules involved in engineering the popular TIM (α/β)(8) motif to modulate its allosteric properties. The PK system exhibits a lot of the properties that will allow mining of the ground rules governing the correlative linkages between sequence-fold-function. In this chapter, we review the approaches to acquire the fundamental functional and structural energetics that establish the linkages among this intricate network of linked multiequilibria. Results from these diverse approaches are integrated to establish a working model to represent the complex network of multiple linked reactions which ultimately leads to the observation of allosteric regulation of PK.
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23
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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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24
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Herman P, Lee JC. Functional energetic landscape in the allosteric regulation of muscle pyruvate kinase. 2. Fluorescence study. Biochemistry 2009; 48:9456-65. [PMID: 19719323 DOI: 10.1021/bi900280u] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The energetic landscape of the allosteric regulatory mechanism of rabbit muscle pyruvate kinase (RMPK) was characterized by isothermal titration calorimetry (ITC). Four novel insights were uncovered. (1) ADP exhibits a dual property. Depending on the temperature, ADP can regulate RMPK activity by switching the enzyme to either the R or T state. (2) The assumption that ligand binding to RMPK is state-dependent is only correct for PEP but not Phe and ADP. (3) The effect of pH on the regulatory behavior of RMPK is partly due to the complex pattern of proton release or absorption linked to the multiple linked equilibria which govern the activity of the enzyme. (4) The R <--> T equilibrium is accompanied by a significant DeltaC(p), rendering RMPK most sensitive to temperature under physiological conditions. To rigorously test the validity of conclusions derived from the ITC data, in this study a fluorescence approach, albeit indirect, that tracks continuous structural perturbations was employed. Intrinsic Trp fluorescence of RMPK in the absence and presence of substrates phosphoenolpyruvate (PEP) and ADP, and the allosteric inhibitor Phe, was measured in the temperature range between 4 and 45 degrees C. For data analysis, the fluorescence data were complemented by ITC experiments to yield an extended data set allowing more complete characterization of the RMPK regulatory mechanism. Twenty-one thermodynamic parameters were derived to define the network of linked interactions involved in regulating the allosteric behavior of RMPK through global analysis of the ITC and fluorescent data sets. In this study, 27 independent curves with more than 1600 experimental points were globally analyzed. Consequently, the consensus results substantiate not only the conclusions derived from the ITC data but also structural information characterizing the transition between the active and inactive states of RMPK and the antagonism between ADP and Phe binding. The latter observation reveals a novel role for ADP in the allosteric regulation of RMPK.
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Affiliation(s)
- Petr Herman
- Faculty of Mathematics and Physics, Institute of Physics, Charles University, Ke Karlovu 5, 121 16 Prague, Czech Republic.
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25
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Herman P, Lee JC. Functional energetic landscape in the allosteric regulation of muscle pyruvate kinase. 1. Calorimetric study. Biochemistry 2009; 48:9448-55. [PMID: 19719244 DOI: 10.1021/bi900279x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Rabbit muscle pyruvate kinase (RMPK) is an important allosteric enzyme of the glycolytic pathway catalyzing a transfer of the phosphate from phosphoenolpyruvate (PEP) to ADP. The energetic landscape of the allosteric regulatory mechanism of RMPK was characterized by isothermal titration calorimetry (ITC) in the temperature range from 4 to 45 degrees C. ITC data for RMPK binding to substrates PEP and ADP, for the allosteric inhibitor Phe, and for combination of ADP and Phe were globally analyzed. The thermodynamic parameters characterizing the linked-multiple-equilibrium system were extracted. Four novel insights were uncovered. (1) The binding preference of ADP for either the T or R state is temperature-dependent, namely, more favorable to the T and R states at high and low temperatures, respectively. This crossover of affinity toward R and T states implies that ADP plays a complex role in modulating the allosteric behavior of RMPK. Depending on the temperature, binding of ADP can regulate RMPK activity by favoring the enzyme to either the R or T state. (2) The binding of Phe is negatively coupled to that of ADP; i.e., Phe and ADP prefer not to bind to the same subunit of RMPK. (3) The release or absorption of protons linked to the various equilibria is specific to the particular reaction. As a consequence, pH will exert a complex effect on these linked equilibria, resulting in the proton being an allosteric regulatory ligand of RMPK. (4) The R <--> T equilibrium is accompanied by a significant DeltaC(p), rendering RMPK most sensitive to temperature under physiological conditions. During muscle activity, both pH and temperature fluctuations are known to happen; thus, results of this study are physiologically relevant.
