The Experts below are selected from a list of 2046 Experts worldwide ranked by ideXlab platform
Alan Aspuruguzik - One of the best experts on this subject based on the ideXlab platform.
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mechanistic regimes of vibronic transport in a heterodimer and the design principle of incoherent vibronic transport in Phycobiliproteins
Journal of Physical Chemistry Letters, 2018Co-Authors: Doran I G Bennett, Christoph Kreisbeck, Alan Aspuruguzik, Pavel Malý, Rienk Van GrondelleAbstract:Following the observation of coherent oscillations in nonlinear spectra of photosynthetic pigment protein complexes, in particular, phycobilliproteins such as PC645, coherent vibronic transport has been suggested as a design principle for novel light-harvesting materials. Vibronic transport between energetically remote pigments is coherent when the presence of a vibration resonant with the electronic energy gap supports transient delocalization between the electronic excited states. We establish the mechanism of vibronic transport for a model heterodimer across a wide range of molecular parameter values. The resulting mechanistic map demonstrates that the molecular parameters of Phycobiliproteins in fact support incoherent vibronic transport. This result points to an important design principle: Incoherent vibronic transport is more efficient than a coherent mechanism when energetic disorder exceeds the coupling between the donor and vibrationally excited acceptor states. Finally, our results suggest that ...
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local protein solvation drives direct down conversion in phycobiliprotein pc645 via incoherent vibronic transport
Proceedings of the National Academy of Sciences of the United States of America, 2018Co-Authors: Samuel M Blau, Doran I G Bennett, Christoph Kreisbeck, Gregory D Scholes, Alan AspuruguzikAbstract:The mechanisms controlling excitation energy transport (EET) in light-harvesting complexes remain controversial. Following the observation of long-lived beats in 2D electronic spectroscopy of PC645, vibronic coherence, the delocalization of excited states between pigments supported by a resonant vibration, has been proposed to enable direct excitation transport from the highest-energy to the lowest-energy pigments, bypassing a collection of intermediate states. Here, we instead show that for phycobiliprotein PC645 an incoherent vibronic transport mechanism is at play. We quantify the solvation dynamics of individual pigments using ab initio quantum mechanics/molecular mechanics (QM/MM) nuclear dynamics. Our atomistic spectral densities reproduce experimental observations ranging from absorption and fluorescence spectra to the timescales and selectivity of down-conversion observed in transient absorption measurements. We construct a general model for vibronic dimers and establish the parameter regimes of coherent and incoherent vibronic transport. We demonstrate that direct down-conversion in PC645 proceeds incoherently, enhanced by large reorganization energies and a broad collection of high-frequency vibrations. We suggest that a similar incoherent mechanism is appropriate across Phycobiliproteins and represents a potential design principle for nanoscale control of EET.
Donald A Bryant - One of the best experts on this subject based on the ideXlab platform.
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far red light allophycocyanin subunits play a role in chlorophyll d accumulation in far red light
Photosynthesis Research, 2020Co-Authors: Nathan Soulier, Gavin M Turner, Ming Yang Ho, Tatiana N Laremore, Gaozhong Shen, Donald A BryantAbstract:Some terrestrial cyanobacteria acclimate to and utilize far-red light (FRL; λ = 700–800 nm) for oxygenic photosynthesis, a process known as far-red light photoacclimation (FaRLiP). A conserved, 20-gene FaRLiP cluster encodes core subunits of Photosystem I (PSI) and Photosystem II (PSII), five phycobiliprotein subunits of FRL-bicylindrical cores, and enzymes for synthesis of chlorophyll (Chl) f and possibly Chl d. Deletion mutants for each of the five apc genes of the FaRLiP cluster were constructed in Synechococcus sp. PCC 7335, and all had similar phenotypes. When the mutants were grown in white (WL) or red (RL) light, the cells closely resembled the wild-type (WT) strain grown under the same conditions. However, the WT and mutant strains were very different when grown under FRL. Mutants grown in FRL were unable to assemble FRL-bicylindrical cores, were essentially devoid of FRL-specific Phycobiliproteins, but retained RL-type phycobilisomes and WL-PSII. The transcript levels for genes of the FaRLiP cluster in the mutants were similar to those in WT. Surprisingly, the Chl d contents of the mutant strains were greatly reduced (~ 60–99%) compared to WT and so were the levels of FRL-PSII. We infer that Chl d may be essential for the assembly of FRL-PSII, which does not accumulate to normal levels in the mutants. We further infer that the cysteine-rich subunits of FRL allophycocyanin may either directly participate in the synthesis of Chl d or that FRL bicylindrical cores stabilize FRL-PSII to prevent loss of Chl d.
