scholarly journals Natively Oxidized Amino Acid Residues in the Spinach PS I-LHC I Supercomplex

2019 ◽  
Author(s):  
Ravindra Kale ◽  
Larry Sallans ◽  
Laurie K. Frankel ◽  
Terry M. Bricker
Keyword(s):  
Amino Acid ◽  
Oxidative Modification ◽  
Ros Generation ◽  
Ros Production ◽  
Amino Acid Residues ◽  
Ps Ii ◽  
Chl A ◽  
Ps I ◽  
Close Proximity ◽  
Oxidatively Modified

AbstractReactive oxygen species (ROS) production is an unavoidable byproduct of electron transport under aerobic conditions. Photosystem II (PS II), the cytochrome b6f complex and Photosystem I (PS I) are all demonstrated sources of ROS. It has been proposed that PS I produces substantial levels of a variety of ROS including 1O2, H2O2 and, possibly, , however, the site(s) of ROS production within PS I has been the subject of significant debate. We hypothesize that amino acid residues close to the sites of ROS generation will be more susceptible to oxidative modification than distant residues. In this study, we have identified oxidized amino acid residues in spinach PS I which was isolated from field-grown spinach. The modified residues were identified by high-resolution tandem mass spectrometry. As expected, many of the modified residues lie on the surface of the complex. However, a well-defined group of oxidized residues, both buried and surface-exposed, lead from the chl a’ of P700 to the surface of PS I. These residues (PsaB: 609F, 611E, 617M, 619W, 620L, and PsaF: 139L, 142A,143D) may identify a preferred route for ROS, probably 1O2, to egress the complex from the vicinity of P700. Additionally, two buried residues located in close proximity to A1B (PsaB:712H and 714S) were modified, which may be consistent with A1B being a source of . Surprisingly, no oxidatively modified residues were identified in close proximity to the 4Fe-FS clusters FX, FA or FB. These cofactors had been identified as a principal targets for ROS damage in the photosystem. Finally, a large number of residues located in the hydrophobic cores of Lhca1-Lhca4 are oxidatively modified. These appear to be the result of 1O2 production by the distal antennae for the photosystem.

scholarly journals Natively Oxidized Amino Acid Residues in the Spinach Cytochrome b6f Complex

2017 ◽  
Author(s):  
Ryan M. Taylor ◽  
Larry Sallans ◽  
Laurie K. Frankel ◽  
Terry M. Bricker
Keyword(s):  
Amino Acid ◽  
Oxidative Modification ◽  
Oxygenic Photosynthesis ◽  
Ros Generation ◽  
Ros Production ◽  
Amino Acid Residues ◽  
Iron Sulfur Cluster ◽  
Iron Sulfur ◽  
The Subject ◽  
Oxidatively Modified

AbstractThe cytochrome b6f complex of oxygenic photosynthesis produces substantial levels of reactive oxygen species (ROS). It has been observed that the ROS production rate by b6f is 10-20 fold higher than that observed for the analogous respiratory cytochrome bc1 complex. The types of ROS produced (O2•−,1O2, and, possibly, H2O2) and the site(s) of ROS production within the b6f complex has been the subject of some debate. Proposed sources of ROS have include the heme bp, PQp•− (possible sources for O2•−), the Rieske iron-sulfur cluster (possible source of O2•− and/or H2O2), Chl a (possible source of 1O2) and heme Cn (possible source of O2•− and/or H2O2). Our working hypothesis is that amino acid residues proximal to the ROS production sites will be more susceptible to oxidative modification than distant residues. In the current study, we have identified natively oxidized amino acid residues in the subunits of the spinach cytochrome b6f complex. The oxidized residues were identified by tandem mass spectrometry using the MassMatrix Program. Our results indicate that numerous residues, principally localized near p-side cofactors and Chl a, were oxidatively modified. We hypothesize that these sites are sources for ROS generation in the spinach cytochrome b6f complex.

scholarly journals Oxidative Modification of LHC II Associated with Photosystem II and PS I-LHC I-LHC II Membranes