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Affiliation(s)
- Petr Herman
- Faculty of Mathematics and Physics, Institute of Physics, Charles University, Ke Karlovu 5, 121 16 Prague, Czech Republic.
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26
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Spoden GA, Morandell D, Ehehalt D, Fiedler M, Jansen-Dürr P, Hermann M, Zwerschke W. The SUMO-E3 ligase PIAS3 targets pyruvate kinase M2. J Cell Biochem 2009; 107:293-302. [PMID: 19308990 DOI: 10.1002/jcb.22125] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Pyruvate kinase M2 (M2-PK) controls the rate-limiting step at the end of the glycolytic pathway in normal proliferating and tumor cells. Other functions of M2-PK in addition to its role in glycolysis are little understood. The aim of this study was to identify new cellular interaction partners of M2-PK in order to discover novel links between M2-PK and cellular functions. Here we show that the SUMO-E3 ligase protein PIAS3 (inhibitor of activated STAT3) physically interacts with M2-PK and its isoenzyme M1-PK. Moreover, we demonstrate that endogenous SUMO-1-M2-PK conjugates exist in mammalian cells. Furthermore, we show that transient expression of PIAS3 but not the RING domain mutant PIAS3 (C299S, H301A) is consistent with nuclear localization of M2-PK and PIAS3 and M2-PK partially co-localize in the nucleus of these cells. This study suggests a link between PIAS3 and nuclear pyruvate kinase.
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Affiliation(s)
- Gilles A Spoden
- Institute for Biomedical Aging Research of the Austrian Academy of Sciences, Innsbruck, Austria
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27
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Akhtar K, Gupta V, Koul A, Alam N, Bhat R, Bamezai RNK. Differential behavior of missense mutations in the intersubunit contact domain of the human pyruvate kinase M2 isozyme. J Biol Chem 2009; 284:11971-81. [PMID: 19265196 DOI: 10.1074/jbc.m808761200] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In this study, we attempted to understand the mechanism of regulation of the activity and allosteric behavior of the pyruvate kinase M(2) enzyme and two of its missense mutations, H391Y and K422R, found in cells from Bloom syndrome patients, prone to develop cancer. Results show that despite the presence of mutations in the intersubunit contact domain, the K422R and H391Y mutant proteins maintained their homotetrameric structure, similar to the wild-type protein, but showed a loss of activity of 75 and 20%, respectively. Interestingly, H391Y showed a 6-fold increase in affinity for its substrate phosphoenolpyruvate and behaved like a non-allosteric protein with compromised cooperative binding. However, the affinity for phosphoenolpyruvate was lost significantly in K422R. Unlike K422R, H391Y showed enhanced thermal stability, stability over a range of pH values, a lesser effect of the allosteric inhibitor Phe, and resistance toward structural alteration upon binding of the activator (fructose 1,6-bisphosphate) and inhibitor (Phe). Both mutants showed a slight shift in the pH optimum from 7.4 to 7.0. Although this study signifies the importance of conserved amino acid residues in long-range communications between the subunits of multimeric proteins, the altered behavior of mutants is suggestive of their probable role in tumor-promoting growth and metabolism in Bloom syndrome patients with defective pyruvate kinase M(2).
