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Delmar S Larsen - One of the best experts on this subject based on the ideXlab platform.
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conservation and diversity in the primary reverse photodynamics of the canonical red green cyanobacteriochrome family
Biochemistry, 2020Co-Authors: Adam J Jenkins, Shelley S Martin, Sean M Gottlieb, Peter W Kim, Chewei Chang, Randeep J Hayer, Samuel J Hanke, Delmar S LarsenAbstract:In this report, we compare the femtosecond to nanosecond primary reverse photodynamics (15EPg → 15ZPr) of eight tetrapyrrole binding photoswitching cyanobacteriochromes in the canonical red/green family from the cyanobacterium Nostoc punctiforme. Three characteristic classes were identified on the basis of the diversity of excited-state and ground-state properties, including the lifetime, photocycle initiation quantum yield, photointermediate stability, spectra, and temporal properties. We observed a correlation between the excited-state lifetime and peak wavelength of the electronic absorption spectrum with higher-energy-absorbing representatives exhibiting both faster excited-state decay times and higher photoisomerization quantum yields. The latter was attributed to both an increased number of structural restraints and differences in H-bonding networks that facilitate photoisomerization. All three classes exhibited primary Lumi-Go intermediates, with class II and III representatives evolving to a secondary Meta-G photointermediate. Class II Meta-GR intermediates were orange absorbing, whereas class III Meta-G had structurally relaxed, red-absorbing chromophores that resemble their dark-adapted 15ZPr states. Differences in the reverse and Forward Reaction mechanisms are discussed within the context of structural constraints.
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primary photodynamics of the green red absorbing photoswitching regulator of the chromatic adaptation e domain from fremyella diplosiphon
Biochemistry, 2013Co-Authors: Sean M Gottlieb, Nathan C Rockwell, Peter W Kim, Yuu Hirose, Masahiko Ikeuchi, Clark J Lagarias, Delmar S LarsenAbstract:Phytochromes are red/far-red photosensory proteins that utilize the photoisomerization of a linear tetrapyrrole (bilin) chromophore to detect the red to far-red light ratio. Cyanobacteriochromes (CBCRs) are distantly related cyanobacterial photosensors with homologous bilin-binding GAF domains, but they exhibit greater spectral diversity. Different CBCR subfamilies have been described, with spectral sensitivity varying across the near-ultraviolet and throughout the visible spectrum, but all known CBCRs utilize photoisomerization of the bilin 15,16-double bond as the primary photochemical event. The first CBCR discovered was RcaE, responsible for tuning light harvesting to the incident color environment (complementary chromatic adaptation) in Fremyella diplosiphon. The green/red RcaE photocycle has recently been described in detail. We now extend this analysis by examining femtosecond photodynamics using ultrafast transient absorption techniques with broadband detection and multicomponent global analysis. Excited-state dynamics in both directions are significantly slower than those recently published for the red/green CBCR NpR6012g4. In the Forward Reaction, the primary Lumi-G photoproduct arises from the longer-lived excited-state populations, leading to a low photoproduct quantum yield. Using dual-excitation wavelength interleaved pump-probe spectroscopy, we observe multiphasic excited-state dynamics in the Forward Reaction ((15Z)Pg → (15E)Pr), which we interpret as arising from ground-state inhomogeneity with different tautomers of the PCB chromophore. The reverse Reaction ((15E)Pr → (15Z)Pg) is characterized via pump-probe spectroscopy and also exhibits slow excited-state decay dynamics and a low photoproduct yield. These results provide the first description of excited-state dynamics for a green/red CBCR.
