Comparative study of the stability of poplar plastocyanin isoforms

Shosheva, Alexandra; Donchev, Anthony A.; Dimitrov, Milen; Kostov, G.; Toromanov, Georgi; Getov, V. I.; Alexov, Emil

doi:10.1016/j.bbapap.2004.12.012

Cited by 14 publications

(14 citation statements)

References 56 publications

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“…It seems likely that apoPC without its cofactor is more rapidly turned over (see discussion in Abdel-Ghany, 2009). It had been suggested based on biophysical studies with isolated PC proteins that the two poplar PC isoforms differed in their thermal stability (Shosheva et al, 2005), and such differences might affect how tight the proteins bind a cofactor, which, in turn, could affect the stability of the polypeptide. The two poplar PC isoforms have very similar mobility on SDS-PAGE and therefore are not as easily distinguished as the Arabidopsis PC1 and PC2 isoforms (Pesaresi et al, 2009).…”

Section: Discussionmentioning

confidence: 99%

Spatiotemporal Analysis of Copper Homeostasis in Populus trichocarpa Reveals an Integrated Molecular Remodeling for a Preferential Allocation of Copper to Plastocyanin in the Chloroplasts of Developing Leaves

et al. 2011

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Plastocyanin, which requires copper (Cu) as a cofactor, is an electron carrier in the thylakoid lumen and essential for photoautotrophic growth of plants. The Cu microRNAs, which are expressed during Cu deprivation, down-regulate several transcripts that encode for Cu proteins. Since plastocyanin is not targeted by the Cu microRNAs, a cofactor economy model has been proposed in which plants prioritize Cu for use in photosynthetic electron transport. However, defects in photosynthesis are classic symptoms of Cu deprivation, and priorities in Cu cofactor delivery have not been determined experimentally. Using hydroponically grown Populus trichocarpa (clone Nisqually-1), we have established a physiological and molecular baseline for the response to Cu deficiency. An integrated analysis showed that Cu depletion strongly reduces the activity of several Cu proteins including plastocyanin, and consequently, photosynthesis and growth are decreased. Whereas plastocyanin mRNA levels were only mildly affected by Cu depletion, this treatment strongly affected the expression of other Cu proteins via Cu microRNA-mediated transcript down-regulation. Polyphenol oxidase was newly identified as Cu regulated and targeted by a novel Cu microRNA, miR1444. Importantly, a spatiotemporal analysis after Cu resupply to previously depleted plants revealed that this micronutrient is preferentially allocated to developing photosynthetic tissues. Plastocyanin and photosynthetic electron transport efficiency were the first to recover after Cu addition, whereas recovery of the other Cu-dependent activities was delayed. Our findings lend new support to the hypothesis that the Cu microRNAs serve to mediate a prioritization of Cu cofactor use. These studies also highlight poplar as an alternative sequenced model for spatiotemporal analyses of nutritional homeostasis.

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Section: Discussionmentioning

confidence: 99%

Spatiotemporal Analysis of Copper Homeostasis in Populus trichocarpa Reveals an Integrated Molecular Remodeling for a Preferential Allocation of Copper to Plastocyanin in the Chloroplasts of Developing Leaves

et al. 2011

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“…75°C). The stability of the copper site in Cupricyclin-1 well compares with that of natural metalloproteins such as azurin and plastocyanin which display complete copper release at temperature values ranging from 70 to 85°C depending on the metal oxidation state and the DSC scanning rate [24]–[26].…”

Section: Resultsmentioning

confidence: 95%

“…No clear endotherm was evident in the thermograms, due to the fact that the peptide almost completely lacks defined structural elements which can yield DSC signals (such as hydrogen bonds). In copper proteins such as azurin and plastocyanin, the exotherm is attributed to copper-dependent redox reactions with cysteines following copper release [24]–[26]. By analogy, DSC results indicate that the metal site of Cupricyclin-1 is stable up to 55°C and that copper release is complete only at 95°C (the T 1/2 for copper release being approx.…”