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Affiliation(s)
- Kamal Akhtar
- National Centre of Applied Human Genetics, School of Life Sciences, New Delhi, India
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28
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van Wijk R, Huizinga EG, van Wesel AC, van Oirschot BA, A. Hadders M, van Solinge WW. Fifteen novel mutations inPKLRassociated with pyruvate kinase (PK) deficiency: Structural implications of amino acid substitutions in PK. Hum Mutat 2009; 30:446-53. [DOI: 10.1002/humu.20915] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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29
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Molecular characterization and expression of the equine M1 and M2-pyruvate kinase gene. Comp Biochem Physiol B Biochem Mol Biol 2008; 151:125-32. [DOI: 10.1016/j.cbpb.2008.06.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2008] [Revised: 06/09/2008] [Accepted: 06/09/2008] [Indexed: 10/22/2022]
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30
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Tulloch LB, Morgan HP, Hannaert V, Michels PAM, Fothergill-Gilmore LA, Walkinshaw MD. Sulphate removal induces a major conformational change in Leishmania mexicana pyruvate kinase in the crystalline state. J Mol Biol 2008; 383:615-26. [PMID: 18775437 DOI: 10.1016/j.jmb.2008.08.037] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2008] [Accepted: 08/14/2008] [Indexed: 11/17/2022]
Abstract
We report X-ray structures of pyruvate kinase from Leishmania mexicana (LmPYK) that are trapped in different conformations. These, together with the previously reported structure of LmPYK in its inactive (T-state) conformation, allow comparisons of three different conformers of the same species of pyruvate kinase (PYK). Four new site point mutants showing the effects of side-chain alteration at subunit interfaces are also enzymatically characterised. The LmPYK tetramer crystals grown with ammonium sulphate as precipitant adopt an active-like conformation, with sulphate ions at the active and effector sites. The sulphates occupy positions similar to those of the phosphates of ligands bound to active (R-state) and constitutively active (nonallosteric) PYKs from several species, and provide insight into the structural roles of the phosphates of the substrates and effectors. Crystal soaking in sulphate-free buffers was found to induce major conformational changes in the tetramer. In particular, the unwinding of the Aalpha6' helix and the inward hinge movement of the B domain are coupled with a significant widening (4 A) of the tetramer caused by lateral movement of the C domains. The two new LmPYK structures and the activity studies of site point mutations described in this article are consistent with a developing picture of allosteric activity in which localised changes in protein flexibility govern the distribution of conformer families adopted by the tetramer in its active and inactive states.
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Affiliation(s)
- Lindsay B Tulloch
- Institute of Structural and Molecular Biology, The University of Edinburgh, Michael Swann Building, The King's Buildings, Edinburgh, UK
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31
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Lee JC. Modulation of allostery of pyruvate kinase by shifting of an ensemble of microstates. Acta Biochim Biophys Sin (Shanghai) 2008; 40:663-9. [PMID: 18604458 DOI: 10.1111/j.1745-7270.2008.00445.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Since the introduction of the concepts of allostery about four decades ago, much advancement has been made in elucidating the structure-function correlation in allostery. However, there are still a number of issues that remain unresolved. In this review we used mammalian pyruvate kinase (PK) as a model system to understand the role of protein dynamics in modulating cooperativity. PK has a triosephosphate isomerase (TIM) (alpha/beta)(8) barrel structural motif. PK is an ideal system to address basic questions regarding regulatory mechanisms about this common (alpha/beta)(8) structural motif. The simplest model accounting for all of the solution thermodynamic and kinetic data on ligand-enzyme interactions involves two conformational states, inactive E(T) and active E(R). These conformational states are represented by domain movements. Further studies provide the first evidence for a differential effect of ligand binding on the dynamics of the structural elements, not major secondary structural changes. These data are consistent with our model that allosteric regulation of PK is the consequence of perturbation of the distribution of an ensemble of states in which the inactive E(T) and active E(R) represent the two extreme end states. Sequence differences and ligands can modulate the distribution of states leading to alterations of functions. The future work includes: defining the network of functionally connected residues; elucidating the chemical principles governing the sequence differences which affect functions; and probing the nature of mutations on the stability of the secondary structural elements, which in turn modulate allostery.