2021 ◽  
Author(s):  
Ravindra S Kale ◽  
Jacob Seep ◽  
Larry Sallans ◽  
Laurie K Frankel ◽  
Terry M. Bricker
Keyword(s):  
Amino Acid ◽  
Photosystem Ii ◽  
Oxidative Modification ◽  
Ros Generation ◽  
Hydrophobic Core ◽  
Amino Acid Residues ◽  
Lhc Ii ◽  
Ps Ii ◽  
Ps I ◽  
Lhc I

Under aerobic conditions the production of Reactive Oxygen Species (ROS) by electron transport chains is unavoidable, and occurs in both autotrophic and heterotrophic organisms. In photosynthetic organisms both Photosystem II (PS II) and Photosystem I (PS I), in addition to the cytochrome b6/f complex, are demonstrated sources of ROS. All of these membrane protein complexes exhibit oxidative damage when isolated from field-grown plant material. An additional possible source of ROS in PS I and PS II is the distal, chlorophyll-containing light-harvesting array LHC II, which is present in both photosystems. These serve as possible sources of 1O2 produced by the interaction of 3O2 with 3chl* produced by intersystem crossing. We have hypothesized that amino acid residues close to the sites of ROS generation will be more susceptible to oxidative modification than distant residues. In this study, we have identified oxidized amino acid residues in a subset of the spinach LHC II proteins (Lhcb1 and Lhcb2) that were associated with either PS II membranes (i.e. BBYs) or PS I-LHC I-LHC II membranes, both of which were isolated from field-grown spinach. We identified oxidatively modified residues by high-resolution tandem mass spectrometry. Interestingly, two different patterns of oxidative modification were evident for the Lhcb1 and Lhcb2 proteins from these different sources. In the LHC II associated with PS II membranes, oxidized residues were identified to be located on the stromal surface of Lhcb1 and, to a much lesser extent, Lhcb2. Relatively few oxidized residues were identified as buried in the hydrophobic core of these proteins. The LHC II associated with PS I-LHC I-LHC II membranes, however, exhibited fewer surface-oxidized residues but, rather a large number of oxidative modifications buried in the hydrophobic core regions of both Lhcb1 and Lhcb2, adjacent to the chlorophyll prosthetic groups. These results appear to indicate that ROS, specifically 1O2, can modify the Lhcb proteins associated with both photosystems and that the LHC II associated with PS II membranes represent a different population from the LHC II associated with PS I-LHC I-LHC II membranes.

scholarly journals Mitochondrial ROS promote macrophage pyroptosis by inducing GSDMD oxidation

2019 ◽  
Vol 11 (12) ◽  
pp. 1069-1082 ◽  
Author(s):  
Yufang Wang ◽  
Peiliang Shi ◽  
Qin Chen ◽  
Zan Huang ◽  
Dayuan Zou ◽  
...  
Keyword(s):  
Amino Acid ◽  
Nlrp3 Inflammasome ◽  
De Novo ◽  
Oxidative Modification ◽  
Ros Generation ◽  
Inflammasome Activation ◽  
Amino Acid Residues ◽  
Caspase 1 ◽  
Hydrogen Peroxide Treatment ◽  
Mitochondrial Ros

Abstract Disrupted mitochondrial membrane potential (MMP) and reactive oxygen species (ROS) generation are often associated with macrophage pyroptosis. It remains unclear how these forms of mitochondrial dysfunction relate to inflammasome activation and gasdermin-D (Gsdmd) cleavage, two central steps of the pyroptotic process. Here, we also found MMP collapse and ROS generation induced by Nlrp3 inflammasome activation as previous studies reported. The elimination of ROS alleviated the cleavage of Gsdmd, suggesting that Gsdmd cleavage occurs downstream of ROS release. Consistent with this result, hydrogen peroxide treatment augmented the cleavage of Gsdmd by caspase-1. Indeed, four amino acid residues of Gsdmd were oxidized under oxidative stress in macrophages. The efficiency of Gsdmd cleavage by inflammatory caspase-1 was dramatically reduced when oxidative modification was blocked by mutation of these amino acid residues. These results demonstrate that Gsdmd oxidation serves as a de novo mechanism by which mitochondrial ROS promote Nlrp3 inflammasome-dependent pyroptotic cell death.