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Primary Photodynamics of the Green/Red-Absorbing Photoswitching Regulator of the Chromatic Adaptation E Domain from Fremyella diplosiphon
2013Co-Authors: Sean M Gottlieb, Nathan C Rockwell, Yuu Hirose, Masahiko Ikeuchi, Clark J Lagarias, Peter W. Kim, Delmar S LarsenAbstract:Phytochromes are red/far-red photosensory proteins that utilize the photoisomerization of a linear tetrapyrrole (bilin) chromophore to detect the red to far-red light ratio. Cyanobacteriochromes (CBCRs) are distantly related cyanobacterial photosensors with homologous bilin-binding GAF domains, but they exhibit greater spectral diversity. Different CBCR subfamilies have been described, with spectral sensitivity varying across the near-ultraviolet and throughout the visible spectrum, but all known CBCRs utilize photoisomerization of the bilin 15,16-double bond as the primary photochemical event. The first CBCR discovered was RcaE, responsible for tuning light harvesting to the incident color environment (complementary chromatic adaptation) in Fremyella diplosiphon. The green/red RcaE photocycle has recently been described in detail. We now extend this analysis by examining femtosecond photodynamics using ultrafast transient absorption techniques with broadband detection and multicomponent global analysis. Excited-state dynamics in both directions are significantly slower than those recently published for the red/green CBCR NpR6012g4. In the Forward Reaction, the primary Lumi-G photoproduct arises from the longer-lived excited-state populations, leading to a low photoproduct quantum yield. Using dual-excitation wavelength interleaved pump–probe spectroscopy, we observe multiphasic excited-state dynamics in the Forward Reaction (15ZPg → 15EPr), which we interpret as arising from ground-state inhomogeneity with different tautomers of the PCB chromophore. The reverse Reaction (15EPr → 15ZPg) is characterized via pump–probe spectroscopy and also exhibits slow excited-state decay dynamics and a low photoproduct yield. These results provide the first description of excited-state dynamics for a green/red CBCR
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second chance Forward isomerization dynamics of the red green cyanobacteriochrome npr6012g4 from nostoc punctiforme
Journal of the American Chemical Society, 2012Co-Authors: Lucy H Freer, Nathan C Rockwell, Shelley S Martin, Delmar S LarsenAbstract:The primary ultrafast Z-to-E isomerization photodynamics of the phytochrome-related cyanobacteriochrome NpR6012g4 from Nostoc punctiforme was studied by transient absorption pump–dump–probe spectroscopy. A 2 ps dump pulse resonant with the stimulated emission band depleted 21% of the excited-state population, while the initial photoproduct Lumi-R was depleted by only 11%. We observed a red-shifted ground-state intermediate (GSI) that we assign to a metastable state that failed to isomerize fully. Multicomponent global analysis implicates the generation of additional Lumi-R from the GSI via crossing over the ground-state thermal barrier for full isomerization, explaining the discrepancy between excited-state and Lumi-R depletion by the dump pulse. This second-chance ground-state dynamics provides a plausible explanation for the unusually high quantum yield of 40% for the primary isomerization step in the Forward Reaction of NpR6012g4.
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femtosecond photodynamics of the red green cyanobacteriochrome npr6012g4 from nostoc punctiforme 1 Forward dynamics
Biochemistry, 2012Co-Authors: Lucy H Freer, Nathan C Rockwell, Shelley S Martin, Delmar S LarsenAbstract:Phytochromes are well-known red/far-red photosensory proteins that utilize the photoisomerization of a linear tetrapyrrole (bilin) chromophore to detect the ratio of red to far-red light. Cyanobacteriochromes (CBCRs) are related photosensory proteins with a bilin-binding GAF domain, but much more diverse spectral sensitivity, with five recognized subfamilies of CBCRs described to date. The mechanisms that underlie this spectral diversity have not yet been fully elucidated. One of the main CBCR subfamilies photoconverts between a red-absorbing ground state, like the familiar Pr state of phytochromes, and a green-absorbing photoproduct (Pg). Here, we examine the ultrafast Forward photodynamics of the red/green CBCR NpR6012g4 from the NpR6012 locus of the nitrogen-fixing cyanobacterium Nostoc punctiforme. Using transient absorption spectroscopy with broadband detection and multicomponent global analysis, we observed multiphasic excited-state dynamics that induces the Forward Reaction (red-absorbing to green-...
Lucy H Freer - One of the best experts on this subject based on the ideXlab platform.