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Affiliation(s)
- J Ching Lee
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, Texas 77555-1055, USA.
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32
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Spoden GA, Mazurek S, Morandell D, Bacher N, Ausserlechner MJ, Jansen-Dürr P, Eigenbrodt E, Zwerschke W. Isotype-specific inhibitors of the glycolytic key regulator pyruvate kinase subtype M2 moderately decelerate tumor cell proliferation. Int J Cancer 2008; 123:312-321. [PMID: 18425820 DOI: 10.1002/ijc.23512] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Tumor cells express the glycolytic regulator pyruvate kinase subtype M2 (M2-PK), which can occur in a tetrameric form with high affinity to its substrate phosphoenolpyruvate (PEP) and a dimeric form with a low PEP affinity. The transition between both conformations contributes to the control of glycolysis and is important for tumor cell proliferation and survival. Here we targeted M2-PK by synthetic peptide aptamers, which specifically bind to M2-PK and shift the isoenzyme into its low affinity dimeric conformation. The aptamer-induced dimerization and inactivation of M2-PK led to a significant decrease in the PK mass-action ratio as well as ATP:ADP ratio in the target cells. Furthermore, the expression of M2-PK-binding peptide aptamers moderately reduced the growth of immortalized NIH3T3 cell populations by decelerating cell proliferation, but without affecting apoptotic cell death. Moreover, the M2-PK-binding peptide aptamers also reduced the proliferation rate of human U-2 OS osteosarcoma cells. In the present study, we developed the first specific inhibitors of the pyruvate kinase isoenzyme type M2 and present evidence that these inhibitors moderately decelerate tumor cell proliferation.
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Affiliation(s)
- Gilles A Spoden
- Cell Metabolism and Differentiation Research Group, Institute for Biomedical Aging Research of the Austrian Academy of Sciences, Innsbruck, Austria.,Tumorvirology Group, Tyrolean Cancer Research Institute, Medical University Innsbruck, Innsbruck, Austria
| | - Sybille Mazurek
- Department for Biochemistry and Endocrinology, Veterinary Faculty, University of Giessen, Giessen, Germany.,ScheBo Biotech AG, Netanyastrasse 3, Giessen, Germany
| | - Dieter Morandell
- Cell Metabolism and Differentiation Research Group, Institute for Biomedical Aging Research of the Austrian Academy of Sciences, Innsbruck, Austria.,Tumorvirology Group, Tyrolean Cancer Research Institute, Medical University Innsbruck, Innsbruck, Austria
| | - Nicole Bacher
- Cell Metabolism and Differentiation Research Group, Institute for Biomedical Aging Research of the Austrian Academy of Sciences, Innsbruck, Austria
| | | | - Pidder Jansen-Dürr
- Department for Molecular and Cellular Biology, Institute for Biomedical Aging Research of the Austrian Academy of Sciences, Innsbruck, Austria.,Molecular Oncology Group, Tyrolean Cancer Research Institute, Medical University Innsbruck, Austria
| | - Erich Eigenbrodt
- Department for Biochemistry and Endocrinology, Veterinary Faculty, University of Giessen, Giessen, Germany
| | - Werner Zwerschke
- Cell Metabolism and Differentiation Research Group, Institute for Biomedical Aging Research of the Austrian Academy of Sciences, Innsbruck, Austria.,Tumorvirology Group, Tyrolean Cancer Research Institute, Medical University Innsbruck, Innsbruck, Austria
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33
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Wu X, Zhou Y, Zhang K, Liu Q, Guo D. Isoform-specific interaction of pyruvate kinase with hepatitis C virus NS5B. FEBS Lett 2008; 582:2155-60. [PMID: 18519040 DOI: 10.1016/j.febslet.2008.05.033] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2008] [Revised: 04/20/2008] [Accepted: 05/07/2008] [Indexed: 10/22/2022]
Abstract
Hepatitis C virus (HCV) replication and pathogenesis involve both virus-encoded proteins and cellular factors. In our study, we showed that NS5B, the HCV RNA-dependent RNA polymerase, interacted with M2 type pyruvate kinase (M2PK) but not L type pyruvate kinase. We confirmed the interaction by GST pull down, coimmunoprecipitation and confocal immunofluorescence analysis in cells with transient expression of NS5B and M2PK as well as in a HCV replicon-bearing cell line. Furthermore shRNA which specifically down-regulated M2PK expression could inhibit the replication of HCV in HCV replicon 9B cells.
