The cytochrome <i>f</i>–plastocyanin complex as a model to study transient interactions between redox proteins

Cruz-Gallardo, Isabel; Dı́az-Moreno, Irene; Díaz-Quintana, Antonio; Rosa, Miguel Á. De la

doi:10.1016/j.febslet.2011.08.035

Cited by 34 publications

(22 citation statements)

References 53 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The phenomenon of co-expression was also observed in miR398- plastocyanin , in which the expression levels of both miR398 and plastocyanin were higher in germinated embryos than in dormant embryos. Plastocyanin functions as a soluble carrier transferring electrons between cytochrome b(6)f and photosystem I [60]. The expression pattern of plastocyanin was consistent with the phenomenon that genes involved in photosynthesis and carbon fixation are upregulated from dormant embryos compared to germinated embryos [61].…”

Section: Discussionsupporting

confidence: 74%

Deciphering Small Noncoding RNAs during the Transition from Dormant Embryo to Germinated Embryo in Larches (Larix leptolepis)

Zhang

Han

et al. 2013

PLoS ONE

View full text Add to dashboard Cite

Small RNAs (sRNAs), as a key component of molecular biology, play essential roles in plant development, hormone signaling, and stress response. However, little is known about the relationships among sRNAs, hormone signaling, and dormancy regulation in gymnosperm embryos. To investigate the roles of sRNAs in embryo dormancy maintenance and release in Larix leptolepis, we deciphered the endogenous “sRNAome” in dormant and germinated embryos. High-throughput sequencing of sRNA libraries showed that dormant embryos exhibited a length bias toward 24-nt while germinated embryos showed a bias toward 21-nt lengths. This might be associated with distinct levels of RNA-dependent RNA polymerase2 (RDR2) and/or RDR6, which is regulated by hormones. Proportions of miRNAs to nonredundant and redundant sRNAs were higher in germinated embryos than in dormant embryos, while the ratio of unknown sRNAs was higher in dormant embryos than in germinated embryos. We identified a total of 160 conserved miRNAs from 38 families, 3 novel miRNAs, and 16 plausible miRNA candidates, of which many were upregulated in germinated embryos relative to dormant embryos. These findings indicate that larches and possibly other gymnosperms have complex mechanisms of gene regulation involving miRNAs and other sRNAs operating transcriptionally and posttranscriptionally during embryo dormancy and germination. We propose that abscisic acid modulates embryo dormancy and germination at least in part through regulation of the expression level of sRNA-biogenesis genes, thus changing the sRNA components.

show abstract

Section: Discussionsupporting

confidence: 74%

Deciphering Small Noncoding RNAs during the Transition from Dormant Embryo to Germinated Embryo in Larches (Larix leptolepis)

Zhang

Han

et al. 2013

PLoS ONE

View full text Add to dashboard Cite

show abstract

“…These differences arise from the experimental crystallographic data usually being recorded at a low temperature (77 K), thereby reducing the dynamics of the protein. A similar example is found in electron transfer complexes, for which the observation of specific salt bridges through molecular dynamic computations [ 46 , 60 ] explained the discrepancies between kinetic analyses of site-directed mutants [ 61 ] and structural data [ 62 ].…”

Section: Discussionmentioning

confidence: 74%

The Dynamics of the Human Leukocyte Antigen Head Domain Modulates Its Recognition by the T-Cell Receptor