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phycobiliprotein biosynthesis in cyanobacteria structure and function of enzymes involved in post translational modification
Advances in Experimental Medicine and Biology, 2010Co-Authors: Wendy M Schluchter, Avijit Biswas, Gaozhong Shen, Richard M Alvey, Nicolle A Saunee, Shervonda R Williams, Crystal A Mille, Donald A BryantAbstract:Cyanobacterial Phycobiliproteins are brilliantly colored due to the presence of covalently attached chromophores called bilins, linear tetrapyrroles derived from heme. For most Phycobiliproteins, these post-translational modifications are catalyzed by enzymes called bilin lyases; these enzymes ensure that the appropriate bilins are attached to the correct cysteine residues with the proper stereochemistry on each phycobiliprotein subunit. Phycobiliproteins also contain a unique, post-translational modification, the methylation of a conserved asparagine (Asn) present at β-72, which occurs on the β-subunits of all Phycobiliproteins. We have identified and characterized several new families of bilin lyases, which are responsible for attaching PCB to Phycobiliproteins as well as the Asn methyl transferase for β-subunits in Synechococcus sp. PCC 7002 and Synechocystis sp. PCC 6803. All of the enzymes responsible for synthesis of holo-Phycobiliproteins are now known for this cyanobacterium, and a brief discussion of each enzyme family and its role in the biosynthesis of Phycobiliproteins is presented here. In addition, the first structure of a bilin lyase has recently been solved (PDB ID: 3BDR). This structure shows that the bilin lyases are most similar to the lipocalin protein structural family, which also includes the bilin-binding protein found in some butterflies.
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cpcm posttranslationally methylates asparagine 71 72 of phycobiliprotein beta subunits in synechococcus sp strain pcc 7002 and synechocystis sp strain pcc 6803
Journal of Bacteriology, 2008Co-Authors: Gaozhong Shen, Wendy M Schluchter, Heidi S Leonard, Donald A BryantAbstract:Cyanobacteria produce phycobilisomes, which are macromolecular light-harvesting complexes mostly assembled from Phycobiliproteins. Phycobiliprotein beta subunits contain a highly conserved gamma-N-methylasparagine residue, which results from the posttranslational modification of Asn71/72. Through comparative genomic analyses, we identified a gene, denoted cpcM, that (i) encodes a protein with sequence similarity to other S-adenosylmethionine-dependent methyltransferases, (ii) is found in all sequenced cyanobacterial genomes, and (iii) often occurs near genes encoding Phycobiliproteins in cyanobacterial genomes. The cpcM genes of Synechococcus sp. strain PCC 7002 and Synechocystis sp. strain PCC 6803 were insertionally inactivated. Mass spectrometric analyses of Phycobiliproteins isolated from the mutants confirmed that the CpcB, ApcB, and ApcF were 14 Da lighter than their wild-type counterparts. Trypsin digestion and mass analyses of Phycobiliproteins isolated from the mutants showed that tryptic peptides from phycocyanin that included Asn72 were also 14 Da lighter than the equivalent peptides from wild-type strains. Thus, CpcM is the methyltransferase that modifies the amide nitrogen of Asn71/72 of CpcB, ApcB, and ApcF. When cells were grown at low light intensity, the cpcM mutants were phenotypically similar to the wild-type strains. However, the mutants were sensitive to high-light stress, and the cpcM mutant of Synechocystis sp. strain PCC 6803 was unable to grow at moderately high light intensities. Fluorescence emission measurements showed that the ability to perform state transitions was impaired in the cpcM mutants and suggested that energy transfer from Phycobiliproteins to the photosystems was also less efficient. The possible functions of asparagine N methylation of Phycobiliproteins are discussed.