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Affiliation(s)
- Xiaoyun Wu
- State Key Laboratory of Virology, the Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, PR China
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34
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Pissard S, Max-Audit I, Skopinski L, Vasson A, Vivien P, Bimet C, Goossens M, Galacteros F, Wajcman H. Pyruvate kinase deficiency in France: a 3-year study reveals 27 new mutations. Br J Haematol 2006; 133:683-9. [PMID: 16704447 DOI: 10.1111/j.1365-2141.2006.06076.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pyruvate kinase (PK) deficiency is the most common enzyme defect affecting the glycolytic pathway of the erythrocyte. Usually, it is clinically silent in heterozygotes but serious disorders are described at birth in homozygotes or compound heterozygotes. Including the mutants herein reported, more than 180 mutations of the PK-LR gene have now been identified. This 3-year study was carried out to detect mutations associated with disease-affecting families. Haematological indices, erythrocyte PK and glucose-6-phosphate dehydrogenase activities were measured. Molecular characterisation of the PK gene mutations included restriction enzyme analysis, mutation scanning and gene sequencing. Among the 56 families studied, nine homozygous cases and 41 different mutations were found. Eight mutations involved a splice site, 31 missense mutations were located in crucial domains of the molecule (catalytic site, cleft between the A and C domains, A/A' interface) and two cases of insertion-deletion were found. In total, 20 new mutations modifying the structure of the enzyme and seven affecting a splice site are reported. PK deficiency is an under diagnosed disease. However, deficiency could be life threatening in perinatal period and we report two lethal cases. These results support the characterisation of PK mutations, and show that prenatal diagnosis can identify affected infants and prepare safer conditions for the birth.
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Affiliation(s)
- Serge Pissard
- Laboratoire de Biochimie et de Génétique, AP-HP, Hôpital Henri-Mondor, Creteil, France.
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35
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Williams R, Holyoak T, McDonald G, Gui C, Fenton AW. Differentiating a ligand's chemical requirements for allosteric interactions from those for protein binding. Phenylalanine inhibition of pyruvate kinase. Biochemistry 2006; 45:5421-9. [PMID: 16634623 DOI: 10.1021/bi0524262] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The isoform of pyruvate kinase from brain and muscle of mammals (M(1)-PYK) is allosterically inhibited by phenylalanine. Initial observations in this model allosteric system indicate that Ala binds competitively with Phe, but elicits a minimal allosteric response. Thus, the allosteric ligand of this system must have requirements for eliciting an allosteric response in addition to the requirements for binding. Phe analogues have been used to dissect what chemical properties of Phe are responsible for eliciting the allosteric response. We first demonstrate that the l-2-aminopropanaldehyde substructure of the amino acid ligand is primarily responsible for binding to M(1)-PYK. Since the allosteric response to Ala is minimal and linear addition of methyl groups beyond the beta-carbon increase the magnitude of the allosteric response, we conclude that moieties beyond the beta-carbon are primarily responsible for allostery. Instead of an all-or-none mechanism of allostery, these findings support the idea that the bulk of the hydrophobic side chain, but not the aromatic nature, is the primary determinant of the magnitude of the observed allosteric inhibition. The use of these results to direct structural studies has resulted in a 1.65 A structure of M(1)-PYK with Ala bound. The coordination of Ala in the allosteric amino acid binding site confirms the binding role of the l-2-aminopropanaldehyde substructure of the ligand. Collectively, this study confirms that a ligand can have chemical regions specific for eliciting the allosteric signal in addition to the chemical regions necessary for binding.
