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Biochemistry. Biokhimiia Mar 1998Structures of proteins in unfolded states have important implications for the protein folding problem and for the translocation of polypeptide chains. Acid-denatured,... (Review)
Review
Structures of proteins in unfolded states have important implications for the protein folding problem and for the translocation of polypeptide chains. Acid-denatured, cold-denatured, and 6 M guanidine hydrochloride (GuHCl) denatured yeast phosphoglycerate kinase (PGK) are ensembles of flexible unfolded molecules with rapidly interconverting structures of the individual polypeptide chains. They differ, however, in their physical properties, such as in coil size and in stiffness over a short distance along the chain. These properties of polypeptide chains can be described well by persistence statistics. A solution containing 0.7 M GuHCl at 4.5 degrees C is nearly a Theta-solvent for PGK. By contrast, 6 M GuHCl is a good solvent for PGK. Acid-denatured PGK at low ionic strength has the most expanded and stiffest chains. The conformation of heat-denatured PGK should be more compact than that of random walk chains at the Theta-point, as can be inferred from measurements on other proteins. Investigations of heat-denatured PGK by scattering methods are unfeasible due to aggregation of the protein. The persistence length as a measure of chain stiffness varies between a = 1.74 nm for cold-denatured PGK and a = 3.0 nm for acid-denatured PGK. The distribution functions of the gyration radii were calculated from the X-ray scattering data for all unfolded states and compared with the radius of gyration of the natively folded molecule.
Topics: Models, Molecular; Phosphoglycerate Kinase; Protein Conformation; Protein Denaturation; Protein Folding; Saccharomyces cerevisiae
PubMed: 9526123
DOI: No ID Found -
Proceedings of the National Academy of... Apr 2023The canonical role of the transcription factor E2F is to control the expression of cell cycle genes by binding to the E2F sites in their promoters. However, the list of...
The canonical role of the transcription factor E2F is to control the expression of cell cycle genes by binding to the E2F sites in their promoters. However, the list of putative E2F target genes is extensive and includes many metabolic genes, yet the significance of E2F in controlling the expression of these genes remains largely unknown. Here, we used the CRISPR/Cas9 technology to introduce point mutations in the E2F sites upstream of five endogenous metabolic genes in . We found that the impact of these mutations on both the recruitment of E2F and the expression of the target genes varied, with the glycolytic gene, (, being mostly affected. The loss of E2F regulation on the gene led to a decrease in glycolytic flux, tricarboxylic acid cycle intermediates levels, adenosine triphosphate (ATP) content, and an abnormal mitochondrial morphology. Remarkably, chromatin accessibility was significantly reduced at multiple genomic regions in mutants. These regions contained hundreds of genes, including metabolic genes that were downregulated in mutants. Moreover, animals had shortened life span and exhibited defects in high-energy consuming organs, such as ovaries and muscles. Collectively, our results illustrate how the pleiotropic effects on metabolism, gene expression, and development in the animals underscore the importance of E2F regulation on a single E2F target, .
Topics: Animals; Chromatin; Drosophila; E2F Transcription Factors; Phosphoglycerate Kinase; Promoter Regions, Genetic; Drosophila Proteins
PubMed: 37011211
DOI: 10.1073/pnas.2220770120 -
Neurochemistry International Oct 2020Patients with Parkinson's disease (PD) show a common progressive neurodegenerative movement disorder characterized by rigidity, tremors, postural instability, and...
Patients with Parkinson's disease (PD) show a common progressive neurodegenerative movement disorder characterized by rigidity, tremors, postural instability, and bradykinesia due to the loss of dopaminergic neurons in the substantia nigra, and is often accompanied by several non-motor symptoms, called parkinsonism. Several lines of recent evidence support the hypothesis that mutations in the gene encoding phosphoglycerate kinase (PGK) play an important role in the PD mechanism. PGK is a key enzyme in the glycolytic pathway that catalyzes the reaction from 1,3-diphosphoglycerate to 3-phosphoglycerate. We herein established a parkinsonism model targeting Drosophila Pgk. Dopaminergic (DA) neuron-specific Pgk knockdown lead to locomotive defects in both young and aged adult flies and was accompanied by progressive DA neuron loss with aging. Pgk knockdown in DA neurons decreased dopamine levels in the central nervous system (CNS) of both young and aged adult flies. These phenotypes are similar to the defects observed in human PD patients, suggesting that the Pgk knockdown flies established herein are a promising model for parkinsonism. Furthermore, pan-neuron-specific Pgk knockdown induced low ATP levels and the accumulation of reactive oxygen species (ROS) in the CNS of third instar larvae. Collectively, these results indicate that a failure in the energy production system of Pgk knockdown flies causes locomotive defects accompanied by neuronal dysfunction and degeneration in DA neurons.