scholarly journals The influence of metals of variable valence on the oxidative modification of albumin amino acid residues

2021 ◽  
Vol 9 (3) ◽  
pp. 369-376
Author(s):  
O.A. Zav’yalova ◽  
◽  
Yu.A. Marsyanova ◽  
Yu.V. Abalenikhinа ◽  
A.F. Ishtulin ◽  
...  
Keyword(s):  
Amino Acid ◽  
Bovine Serum Albumin ◽  
Serum Albumin ◽  
Bovine Serum ◽  
Mixed Valence ◽  
Oxidative Modification ◽  
Amino Acid Residues ◽  
Variable Valence ◽  
Carbonyl Derivatives ◽  
Derivatives Of

BACKGROUND: The constancy of the protein composition of the body is one of the most important conditions for normal vital activity. Deviations in the content of the main bioelements, in particular, mixed valence metals, caused by environmental factors, improper nutrition and other factors, lead to various disorders. One of the properties of metals of mixed valence is the abil-ity to cause metal-catalyzed oxidation of proteins in joint action with active forms of oxygen. It seems interesting to study the oxidative modification of the amino acid residues of albumin and the change in its properties. AIM: To study the effect of reactive oxygen intermediates generated by the Fenton reaction in the presence of Fe2+ and Cu2+ on the oxidative modification of amino acid residues of bovine serum albumin. MATERIALS AND METHODS: The study was carried out on bovine serum albumin (BSA), which was incubated for 2 hours in a mixture of Fenton's reagents – FeSO4 + H2O2 and in a mixture of СuSO4 + H2O2. The quantitative protein content in the samples was determined with the bromcresol green reagent (Albumin-Olvex). The content of carbonyl derivatives of proteins was estimated by the method of R.L. Levine modified by E.E. Dubinina. The content of thiol groups in albumin samples from the control and experimental groups was determined by the Ellman method with DTNB (under non-denaturing conditions. RESULTS: The presented results demonstrate that under the action of Cu2+ ions, the formation of carbonyl derivatives of aliphatic amino acids of albumin is less than in the presence of Fe2+, which can be explained by the different degrees of albumin affinity to metals of variable valence. The rate of mobility of oxidatively modified albumin in polyacrylamide gel decreases, which is explained by protein aggregation due to bityrosine cross-links. CONCLUSION: Variable valence metals affect the modification of albumin. The change in the functional properties of the protein is of physiological significance, including the case of extracellular mobilization of iron and copper.

scholarly journals Decoding Essential Amino Acid Residues in the Substrate Groove of a Non-Specific Nuclease from Pseudomonas syringae

Catalysts ◽  
2019 ◽  
Vol 9 (11) ◽  
pp. 941 ◽  
Author(s):  
Lynn Sophie Schwardmann ◽  
Sarah Schmitz ◽  
Volker Nölle ◽  
Skander Elleuche
Keyword(s):  
Amino Acid ◽  
Pseudomonas Syringae ◽  
Metal Ion ◽  
Homology Model ◽  
Downstream Processing ◽  
Outer Ring ◽  
Amino Acid Residues ◽  
Independent Manner ◽  
Identify Amino Acid ◽  
Close Proximity

Non-specific nucleases (NSN) are of interest for biotechnological applications, including industrial downstream processing of crude protein extracts or cell-sorting approaches in microfabricated channels. Bacterial nucleases belonging to the superfamily of phospholipase D (PLD) are featured for their ability to catalyze the hydrolysis of nucleic acids in a metal-ion-independent manner. In order to gain a deeper insight into the composition of the substrate groove of a NSN from Pseudomonas syringae, semi-rational mutagenesis based on a structure homology model was applied to identify amino acid residues on the protein’s surface adjacent to the catalytic region. A collection of 12 mutant enzymes each with a substitution to a positively charged amino acid (arginine or lysine) was produced in recombinant form and biochemically characterized. Mutations in close proximity to the catalytic region (inner ring) either dramatically impaired or completely abolished the enzymatic performance, while amino acid residues located at the border of the substrate groove (outer ring) only had limited or no effects. A K119R substitution mutant displayed a relative turnover rate of 112% compared to the original nuclease. In conclusion, the well-defined outer ring of the substrate groove is a potential target for modulation of the enzymatic performance of NSNs belonging to the PLD superfamily.