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Affiliation(s)
- Rachel Williams
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas 66160, USA
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36
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Glaser F, Rosenberg Y, Kessel A, Pupko T, Ben-Tal N. The ConSurf-HSSP database: the mapping of evolutionary conservation among homologs onto PDB structures. Proteins 2006; 58:610-7. [PMID: 15614759 DOI: 10.1002/prot.20305] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The HSSP (Homology-Derived Secondary Structure of Proteins) database provides multiple sequence alignments (MSAs) for proteins of known three-dimensional (3D) structure in the Protein Data Bank (PDB). The database also contains an estimate of the degree of evolutionary conservation at each amino acid position. This estimate, which is based on the relative entropy, correlates with the functional importance of the position; evolutionarily conserved positions (i.e., positions with limited variability and low entropy) are occasionally important to maintain the 3D structure and biological function(s) of the protein. We recently developed the Rate4Site algorithm for scoring amino acid conservation based on their calculated evolutionary rate. This algorithm takes into account the phylogenetic relationships between the homologs and the stochastic nature of the evolutionary process. Here we present the ConSurf-HSSP database of Rate4Site estimates of the evolutionary rates of the amino acid positions, calculated using HSSP's MSAs. The database provides precalculated evolutionary rates for nearly all of the PDB. These rates are projected, using a color code, onto the protein structure, and can be viewed online using the ConSurf server interface. To exemplify the database, we analyzed in detail the conservation pattern obtained for pyruvate kinase and compared the results with those observed using the relative entropy scores of the HSSP database. It is reassuring to know that the main functional region of the enzyme is detectable using both conservation scores. Interestingly, the ConSurf-HSSP calculations mapped additional functionally important regions, which are moderately conserved and were overlooked by the original HSSP estimate. The ConSurf-HSSP database is available online (http://consurf-hssp.tau.ac.il).
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Affiliation(s)
- Fabian Glaser
- Department of Biochemistry, Tel Aviv University, Tel Aviv, Israel
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37
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van Wijk R, van Solinge WW. The energy-less red blood cell is lost: erythrocyte enzyme abnormalities of glycolysis. Blood 2005; 106:4034-42. [PMID: 16051738 DOI: 10.1182/blood-2005-04-1622] [Citation(s) in RCA: 205] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The red blood cell depends solely on the anaerobic conversion of glucose by the Embden-Meyerhof pathway for the generation and storage of high-energy phosphates, which is necessary for the maintenance of a number of vital functions. Many red blood cell enzymopathies have been described that disturb the erythrocyte's integrity, shorten its cellular survival, and result in hemolytic anemia. By far the majority of these enzymopathies are hereditary in nature. In this review, we summarize the current knowledge regarding the genetic, biochemical, and structural features of clinically relevant red blood cell enzymopathies involved in the Embden-Meyerhof pathway and the Rapoport-Luebering shunt.
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Affiliation(s)
- Richard van Wijk
- Department of Laboratory Medicine, Rm G03.550, University Medical Center Utrecht, PO Box 85500, 3508 GA, Utrecht, The Netherlands
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38
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Senkovich O, Speed H, Grigorian A, Bradley K, Ramarao CS, Lane B, Zhu G, Chattopadhyay D. Crystallization of three key glycolytic enzymes of the opportunistic pathogen Cryptosporidium parvum. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2005; 1750:166-72. [PMID: 15953771 DOI: 10.1016/j.bbapap.2005.04.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2004] [Revised: 04/16/2005] [Accepted: 04/18/2005] [Indexed: 11/17/2022]
Abstract
Cryptosporidium parvum is one of the major causes of waterborne diseases worldwide. This protozoan parasite depends mainly on the anaerobic oxidation of glucose for energy production. In order to identify the differences in the three-dimensional structure of key glycolytic enzymes of C. parvum and its human host, we have expressed, purified and crystallized recombinant versions of three important glycolytic enzymes of the parasite, namely, glyceraldehyde 3-phosphate dehydrogenase, pyruvate kinase and lactate dehydrogenase. Lactate dehydrogenase has been crystallized in the absence and in the presence of its substrates and cofactors, while pyruvate kinase and glyceraldehyde 3-phosphate dehydrogenase were crystallized only in the apo-form. X-ray diffraction data have been collected for all crystals.