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biogenesis of Phycobiliproteins iii cpcm is the asparagine methyltransferase for phycobiliprotein β subunits in cyanobacteria
Journal of Biological Chemistry, 2008Co-Authors: Crystal A Miller, Gaozhong Shen, Donald A Bryant, Shervonda R Williams, Heidi S Leonard, Ivan G Pinsky, Brandy M Turner, Leon Harrison, Ariane F Fletcher, Wendy M SchluchterAbstract:All Phycobiliproteins contain a conserved, post-translational modification on asparagine 72 of their β-subunits. Methylation of this Asn to produce γ-N-methylasparagine has been shown to increase energy transfer efficiency within the phycobilisome and to prevent photoinhibition. We report here the biochemical characterization of the product of sll0487, which we have named cpcM, from the cyanobacterium Synechocystis sp. PCC 6803. Recombinant apo-phycocyanin and apo-allophycocyanin subunits were used as the substrates for assays with [methyl-3H]S-adenosylmethionine and recombinant CpcM. CpcM methylated the β-subunits of Phycobiliproteins (CpcB, ApcB, and ApcF) and did not methylate the corresponding α-subunits (CpcA, ApcA, and ApcD), although they are similar in primary and tertiary structure. CpcM preferentially methylated its CpcB substrate after chromophorylation had occurred at Cys82. CpcM exhibited lower activity on trimeric phycocyanin after complete chromophorylation and oligomerization had occurred. Based upon these in vitro studies, we conclude that this post-translational modification probably occurs after chromophorylation but before trimer assembly in vivo.
Doran I G Bennett - One of the best experts on this subject based on the ideXlab platform.
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mechanistic regimes of vibronic transport in a heterodimer and the design principle of incoherent vibronic transport in Phycobiliproteins
Journal of Physical Chemistry Letters, 2018Co-Authors: Doran I G Bennett, Christoph Kreisbeck, Alan Aspuruguzik, Pavel Malý, Rienk Van GrondelleAbstract:Following the observation of coherent oscillations in nonlinear spectra of photosynthetic pigment protein complexes, in particular, phycobilliproteins such as PC645, coherent vibronic transport has been suggested as a design principle for novel light-harvesting materials. Vibronic transport between energetically remote pigments is coherent when the presence of a vibration resonant with the electronic energy gap supports transient delocalization between the electronic excited states. We establish the mechanism of vibronic transport for a model heterodimer across a wide range of molecular parameter values. The resulting mechanistic map demonstrates that the molecular parameters of Phycobiliproteins in fact support incoherent vibronic transport. This result points to an important design principle: Incoherent vibronic transport is more efficient than a coherent mechanism when energetic disorder exceeds the coupling between the donor and vibrationally excited acceptor states. Finally, our results suggest that ...
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local protein solvation drives direct down conversion in phycobiliprotein pc645 via incoherent vibronic transport
Proceedings of the National Academy of Sciences of the United States of America, 2018Co-Authors: Samuel M Blau, Doran I G Bennett, Christoph Kreisbeck, Gregory D Scholes, Alan AspuruguzikAbstract:The mechanisms controlling excitation energy transport (EET) in light-harvesting complexes remain controversial. Following the observation of long-lived beats in 2D electronic spectroscopy of PC645, vibronic coherence, the delocalization of excited states between pigments supported by a resonant vibration, has been proposed to enable direct excitation transport from the highest-energy to the lowest-energy pigments, bypassing a collection of intermediate states. Here, we instead show that for phycobiliprotein PC645 an incoherent vibronic transport mechanism is at play. We quantify the solvation dynamics of individual pigments using ab initio quantum mechanics/molecular mechanics (QM/MM) nuclear dynamics. Our atomistic spectral densities reproduce experimental observations ranging from absorption and fluorescence spectra to the timescales and selectivity of down-conversion observed in transient absorption measurements. We construct a general model for vibronic dimers and establish the parameter regimes of coherent and incoherent vibronic transport. We demonstrate that direct down-conversion in PC645 proceeds incoherently, enhanced by large reorganization energies and a broad collection of high-frequency vibrations. We suggest that a similar incoherent mechanism is appropriate across Phycobiliproteins and represents a potential design principle for nanoscale control of EET.
Gaozhong Shen - One of the best experts on this subject based on the ideXlab platform.