scholarly journals Conformational stability of bovine α-crystallin. Evidence for a destabilizing effect of ascorbate

1992 ◽  
Vol 287 (1) ◽  
pp. 107-112 ◽  
Author(s):  
S A Santini ◽  
A Mordente ◽  
E Meucci ◽  
G A D Miggiano ◽  
G E Martorana
Keyword(s):  
Amino Acid ◽  
Conformational Stability ◽  
Gel Filtration ◽  
Protein Molecule ◽  
Oxidative Modification ◽  
Amino Acid Residues ◽  
Alpha Crystallin ◽  
Protein Dissociation ◽  
Covalent Adducts ◽  
Polypeptide Chains

Short-term incubation of bovine alpha-crystallin with ascorbate alters the protein conformational stability. The denaturation curves with urea and guanidinium-chloride show different patterns, suggesting a deviation from a two-state mechanism owing to the presence of one or more intermediates in the unfolding of ascorbate-modified alpha-crystallin. Furthermore, the latter protein profiles are shifted to lower denaturant concentrations indicating a destabilizing action of ascorbate, which is capable of facilitating protein dissociation into subunits as demonstrated by gel filtration with 1.5 M-urea. The decrease in conformational stability cannot be ascribed to any major structural alteration, but rather to localized changes in the protein molecule. In fact, no difference between native and ascorbate-treated alpha-crystallin can be detected by amino acid analysis but perturbation of the tryptophan and tyrosine environment is indicated by alterations in intrinsic fluorescence. Furthermore, turbidity and light-scattering measurements suggest an involvement of the lysine side chains, since aggregability patterns with acetylsalicylic acid are significantly altered. The ascorbate-destabilizing effect on the conformational stability of alpha-crystallin, probably exerted through oxidative modification of amino acid residues and/or the formation of covalent adducts, provokes unfavourable steric interactions between residues along the polypeptide chains, thus favouring aggregation and insolubilization of crystallins which can lead to cataract formation, as also demonstrated by proteolytic digestion patterns which show a lower rate of degradation of the ascorbate-modified alpha-crystallin.

scholarly journals Hypochlorite-induced oxidative modification of fibrinogen

2019 ◽  
Vol 484 (3) ◽  
pp. 367-371
Author(s):  
L. V. Yurina ◽  
A. D. Vasilyeva ◽  
A. E. Bugrova ◽  
M. I. Indeykina ◽  
A. S. Kononikhin ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Amino Acid ◽  
Oxidative Damage ◽  
Self Assembly ◽  
Protein Electrophoresis ◽  
Oxidative Modification ◽  
Cross Linking ◽  
Amino Acid Residues ◽  
Fibrin Network

Oxidation of fibrinogen with hypochlorite inhibited the fibrin network self-assembly even at the lowest concentration of the oxidant. The analysis of the results of protein electrophoresis at this hypochlorite concentration showed the absence of fragmentation of the protein and covalent cross-linking of its chains. The study of the areas responsible for the conversion of fibrinogen into fibrin by mass spectrometry showed that they are not subject to oxidative damage. However, we identified oxidized amino acid residues, which could affect the protofibril aggregation.

scholarly journals Amino acid oxidation of the D1 and D2 proteins by oxygen radicals during photoinhibition of Photosystem II

2017 ◽  
Vol 114 (11) ◽  
pp. 2988-2993 ◽  
Author(s):  
Ravindra Kale ◽  
Annette E. Hebert ◽  
Laurie K. Frankel ◽  
Larry Sallans ◽  
Terry M. Bricker ◽  
...  
Keyword(s):  
Reactive Oxygen Species ◽  
Amino Acid ◽  
Photosystem Ii ◽  
Light Stress ◽  
Reactive Oxygen ◽  
Nonheme Iron ◽  
Oxidative Modification ◽  
Oxygen Species ◽  
Oxidatively Modified ◽  
D1 And D2 Proteins