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second chance Forward isomerization dynamics of the red green cyanobacteriochrome npr6012g4 from nostoc punctiforme
Journal of the American Chemical Society, 2012Co-Authors: Lucy H Freer, Nathan C Rockwell, Shelley S Martin, Delmar S LarsenAbstract:The primary ultrafast Z-to-E isomerization photodynamics of the phytochrome-related cyanobacteriochrome NpR6012g4 from Nostoc punctiforme was studied by transient absorption pump–dump–probe spectroscopy. A 2 ps dump pulse resonant with the stimulated emission band depleted 21% of the excited-state population, while the initial photoproduct Lumi-R was depleted by only 11%. We observed a red-shifted ground-state intermediate (GSI) that we assign to a metastable state that failed to isomerize fully. Multicomponent global analysis implicates the generation of additional Lumi-R from the GSI via crossing over the ground-state thermal barrier for full isomerization, explaining the discrepancy between excited-state and Lumi-R depletion by the dump pulse. This second-chance ground-state dynamics provides a plausible explanation for the unusually high quantum yield of 40% for the primary isomerization step in the Forward Reaction of NpR6012g4.
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femtosecond photodynamics of the red green cyanobacteriochrome npr6012g4 from nostoc punctiforme 1 Forward dynamics
Biochemistry, 2012Co-Authors: Lucy H Freer, Nathan C Rockwell, Shelley S Martin, Delmar S LarsenAbstract:Phytochromes are well-known red/far-red photosensory proteins that utilize the photoisomerization of a linear tetrapyrrole (bilin) chromophore to detect the ratio of red to far-red light. Cyanobacteriochromes (CBCRs) are related photosensory proteins with a bilin-binding GAF domain, but much more diverse spectral sensitivity, with five recognized subfamilies of CBCRs described to date. The mechanisms that underlie this spectral diversity have not yet been fully elucidated. One of the main CBCR subfamilies photoconverts between a red-absorbing ground state, like the familiar Pr state of phytochromes, and a green-absorbing photoproduct (Pg). Here, we examine the ultrafast Forward photodynamics of the red/green CBCR NpR6012g4 from the NpR6012 locus of the nitrogen-fixing cyanobacterium Nostoc punctiforme. Using transient absorption spectroscopy with broadband detection and multicomponent global analysis, we observed multiphasic excited-state dynamics that induces the Forward Reaction (red-absorbing to green-...
Shelley S Martin - One of the best experts on this subject based on the ideXlab platform.
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conservation and diversity in the primary reverse photodynamics of the canonical red green cyanobacteriochrome family
Biochemistry, 2020Co-Authors: Adam J Jenkins, Shelley S Martin, Sean M Gottlieb, Peter W Kim, Chewei Chang, Randeep J Hayer, Samuel J Hanke, Delmar S LarsenAbstract:In this report, we compare the femtosecond to nanosecond primary reverse photodynamics (15EPg → 15ZPr) of eight tetrapyrrole binding photoswitching cyanobacteriochromes in the canonical red/green family from the cyanobacterium Nostoc punctiforme. Three characteristic classes were identified on the basis of the diversity of excited-state and ground-state properties, including the lifetime, photocycle initiation quantum yield, photointermediate stability, spectra, and temporal properties. We observed a correlation between the excited-state lifetime and peak wavelength of the electronic absorption spectrum with higher-energy-absorbing representatives exhibiting both faster excited-state decay times and higher photoisomerization quantum yields. The latter was attributed to both an increased number of structural restraints and differences in H-bonding networks that facilitate photoisomerization. All three classes exhibited primary Lumi-Go intermediates, with class II and III representatives evolving to a secondary Meta-G photointermediate. Class II Meta-GR intermediates were orange absorbing, whereas class III Meta-G had structurally relaxed, red-absorbing chromophores that resemble their dark-adapted 15ZPr states. Differences in the reverse and Forward Reaction mechanisms are discussed within the context of structural constraints.