Topics: Amino Acid Sequence; Animals; Animals, Genetically Modified; Dopaminergic Neurons; Drosophila; Drosophila Proteins; Humans; Parkinsonian Disorders; Phosphoglycerate Kinase
PubMed: 32758590
DOI: 10.1016/j.neuint.2020.104816 -
Journal of Biomolecular Structure &... Nov 2023In the glycolysis pathway, phosphoglycerate kinase 1 (PGK1) transfers one phosphoryl-group from 1,3-diphosphoglycerate (1,3BPG) to ADP to product 3-phosphoglycerate...
In the glycolysis pathway, phosphoglycerate kinase 1 (PGK1) transfers one phosphoryl-group from 1,3-diphosphoglycerate (1,3BPG) to ADP to product 3-phosphoglycerate (3PG) and ATP. The catalytic process is accompanied with the conversion between the open conformation and the closed conformation of PGK1. However, the dynamic collaboration mechanism between the PGK1 conformation transition and the products releasing process remains poorly understood. Here using molecular dynamics simulations combined with molecular mechanics generalized born surface area (MM/GBSA) analysis, we demonstrated that PGK1 in the closed conformation first releases the product ATP to reach a semi-open conformation, and releases the product 3PG to achieve the full open conformation, which could accept new substrates ADP and 1,3BPG for the next cycle. It is noteworthy that the phosphorylation of PGK1 at T243 causes the loop region (residues L248-E260) flip outside the protein, and the phosphorylation of Y324 leads PGK1 become looser. Both modifications cause the exposure of the ADP/ATP binding site, which was beneficial for the substrates/products binding/releasing of PGK1. In addition, the other post translational modifications (PTMs) were also able to regulate the ligands binding/releasing with different effects. Our results revealed the dynamic cooperative molecular mechanism of PGK1 conformational transition with products releasing, as well as the influence of PTMs, which would contribute to the understanding of PGK1 substrates/products conversion process and the development of small molecule drugs targeting PGK1.Communicated by Ramaswamy H. Sarma.
Topics: Phosphoglycerate Kinase; Phosphorylation; Signal Transduction; Protein Processing, Post-Translational; Adenosine Triphosphate
PubMed: 36455998
DOI: 10.1080/07391102.2022.2152870 -
Hoppe-Seyler's Zeitschrift Fur... Nov 1974
Topics: Adenosine Diphosphate; Adenosine Monophosphate; Amino Acids; Animals; Benzoates; Cattle; Chromatography, Gel; Chromatography, Ion Exchange; Hydrogen-Ion Concentration; Kidney; Kinetics; Molecular Weight; Nitro Compounds; Phosphoglycerate Kinase; Protein Conformation; Sulfhydryl Compounds
PubMed: 4461641
DOI: 10.1515/bchm2.1974.355.2.1405 -
Bailliere's Best Practice & Research.... Mar 2000Phosphoglycerate kinase (PGK) deficiency is associated with hereditary haemolytic anaemia and often with central nervous system dysfunction and/or myopathy. Twenty-three... (Review)
Review
Phosphoglycerate kinase (PGK) deficiency is associated with hereditary haemolytic anaemia and often with central nervous system dysfunction and/or myopathy. Twenty-three families have been discovered with this condition. Nine have manifested both symptoms, six only haemolysis, and seven central nervous system dysfunction and/or myopathy without haemolysis; one case is asymptomatic. Among them, the structural abnormalities of 14 mutants, including 11 missense mutations, 1 gene deletion, 1 gene insertion, and 1 splicing mutation, have been identified. The correlation between the phenotypic and structural differences in PGK deficiency remains to be defined. Splenectomy obviates transfusion in most patients but does not correct the haemolytic disorder. Phosphofructokinase (PFK) deficiency is associated with myopathy and/or haemolysis. More than half reported had the typical features of glycogen storage disease type VII (Tarui disease). The other cases exhibited myopathy alone, haemolytic anaemia alone, or no clinical symptom at all. Eight missense, 1 nonsense, 1 frameshift and 5 splicing mutations have been determined in the PFK-M gene. In classic PFK-M deficiency, the avoidance of undue exertion is the key to prevent muscle symptoms.