The Photosystem II reaction center is vulnerable to photoinhibition. The D1 and D2 proteins, lying at the core of the photosystem, are susceptible to oxidative modification by reactive oxygen species that are formed by the photosystem during illumination. Using spin probes and EPR spectroscopy, we have determined that both O2•− and HO• are involved in the photoinhibitory process. Using tandem mass spectroscopy, we have identified a number of oxidatively modified D1 and D2 residues. Our analysis indicates that these oxidative modifications are associated with formation of HO• at both the Mn4O5Ca cluster and the nonheme iron. Additionally, O2•− appears to be formed by the reduction of O2 at either PheoD1 or QA. Early oxidation of D1:332H, which is coordinated with the Mn1 of the Mn4O5Ca cluster, appears to initiate a cascade of oxidative events that lead to the oxidative modification of numerous residues in the C termini of the D1 and D2 proteins on the donor side of the photosystem. Oxidation of D2:244Y, which is a bicarbonate ligand for the nonheme iron, induces the propagation of oxidative reactions in residues of the D-de loop of the D2 protein on the electron acceptor side of the photosystem. Finally, D1:130E and D2:246M are oxidatively modified by O2•− formed by the reduction of O2 either by PheoD1•− or QA•−. The identification of specific amino acid residues oxidized by reactive oxygen species provides insights into the mechanism of damage to the D1 and D2 proteins under light stress.

scholarly journals Significant role of Asn-247 and Arg-64 residues in close proximity of the active site in maintaining the catalytic function of CTX-M-15 type β-lactamase

RSC Advances ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 5325-5337 ◽  
Author(s):  
Lubna Maryam ◽  
Shamsi Khalid ◽  
Abid Ali ◽  
Asad U. Khan
Keyword(s):  
Amino Acid ◽  
Significant Role ◽  
Active Site ◽  
Catalytic Efficiency ◽  
Beta Lactamase ◽  
Amino Acid Residues ◽  
Catalytic Function ◽  
Close Proximity

Mutations of amino acid residues present near active site decrease the catalytic efficiency of beta lactamase enzymes.

The impact of specific oxidized amino acids on protein turnover in J774 cells

2008 ◽  
Vol 410 (1) ◽  
pp. 131-140 ◽  
Author(s):  
Rachael A. Dunlop ◽  
Roger T. Dean ◽  
Kenneth J. Rodgers
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Oxidative Modification ◽  
Amino Acid Residues ◽  
Protein Deposition ◽  
In Situ Modification ◽  
Age Related ◽  
The Impact

Oxidized protein deposition and accumulation have been implicated in the aetiology of a wide variety of age-related pathologies. Protein oxidation in vivo commonly results in the in situ modification of amino acid side chains, generating new oxidized amino acid residues in proteins. We have demonstrated previously that certain oxidized amino acids can be (mis)incorporated into cell proteins in vitro via protein synthesis. In the present study, we show that incorporation of o- and m-tyrosine resulted in increased protein catabolism, whereas dopa incorporation generated proteins that were inefficiently degraded by cells. Incorporation of higher levels of L-dopa into proteins resulted in an increase in the activity of lysosomal cathepsins, increased autofluorescence and the generation of high-molecular-mass SDS-stable complexes, indicative of protein aggregation. These effects were due to proteins containing incorporated L-dopa, since they were not seen with the stereoisomer D-dopa, which enters the cell and generates the same reactive species as L-dopa, but cannot be incorporated into proteins. The present study highlights how the nature of the oxidative modification to the protein can determine the efficiency of its removal from the cell by proteolysis. Protection against the generation of dopa and other species that promote resistance to proteolysis might prove to be critical in preventing toxicity from oxidative stress in pathologies associated with protein deposition, such as atherosclerosis, Alzheimer's disease and Parkinson's disease.

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