Section: Resultsmentioning

confidence: 99%

Cupricyclins, Novel Redox-Active Metallopeptides Based on Conotoxins Scaffold

et al. 2012

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Highly stable natural scaffolds which tolerate multiple amino acid substitutions represent the ideal starting point for the application of rational redesign strategies to develop new catalysts of potential biomedical and biotechnological interest. The knottins family of disulphide-constrained peptides display the desired characteristics, being highly stable and characterized by hypervariability of the inter-cysteine loops. The potential of knottins as scaffolds for the design of novel copper-based biocatalysts has been tested by engineering a metal binding site on two different variants of an ω-conotoxin, a neurotoxic peptide belonging to the knottins family. The binding site has been designed by computational modelling and the redesigned peptides have been synthesized and characterized by optical, fluorescence, electron spin resonance and nuclear magnetic resonance spectroscopy. The novel peptides, named Cupricyclin-1 and -2, bind one Cu2+ ion per molecule with nanomolar affinity. Cupricyclins display redox activity and catalyze the dismutation of superoxide anions with an activity comparable to that of non-peptidic superoxide dismutase mimics. We thus propose knottins as a novel scaffold for the design of catalytically-active mini metalloproteins.

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“…Statistical studies of pair wise interactions in native proteins have shown that favorable interactions do not occur by chance, but rather are optimized. 44,45 Thus the probability of producing a structurally wrong model having optimized pair wise interactions is negligible small. The basic groups behave differentlypractically all arginines have elevated pK a 's (positive ∆pK a ) and are exposed or slightly buried (zero or small ∆pK sol ).…”

Section: Calculating the Pk A 'S Of The Ionizable Groups Using Homolomentioning

confidence: 98%

Assessing the Quality of the Homology-Modeled 3d Structures From Electrostatic Standpoint: Test on Bacterial Nucleoside Monophosphate Kinase Families

Kundrotas

Georgieva

Shosheva

et al. 2007

J. Bioinform. Comput. Biol.

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In this study, we address the issue of performing meaningful pK(a) calculations using homology modeled three-dimensional (3D) structures and analyze the possibility of using the calculated pK(a) values to detect structural defects in the models. For this purpose, the 3D structure of each member of five large protein families of a bacterial nucleoside monophosphate kinases (NMPK) have been modeled by means of homology-based approach. Further, we performed pK(a) calculations for the each model and for the template X-ray structures. Each bacterial NMPK family used in the study comprised on average 100 members providing a pool of sequences and 3D models large enough for reliable statistical analysis. It was shown that pK(a) values of titratable groups, which are highly conserved within a family, tend to be conserved among the models too. We demonstrated that homology modeled structures with sequence identity larger than 35% and gap percentile smaller than 10% can be used for meaningful pK(a) calculations. In addition, it was found that some highly conserved titratable groups either exhibit large pK(a) fluctuations among the models or have pK(a) values shifted by several pH units with respect to the pK(a) calculated for the X-ray structure. We demonstrated that such case usually indicates structural errors associated with the model. Thus, we argue that pK(a) calculations can be used for assessing the quality of the 3D models by monitoring fluctuations of the pK(a) values for highly conserved titratable residues within large sets of homologous proteins.

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Comparative study of the stability of poplar plastocyanin isoforms

Cited by 14 publications

References 56 publications

Spatiotemporal Analysis of Copper Homeostasis in Populus trichocarpa Reveals an Integrated Molecular Remodeling for a Preferential Allocation of Copper to Plastocyanin in the Chloroplasts of Developing Leaves

Spatiotemporal Analysis of Copper Homeostasis in Populus trichocarpa Reveals an Integrated Molecular Remodeling for a Preferential Allocation of Copper to Plastocyanin in the Chloroplasts of Developing Leaves

Cupricyclins, Novel Redox-Active Metallopeptides Based on Conotoxins Scaffold

Assessing the Quality of the Homology-Modeled 3d Structures From Electrostatic Standpoint: Test on Bacterial Nucleoside Monophosphate Kinase Families

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