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far red light allophycocyanin subunits play a role in chlorophyll d accumulation in far red light
Photosynthesis Research, 2020Co-Authors: Nathan Soulier, Gavin M Turner, Ming Yang Ho, Tatiana N Laremore, Gaozhong Shen, Donald A BryantAbstract:Some terrestrial cyanobacteria acclimate to and utilize far-red light (FRL; λ = 700–800 nm) for oxygenic photosynthesis, a process known as far-red light photoacclimation (FaRLiP). A conserved, 20-gene FaRLiP cluster encodes core subunits of Photosystem I (PSI) and Photosystem II (PSII), five phycobiliprotein subunits of FRL-bicylindrical cores, and enzymes for synthesis of chlorophyll (Chl) f and possibly Chl d. Deletion mutants for each of the five apc genes of the FaRLiP cluster were constructed in Synechococcus sp. PCC 7335, and all had similar phenotypes. When the mutants were grown in white (WL) or red (RL) light, the cells closely resembled the wild-type (WT) strain grown under the same conditions. However, the WT and mutant strains were very different when grown under FRL. Mutants grown in FRL were unable to assemble FRL-bicylindrical cores, were essentially devoid of FRL-specific Phycobiliproteins, but retained RL-type phycobilisomes and WL-PSII. The transcript levels for genes of the FaRLiP cluster in the mutants were similar to those in WT. Surprisingly, the Chl d contents of the mutant strains were greatly reduced (~ 60–99%) compared to WT and so were the levels of FRL-PSII. We infer that Chl d may be essential for the assembly of FRL-PSII, which does not accumulate to normal levels in the mutants. We further infer that the cysteine-rich subunits of FRL allophycocyanin may either directly participate in the synthesis of Chl d or that FRL bicylindrical cores stabilize FRL-PSII to prevent loss of Chl d.
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phycobiliprotein biosynthesis in cyanobacteria structure and function of enzymes involved in post translational modification
Advances in Experimental Medicine and Biology, 2010Co-Authors: Wendy M Schluchter, Avijit Biswas, Gaozhong Shen, Richard M Alvey, Nicolle A Saunee, Shervonda R Williams, Crystal A Mille, Donald A BryantAbstract:Cyanobacterial Phycobiliproteins are brilliantly colored due to the presence of covalently attached chromophores called bilins, linear tetrapyrroles derived from heme. For most Phycobiliproteins, these post-translational modifications are catalyzed by enzymes called bilin lyases; these enzymes ensure that the appropriate bilins are attached to the correct cysteine residues with the proper stereochemistry on each phycobiliprotein subunit. Phycobiliproteins also contain a unique, post-translational modification, the methylation of a conserved asparagine (Asn) present at β-72, which occurs on the β-subunits of all Phycobiliproteins. We have identified and characterized several new families of bilin lyases, which are responsible for attaching PCB to Phycobiliproteins as well as the Asn methyl transferase for β-subunits in Synechococcus sp. PCC 7002 and Synechocystis sp. PCC 6803. All of the enzymes responsible for synthesis of holo-Phycobiliproteins are now known for this cyanobacterium, and a brief discussion of each enzyme family and its role in the biosynthesis of Phycobiliproteins is presented here. In addition, the first structure of a bilin lyase has recently been solved (PDB ID: 3BDR). This structure shows that the bilin lyases are most similar to the lipocalin protein structural family, which also includes the bilin-binding protein found in some butterflies.
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cpcm posttranslationally methylates asparagine 71 72 of phycobiliprotein beta subunits in synechococcus sp strain pcc 7002 and synechocystis sp strain pcc 6803
Journal of Bacteriology, 2008Co-Authors: Gaozhong Shen, Wendy M Schluchter, Heidi S Leonard, Donald A BryantAbstract:Cyanobacteria produce phycobilisomes, which are macromolecular light-harvesting complexes mostly assembled from Phycobiliproteins. Phycobiliprotein beta subunits contain a highly conserved gamma-N-methylasparagine residue, which results from the posttranslational modification of Asn71/72. Through comparative genomic analyses, we identified a gene, denoted cpcM, that (i) encodes a protein with sequence similarity to other S-adenosylmethionine-dependent methyltransferases, (ii) is found in all sequenced cyanobacterial genomes, and (iii) often occurs near genes encoding Phycobiliproteins in cyanobacterial genomes. The cpcM genes of Synechococcus sp. strain PCC 7002 and Synechocystis sp. strain PCC 6803 were insertionally inactivated. Mass spectrometric analyses of Phycobiliproteins isolated from the mutants confirmed that the CpcB, ApcB, and ApcF were 14 Da lighter than their wild-type counterparts. Trypsin digestion and mass analyses of Phycobiliproteins isolated from the mutants showed that tryptic peptides from phycocyanin that included Asn72 were also 14 Da lighter than the equivalent peptides from wild-type strains. Thus, CpcM is the methyltransferase that modifies the amide nitrogen of Asn71/72 of CpcB, ApcB, and ApcF. When cells were grown at low light intensity, the cpcM mutants were phenotypically similar to the wild-type strains. However, the mutants were sensitive to high-light stress, and the cpcM mutant of Synechocystis sp. strain PCC 6803 was unable to grow at moderately high light intensities. Fluorescence emission measurements showed that the ability to perform state transitions was impaired in the cpcM mutants and suggested that energy transfer from Phycobiliproteins to the photosystems was also less efficient. The possible functions of asparagine N methylation of Phycobiliproteins are discussed.