Topics: Anemia, Hemolytic, Congenital; Animals; Erythrocytes; Humans; Models, Molecular; Molecular Structure; Mutation; Phosphofructokinase-1; Phosphoglycerate Kinase
PubMed: 10916683
DOI: 10.1053/beha.1999.0062 -
British Journal of Haematology Jan 2007Phosphoglycerate kinase (PGK) deficiency is one of the relatively uncommon causes of hereditary non-spherocytic haemolytic anaemia (HNSHA). The gene encoding the... (Review)
Review
Phosphoglycerate kinase (PGK) deficiency is one of the relatively uncommon causes of hereditary non-spherocytic haemolytic anaemia (HNSHA). The gene encoding the erythrocyte enzyme PGK1, is X-linked. Mutations of this gene may cause chronic haemolysis with or without mental retardation and they may cause myopathies, often with episodes of myoglobinuria, or a combination of these clinical manifestations. Twenty-six families have been described and in 20 of these the mutations are known. The reason for different clinical manifestations of mutations of the same gene remains unknown.
Topics: Anemia, Hemolytic, Congenital Nonspherocytic; Base Sequence; Genetic Diseases, X-Linked; Humans; Molecular Sequence Data; Mutation; Phosphoglycerate Kinase; Protein Conformation
PubMed: 17222195
DOI: 10.1111/j.1365-2141.2006.06351.x -
Methods in Enzymology 1982
Topics: Amino Acids; Geobacillus stearothermophilus; Kinetics; Molecular Weight; NAD; Phosphoglycerate Kinase; Spectrophotometry, Ultraviolet; Substrate Specificity
PubMed: 7154941
DOI: 10.1016/s0076-6879(82)90118-5 -
Journal of Biochemistry Oct 1974
Comparative Study
Topics: Amino Acids; Bacillus; Cations, Divalent; Cations, Monovalent; Chromatography, DEAE-Cellulose; Chromatography, Gel; Drug Stability; Electrophoresis, Disc; Hot Temperature; Hydrogen-Ion Concentration; Kinetics; Molecular Weight; Phosphoglycerate Kinase; Protein Binding; Protein Conformation; Protein Denaturation; Ribonucleotides; Species Specificity; Spectrophotometry, Ultraviolet; Streptomycin; Structure-Activity Relationship; Sulfhydryl Compounds; Urea
PubMed: 4436288
DOI: No ID Found -
Proceedings of the National Academy of... Dec 2021Glycolysis plays a fundamental role in energy production and metabolic homeostasis. The intracellular [adenosine triphosphate]/[adenosine diphosphate] ([ATP]/[ADP])...
Glycolysis plays a fundamental role in energy production and metabolic homeostasis. The intracellular [adenosine triphosphate]/[adenosine diphosphate] ([ATP]/[ADP]) ratio controls glycolytic flux; however, the regulatory mechanism underlying reactions catalyzed by individual glycolytic enzymes enabling flux adaptation remains incompletely understood. Phosphoglycerate kinase (PGK) catalyzes the reversible phosphotransfer reaction, which directly produces ATP in a near-equilibrium step of glycolysis. Despite extensive studies on the transcriptional regulation of PGK expression, the mechanism in response to changes in the [ATP]/[ADP] ratio remains obscure. Here, we report a protein-level regulation of human PGK (hPGK) by utilizing the switching ligand-binding cooperativities between adenine nucleotides and 3-phosphoglycerate (3PG). This was revealed by nuclear magnetic resonance (NMR) spectroscopy at physiological salt concentrations. MgADP and 3PG bind to hPGK with negative cooperativity, whereas MgAMPPNP (a nonhydrolyzable ATP analog) and 3PG bind to hPGK with positive cooperativity. These opposite cooperativities enable a shift between different ligand-bound states depending on the intracellular [ATP]/[ADP] ratio. Based on these findings, we present an atomic-scale description of the reaction scheme for hPGK under physiological conditions. Our results indicate that hPGK intrinsically modulates its function via ligand-binding cooperativities that are finely tuned to respond to changes in the [ATP]/[ADP] ratio. The alteration of ligand-binding cooperativities could be one of the self-regulatory mechanisms for enzymes in bidirectional pathways, which enables rapid adaptation to changes in the intracellular environment.
Topics: Adenosine Diphosphate; Adenosine Triphosphate; Catalysis; Catalytic Domain; Escherichia coli; Gene Expression Regulation, Enzymologic; Glyceric Acids; Glycolysis; Humans; Models, Molecular; Phosphoglycerate Kinase; Protein Binding; Protein Conformation
PubMed: 34893542
DOI: 10.1073/pnas.2112986118