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second chance Forward isomerization dynamics of the red green cyanobacteriochrome npr6012g4 from nostoc punctiforme
Journal of the American Chemical Society, 2012Co-Authors: Lucy H Freer, Nathan C Rockwell, Shelley S Martin, Delmar S LarsenAbstract:The primary ultrafast Z-to-E isomerization photodynamics of the phytochrome-related cyanobacteriochrome NpR6012g4 from Nostoc punctiforme was studied by transient absorption pump–dump–probe spectroscopy. A 2 ps dump pulse resonant with the stimulated emission band depleted 21% of the excited-state population, while the initial photoproduct Lumi-R was depleted by only 11%. We observed a red-shifted ground-state intermediate (GSI) that we assign to a metastable state that failed to isomerize fully. Multicomponent global analysis implicates the generation of additional Lumi-R from the GSI via crossing over the ground-state thermal barrier for full isomerization, explaining the discrepancy between excited-state and Lumi-R depletion by the dump pulse. This second-chance ground-state dynamics provides a plausible explanation for the unusually high quantum yield of 40% for the primary isomerization step in the Forward Reaction of NpR6012g4.
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femtosecond photodynamics of the red green cyanobacteriochrome npr6012g4 from nostoc punctiforme 1 Forward dynamics
Biochemistry, 2012Co-Authors: Lucy H Freer, Nathan C Rockwell, Shelley S Martin, Delmar S LarsenAbstract:Phytochromes are well-known red/far-red photosensory proteins that utilize the photoisomerization of a linear tetrapyrrole (bilin) chromophore to detect the ratio of red to far-red light. Cyanobacteriochromes (CBCRs) are related photosensory proteins with a bilin-binding GAF domain, but much more diverse spectral sensitivity, with five recognized subfamilies of CBCRs described to date. The mechanisms that underlie this spectral diversity have not yet been fully elucidated. One of the main CBCR subfamilies photoconverts between a red-absorbing ground state, like the familiar Pr state of phytochromes, and a green-absorbing photoproduct (Pg). Here, we examine the ultrafast Forward photodynamics of the red/green CBCR NpR6012g4 from the NpR6012 locus of the nitrogen-fixing cyanobacterium Nostoc punctiforme. Using transient absorption spectroscopy with broadband detection and multicomponent global analysis, we observed multiphasic excited-state dynamics that induces the Forward Reaction (red-absorbing to green-...
Nathan C Rockwell - One of the best experts on this subject based on the ideXlab platform.
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primary photodynamics of the green red absorbing photoswitching regulator of the chromatic adaptation e domain from fremyella diplosiphon
Biochemistry, 2013Co-Authors: Sean M Gottlieb, Nathan C Rockwell, Peter W Kim, Yuu Hirose, Masahiko Ikeuchi, Clark J Lagarias, Delmar S LarsenAbstract:Phytochromes are red/far-red photosensory proteins that utilize the photoisomerization of a linear tetrapyrrole (bilin) chromophore to detect the red to far-red light ratio. Cyanobacteriochromes (CBCRs) are distantly related cyanobacterial photosensors with homologous bilin-binding GAF domains, but they exhibit greater spectral diversity. Different CBCR subfamilies have been described, with spectral sensitivity varying across the near-ultraviolet and throughout the visible spectrum, but all known CBCRs utilize photoisomerization of the bilin 15,16-double bond as the primary photochemical event. The first CBCR discovered was RcaE, responsible for tuning light harvesting to the incident color environment (complementary chromatic adaptation) in Fremyella diplosiphon. The green/red RcaE photocycle has recently been described in detail. We now extend this analysis by examining femtosecond photodynamics using ultrafast transient absorption techniques with broadband detection and multicomponent global analysis. Excited-state dynamics in both directions are significantly slower than those recently published for the red/green CBCR NpR6012g4. In the Forward Reaction, the primary Lumi-G photoproduct arises from the longer-lived excited-state populations, leading to a low photoproduct quantum yield. Using dual-excitation wavelength interleaved pump-probe spectroscopy, we observe multiphasic excited-state dynamics in the Forward Reaction ((15Z)Pg → (15E)Pr), which we interpret as arising from ground-state inhomogeneity with different tautomers of the PCB chromophore. The reverse Reaction ((15E)Pr → (15Z)Pg) is characterized via pump-probe spectroscopy and also exhibits slow excited-state decay dynamics and a low photoproduct yield. These results provide the first description of excited-state dynamics for a green/red CBCR.