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biogenesis of Phycobiliproteins iii cpcm is the asparagine methyltransferase for phycobiliprotein β subunits in cyanobacteria
Journal of Biological Chemistry, 2008Co-Authors: Crystal A Miller, Gaozhong Shen, Donald A Bryant, Shervonda R Williams, Heidi S Leonard, Ivan G Pinsky, Brandy M Turner, Leon Harrison, Ariane F Fletcher, Wendy M SchluchterAbstract:All Phycobiliproteins contain a conserved, post-translational modification on asparagine 72 of their β-subunits. Methylation of this Asn to produce γ-N-methylasparagine has been shown to increase energy transfer efficiency within the phycobilisome and to prevent photoinhibition. We report here the biochemical characterization of the product of sll0487, which we have named cpcM, from the cyanobacterium Synechocystis sp. PCC 6803. Recombinant apo-phycocyanin and apo-allophycocyanin subunits were used as the substrates for assays with [methyl-3H]S-adenosylmethionine and recombinant CpcM. CpcM methylated the β-subunits of Phycobiliproteins (CpcB, ApcB, and ApcF) and did not methylate the corresponding α-subunits (CpcA, ApcA, and ApcD), although they are similar in primary and tertiary structure. CpcM preferentially methylated its CpcB substrate after chromophorylation had occurred at Cys82. CpcM exhibited lower activity on trimeric phycocyanin after complete chromophorylation and oligomerization had occurred. Based upon these in vitro studies, we conclude that this post-translational modification probably occurs after chromophorylation but before trimer assembly in vivo.
Hiroki Saeki - One of the best experts on this subject based on the ideXlab platform.
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anti inflammatory effects of dulse palmaria palmata resulting from the simultaneous water extraction of Phycobiliproteins and chlorophyll a
Food Research International, 2017Co-Authors: Mizuho Nishizawa, Yutaka Shimizu, Hiroki SaekiAbstract:The use of dulse (Palmaria palmata) as a source of edible anti-inflammatory products was evaluated in this study. Phycobiliproteins and chlorophyll a were simultaneously extracted from lyophilized dulse leaves via water-extraction, and subjected to thermolysin digestion to produce thermolysin-digested water-extract (d-DWE). d-DWE significantly reduced tumor necrosis factor-α, interleukin-6, and nitric oxide in LPS-stimulated murine macrophages (RAW 264.7 cells), and orally administered d-DWE mitigated acute inflammation in carrageenan-induced paw edema of mice. Mass spectrometry revealed d-DWE contained peptide LRDGEIILRY (derived from phycoerythrin β-chain) and chlorophyll a decomposition products, and they individually reduced the secretion of the proinflammatory mediators in LPS-stimulated RAW 264.7 cells. These results indicate the anti-inflammatory activity could be from a combined effect of phycobiliprotein and chlorophyll a decomposition products prepared from the water-extract of dulse. Thus, inexpensive and safe water-extraction method is effective for the extraction of anti-inflammatory components from dulse.
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anti inflammatory effects of dulse palmaria palmata resulting from the simultaneous water extraction of Phycobiliproteins and chlorophyll a
Food Research International, 2017Co-Authors: Mizuho Nishizawa, Yutaka Shimizu, Hiroki SaekiAbstract:The use of dulse (Palmaria palmata) as a source of edible anti-inflammatory products was evaluated in this study. Phycobiliproteins and chlorophyll a were simultaneously extracted from lyophilized dulse leaves via water-extraction, and subjected to thermolysin digestion to produce thermolysin-digested water-extract (d-DWE). d-DWE significantly reduced tumor necrosis factor-α, interleukin-6, and nitric oxide in LPS-stimulated murine macrophages (RAW 264.7 cells), and orally administered d-DWE mitigated acute inflammation in carrageenan-induced paw edema of mice. Mass spectrometry revealed d-DWE contained peptide LRDGEIILRY (derived from phycoerythrin β-chain) and chlorophyll a decomposition products, and they individually reduced the secretion of the proinflammatory mediators in LPS-stimulated RAW 264.7 cells. These results indicate the anti-inflammatory activity could be from a combined effect of phycobiliprotein and chlorophyll a decomposition products prepared from the water-extract of dulse. Thus, inexpensive and safe water-extraction method is effective for the extraction of anti-inflammatory components from dulse.