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Affiliation(s)
- Olga Senkovich
- Center for Biophysical Sciences and Engineering, University of Alabama at Birmingham, Birmingham, AL-35294, USA
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39
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Yu S, Lee LLY, Lee JC. Effects of metabolites on the structural dynamics of rabbit muscle pyruvate kinase. Biophys Chem 2003; 103:1-11. [PMID: 12504250 DOI: 10.1016/s0301-4622(02)00146-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The activity of rabbit muscle pyruvate kinase (PK) is regulated by metabolites. Besides requiring the presence of its substrates, PEP and ADP, the enzyme requires Mg(2+) and K(+) for activity. PK is allosterically inhibited by Phe for activity. The presence of PEP or Phe has opposing effects on the hydrodynamic properties of the enzyme without an apparent change in secondary structure. In this study, the structural perturbation induced by ligand binding was investigated by Fourier transform infrared (FT-IR) spectroscopy. Furthermore, the structural dynamics of PK was probed by H/D exchange monitored by FT-IR. Substrates and activating metal ions induce PK to assume a more dynamic structure while Phe exerts an opposite effect. In all cases there is no significant interconversion of secondary structures. PEP is the most efficient ligand in inducing a change in the microenvironments of both helices and sheets so much so that they can be detected spectroscopically as separate bands. These results provide the first evidence for a differential effect of ligand binding on the dynamics of structural elements in PK. Furthermore, the data support the model that allosteric regulation of PK is the consequence of perturbation of the distribution of an ensemble of states in which the observed change in hydrodynamic properties represent the two extreme end states.
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Affiliation(s)
- Shaoning Yu
- Department of Human Biological Chemistry and Genetics, University of Texas Medical Branch, Galveston, TX 77555-1055, USA
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40
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Valentini G, Chiarelli LR, Fortin R, Dolzan M, Galizzi A, Abraham DJ, Wang C, Bianchi P, Zanella A, Mattevi A. Structure and function of human erythrocyte pyruvate kinase. Molecular basis of nonspherocytic hemolytic anemia. J Biol Chem 2002; 277:23807-14. [PMID: 11960989 DOI: 10.1074/jbc.m202107200] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Deficiency of human erythrocyte isozyme (RPK) is, together with glucose-6-phosphate dehydrogenase deficiency, the most common cause of the nonspherocytic hemolytic anemia. To provide a molecular framework to the disease, we have solved the 2.7 A resolution crystal structure of human RPK in complex with fructose 1,6-bisphosphate, the allosteric activator, and phosphoglycolate, a substrate analogue, and we have functionally and structurally characterized eight mutants (G332S, G364D, T384M, D390N, R479H, R486W, R504L, and R532W) found in RPK-deficient patients. The mutations target distinct regions of RPK structure, including domain interfaces and catalytic and allosteric sites. The mutations affect to a different extent thermostability, catalytic efficiency, and regulatory properties. These studies are the first to correlate the clinical symptoms with the molecular properties of the mutant enzymes. Mutations greatly impairing thermostability and/or activity are associated with severe anemia. Some mutant proteins exhibit moderate changes in the kinetic parameters, which are sufficient to cause mild to severe anemia, underlining the crucial role of RPK for erythrocyte metabolism. Prediction of the effects of mutations is difficult because there is no relation between the nature and location of the replaced amino acid and the type of molecular perturbation. Characterization of mutant proteins may serve as a valuable tool to assist with diagnosis and genetic counseling.
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Affiliation(s)
- Giovanna Valentini
- Dipartimento di Genetica e Microbiologia, Università di Pavia, via Abbiategrasso 207, 27100 Pavia, Italy.
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