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Primary Photodynamics of the Green/Red-Absorbing Photoswitching Regulator of the Chromatic Adaptation E Domain from Fremyella diplosiphon
2013Co-Authors: Sean M Gottlieb, Nathan C Rockwell, Yuu Hirose, Masahiko Ikeuchi, Clark J Lagarias, Peter W. Kim, Delmar S LarsenAbstract:Phytochromes are red/far-red photosensory proteins that utilize the photoisomerization of a linear tetrapyrrole (bilin) chromophore to detect the red to far-red light ratio. Cyanobacteriochromes (CBCRs) are distantly related cyanobacterial photosensors with homologous bilin-binding GAF domains, but they exhibit greater spectral diversity. Different CBCR subfamilies have been described, with spectral sensitivity varying across the near-ultraviolet and throughout the visible spectrum, but all known CBCRs utilize photoisomerization of the bilin 15,16-double bond as the primary photochemical event. The first CBCR discovered was RcaE, responsible for tuning light harvesting to the incident color environment (complementary chromatic adaptation) in Fremyella diplosiphon. The green/red RcaE photocycle has recently been described in detail. We now extend this analysis by examining femtosecond photodynamics using ultrafast transient absorption techniques with broadband detection and multicomponent global analysis. Excited-state dynamics in both directions are significantly slower than those recently published for the red/green CBCR NpR6012g4. In the Forward Reaction, the primary Lumi-G photoproduct arises from the longer-lived excited-state populations, leading to a low photoproduct quantum yield. Using dual-excitation wavelength interleaved pump–probe spectroscopy, we observe multiphasic excited-state dynamics in the Forward Reaction (15ZPg → 15EPr), which we interpret as arising from ground-state inhomogeneity with different tautomers of the PCB chromophore. The reverse Reaction (15EPr → 15ZPg) is characterized via pump–probe spectroscopy and also exhibits slow excited-state decay dynamics and a low photoproduct yield. These results provide the first description of excited-state dynamics for a green/red CBCR
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second chance Forward isomerization dynamics of the red green cyanobacteriochrome npr6012g4 from nostoc punctiforme
Journal of the American Chemical Society, 2012Co-Authors: Lucy H Freer, Nathan C Rockwell, Shelley S Martin, Delmar S LarsenAbstract:The primary ultrafast Z-to-E isomerization photodynamics of the phytochrome-related cyanobacteriochrome NpR6012g4 from Nostoc punctiforme was studied by transient absorption pump–dump–probe spectroscopy. A 2 ps dump pulse resonant with the stimulated emission band depleted 21% of the excited-state population, while the initial photoproduct Lumi-R was depleted by only 11%. We observed a red-shifted ground-state intermediate (GSI) that we assign to a metastable state that failed to isomerize fully. Multicomponent global analysis implicates the generation of additional Lumi-R from the GSI via crossing over the ground-state thermal barrier for full isomerization, explaining the discrepancy between excited-state and Lumi-R depletion by the dump pulse. This second-chance ground-state dynamics provides a plausible explanation for the unusually high quantum yield of 40% for the primary isomerization step in the Forward Reaction of NpR6012g4.
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femtosecond photodynamics of the red green cyanobacteriochrome npr6012g4 from nostoc punctiforme 1 Forward dynamics
Biochemistry, 2012Co-Authors: Lucy H Freer, Nathan C Rockwell, Shelley S Martin, Delmar S LarsenAbstract:Phytochromes are well-known red/far-red photosensory proteins that utilize the photoisomerization of a linear tetrapyrrole (bilin) chromophore to detect the ratio of red to far-red light. Cyanobacteriochromes (CBCRs) are related photosensory proteins with a bilin-binding GAF domain, but much more diverse spectral sensitivity, with five recognized subfamilies of CBCRs described to date. The mechanisms that underlie this spectral diversity have not yet been fully elucidated. One of the main CBCR subfamilies photoconverts between a red-absorbing ground state, like the familiar Pr state of phytochromes, and a green-absorbing photoproduct (Pg). Here, we examine the ultrafast Forward photodynamics of the red/green CBCR NpR6012g4 from the NpR6012 locus of the nitrogen-fixing cyanobacterium Nostoc punctiforme. Using transient absorption spectroscopy with broadband detection and multicomponent global analysis, we observed multiphasic excited-state dynamics that induces the Forward Reaction (red-absorbing to green-...