et al. 2016

Self Cite

View full text Add to dashboard Cite

Generating the immune response requires the discrimination of peptides presented by the human leukocyte antigen complex (HLA) through the T-cell receptor (TCR). However, how a single amino acid substitution in the antigen bonded to HLA affects the response of T cells remains uncertain. Hence, we used molecular dynamics computations to analyze the molecular interactions between peptides, HLA and TCR. We compared immunologically reactive complexes with non-reactive and weakly reactive complexes. MD trajectories were produced to simulate the behavior of isolated components of the various p-HLA-TCR complexes. Analysis of the fluctuations showed that p-HLA binding barely restrains TCR motions, and mainly affects the CDR3 loops. Conversely, inactive p-HLA complexes displayed significant drop in their dynamics when compared with its free versus ternary forms (p-HLA-TCR). In agreement, the free non-reactive p-HLA complexes showed a lower amount of salt bridges than the responsive ones. This resulted in differences between the electrostatic potentials of reactive and inactive p-HLA species and larger vibrational entropies in non-elicitor complexes. Analysis of the ternary p-HLA-TCR complexes also revealed a larger number of salt bridges in the responsive complexes. To summarize, our computations indicate that the affinity of each p-HLA complex towards TCR is intimately linked to both, the dynamics of its free species and its ability to form specific intermolecular salt-bridges in the ternary complexes. Of outstanding interest is the emerging concept of antigen reactivity involving its interplay with the HLA head sidechain dynamics by rearranging its salt-bridges.

show abstract

“…The role of electrostatic interactions in the formation of the oxidation-reduction complex of two proteins was studied in the interaction model of the well-studied pair of photosynthetic electron transfer proteins, Pc and Cyt f. This pair of proteins is a classic object of experimental research (reviewed by Cruz-Gallardo et al [25], and Khruschev et al [12]) and Brownian dynamics studies [13,18,23,24,[26][27][28][29]. The physiological function of the protein Pc consists of the shuttle electron transfer between the subunit f of cytochrome complex b6-f and the photosystem I in all higher plants and some algae.…”

Section: Productive and Non-productive Encounter Complexesmentioning

confidence: 99%

Photosynthetic Electron Transfer by Dint of Protein Mobile Carriers. Multi-particle Brownian and Molecular Modeling

et al. 2019

View full text Add to dashboard Cite

The paper presents the review of works on modeling the interaction of photosynthetic proteins using the multiparticle Brownian dynamics method developed at the Department of Biophysics, Biological Faculty, Lomonosov Moscow State University. The method describes the displacement of individual macromolecules – mobile electron carriers, and their electrostatic interactions between each other and with pigment-protein complexes embedded in photosynthetic membrane. Three-dimensional models of the protein molecules were constructed on the basis of the data from the Protein Data Bank. We applied the Brownian methods coupled to molecular dynamic simulations to reveal the role of electrostatic interactions and conformational motions in the transfer of an electron from the cytochrome complex Cyt b6f) membrane we developed the model which combines events of proteins Pc diffusion along the thylakoid membrane, electrostatic interactions of Pc with the membrane charges, formation of Pc super-complexes with multienzyme complexes of Photosystem I and to the molecule of the mobile carrier plastocyanin (Pc) in plants, green algae and cyanic bacteria. Taking into account the interior of photosynthetic membrane we developed the model which combines events of proteins Pc diffusion along the thylakoid membrane, electrostatic interactions of Pc with the membrane charges, formation of Pc super-complexes with multienzyme complexes of Photosystem I and Cyt b6f, embedded in photosynthetic membrane, electron transfer and complex dissociation. Multiparticle Brownian simulation method can be used to consider the processes of protein interactions in subcellular systems in order to clarify the role of individual stages and the biophysical mechanisms of these processes.

show abstract

The cytochrome f–plastocyanin complex as a model to study transient interactions between redox proteins

Cited by 34 publications

References 53 publications

Deciphering Small Noncoding RNAs during the Transition from Dormant Embryo to Germinated Embryo in Larches (Larix leptolepis)

Deciphering Small Noncoding RNAs during the Transition from Dormant Embryo to Germinated Embryo in Larches (Larix leptolepis)

The Dynamics of the Human Leukocyte Antigen Head Domain Modulates Its Recognition by the T-Cell Receptor

Photosynthetic Electron Transfer by Dint of Protein Mobile Carriers. Multi-particle Brownian and Molecular Modeling

Contact Info

Product

Resources

About