Yuqi Wang - One of the best experts on this subject based on the ideXlab platform.
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perturbation of phosphoglycerate kinase 1 pgk1 only marginally affects glycolysis in cancer cells
Journal of Biological Chemistry, 2020Co-Authors: Hao Wu, Yuqi Wang, Xun HuAbstract:Phosphoglycerate kinase 1 (PGK1) plays important roles in glycolysis, yet its Forward Reaction kinetics are unknown, and its role especially in regulating cancer cell glycolysis is unclear. Here, we developed an enzyme assay to measure the kinetic parameters of the PGK1-catalyzed Forward Reaction. The Km values for 1,3-bisphosphoglyceric acid (1,3-BPG, the Forward Reaction substrate) were 4.36 muM (yeast PGK1) and 6.86 muM (human PKG1). The Km values for 3-phosphoglycerate (3-PG, the reverse Reaction substrate and a serine precursor) were 146 muM (yeast PGK1) and 186 muM (human PGK1). The Vmax of the Forward Reaction was about 3.5- and 5.8-fold higher than that of the reverse Reaction for the human and yeast enzymes, respectively. Consistently, the intracellular steady-state concentrations of 3-PG were between 180 and 550 muM in cancer cells, providing a basis for glycolysis to shuttle 3-PG to the serine synthesis pathway. Using siRNA-mediated PGK1-specific knockdown in five cancer cell lines derived from different tissues, along with titration of PGK1 in a cell-free glycolysis system, we found that the perturbation of PGK1 had no or only marginal effects on the glucose consumption and lactate generation. The PGK1 knockdown increased the concentrations of fructose 1,6-bisphosphate (FBP), dihydroxyacetone phosphate (DHAP), glyceraldehyde 3-phosphate (GA3P), and 1,3-BPG in nearly equal proportions, controlled by the kinetic and thermodynamic states of glycolysis. We conclude that perturbation of PGK1 in cancer cells insignificantly affects the conversion of glucose to lactate in glycolysis.
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perturbation of phosphoglycerate kinase 1 pgk1 only marginally affects glycolysis in cancer cells
Journal of Biological Chemistry, 2020Co-Authors: Chengmeng Jin, Xiaobing Zhu, Yuqi WangAbstract:Phosphoglycerate kinase 1 (PGK1) plays important roles in glycolysis, yet its Forward Reaction kinetics are unknown, and its role especially in regulating cancer cell glycolysis is unclear. Here, we developed an enzyme assay to measure the kinetic parameters of the PGK1-catalyzed Forward Reaction. The Km values for 1,3-bisphosphoglyceric acid (1,3-BPG, the Forward Reaction substrate) were 4.36 μm (yeast PGK1) and 6.86 μm (human PKG1). The Km values for 3-phosphoglycerate (3-PG, the reverse Reaction substrate and a serine precursor) were 146 μm (yeast PGK1) and 186 μm (human PGK1). The Vmax of the Forward Reaction was about 3.5- and 5.8-fold higher than that of the reverse Reaction for the human and yeast enzymes, respectively. Consistently, the intracellular steady-state concentrations of 3-PG were between 180 and 550 μm in cancer cells, providing a basis for glycolysis to shuttle 3-PG to the serine synthesis pathway. Using siRNA-mediated PGK1-specific knockdown in five cancer cell lines derived from different tissues, along with titration of PGK1 in a cell-free glycolysis system, we found that the perturbation of PGK1 had no effect or only marginal effects on the glucose consumption and lactate generation. The PGK1 knockdown increased the concentrations of fructose 1,6-bisphosphate, dihydroxyacetone phosphate, glyceraldehyde 3-phosphate, and 1,3-BPG in nearly equal proportions, controlled by the kinetic and thermodynamic states of glycolysis. We conclude that perturbation of PGK1 in cancer cells insignificantly affects the conversion of glucose to lactate in glycolysis.
