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Cytochrome c delicately tilts the balance between cell life (respiration) and cell death (apoptosis). Whereas cell life is governed by transient electron transfer interactions of cytochrome c inside the mitochondria, the cytoplasmic adducts of cytochrome c that lead to cell death are amazingly stable. Interestingly, the contacts of cytochrome c with its counterparts shift from the area surrounding the heme crevice for the redox complexes to the opposite molecule side when the electron flow is not necessary. The cytochrome c signalosome shows a higher level of regulation by post-translational modifications-nitration and phosphorylation-of the hemeprotein. Understanding protein interfaces, as well as protein modifications, would puzzle the mitochondrial cytochrome c-controlled pathways out and enable the design of novel drugs to silence the action of pro-survival and pro-apoptotic partners of cytochrome c. © 2011 European Biophysical Societies' Association. ; The authors wish to thank Jonathan Martínez-Fábregas for helpful advice and critical reading of the manuscript. This work was funded by the Spanish Ministry of Science and Innovation (BFU2009-07190) and the Andalusian Government (BIO198 and P08-CVI-3876). ; Peer Reviewed

7 páginas, 4 figuras, 1 tabla. ; Identifying the factors that govern the thermal resistance of cupredoxins is essential for understanding their folding and stability, and for improving our ability to design highly stable enzymes with potential biotechnological applications. Here, we show that the thermal unfolding of plastocyanins from two cyanobacteria—the mesophilic Synechocystis and the thermophilic Phormidium—is closely related to the short-range structure around the copper center. Cu K-edge X-ray absorption spectroscopy shows that the bond length between Cu and the S atom from the cysteine ligand is a key structural factor that correlates with the thermal stability of the cupredoxins in both oxidized and reduced states. These findings were confirmed by an additional study of a site-directed mutant of Phormidium plastocyanin showing a reverse effect of the redox state on the thermal stability of the protein. ; This work was partially supported by CICYT-MAT2008-06542-C04 and BFU2009-07190 grants of the Spanish Ministry of Science and Innovation, and by the Andalusian Government (BIO-198 and P06-CVI-01713). ; Peer reviewed

6 pages, 1 table, 3 figures. ; PMC1769345 ; The transient complex between cytochrome f and plastocyanin from the cyanobacterium Nostoc sp. PCC 7119 has been analysed by X-ray Absorption Spectroscopy in solution, using both proteins in their oxidized and reduced states. Fe K-edge data mainly shows that the atypical metal coordination geometry of cytochrome f, in which the N-terminal amino acid acts as an axial ligand of the heme group, remains unaltered upon binding to its redox partner, plastocyanin. This fact suggests that cytochrome f provides a stable binding site for plastocyanin and minimizes the reorganization energy required in the transient complex formation, which could facilitate the electron transfer between the two redox partners. ; This work was supported by the European Synchrotron Radiation Facility (ESRF SC-1366), the Spanish Ministry of Education and Science (AP2000–2937, BMC2003–00458 and MAT02–01221) and the Andalusian Government (PAI, CVI-0198). ; Peer reviewed

10 páginas, 9 figuras, 1 tabla ; Many fleeting macromolecular interactions, like those being involved in electron transport, are essential in biology. However, little is known about the behaviour of the partners and their dynamics within their short-lived complex. To tackle such issue, we have performed molecular dynamics simulations on an electron transfer complex formed by plastocyanin and cytochrome f from the cyanobacterium Phormidium laminosum. Besides simulations of the isolated partners, two independent trajectories of the complex were calculated, starting from the two different conformations in the NMR ensemble. The first one leads to a more stable ensemble with a shorter distance between the metal sites of the two partners. The second experiences a significant drift of the complex conformation. Analyses of the distinct calculations show that the conformation of cytochrome f is strained upon binding of its partner, and relaxes upon its release. Interestingly, the principal component analysis of the trajectories indicates that plastocyanin displays a concerted motion with the small domain of cytochrome f that can be attributed to electrostatic interactions between the two proteins. ; This work was supported in part by research grants from the Spanish Ministry of Science and Innovation (BFU2006-01361) and the Andalusian Government (BIO-198 and P06-CVI-01713). FJML is the recipient of a FPI fellowship (BES-2005-10404) from the Spanish Ministry of Science and Innovation. ; Peer reviewed

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 ; Financial support was provided by the Spanish Ministry of Economy and Competiveness (Grant No. BFU2012-31670/BMC); The Andalusian Government (Grant PAI, BIO198); The Spanish Fund for Health Research (FIS; code PI11/02366, FI12/00189) and the Ramón Areces Foundation. ; Peer reviewed

Despite the importance of electron transfer (ET) between redox proteins in photosynthesis and respiration, the inter-protein ET rate between redox partner proteins has never been measured as a function of their separation in aqueous solution. Here we use electrochemical tunneling spectroscopy to show that the current between two protein partners decays along more than 10 nm in the solution. Molecular dynamics simulations reveal a reduced ionic density and extended electric field in the volume confined between the proteins. The distance-decay factor and the calculated local barrier for ET are regulated by the electrochemical potential applied to the proteins. Redox partners could use electrochemically gated, long distance ET through the solution in order to conciliate high ET specificity with weak binding, thus keeping high turnover rates in the crowded environment of cells. ; The project was funded by CERCA, FEDER, and Networking Biomedical Research Center (CIBER), Spain. CIBER is an initiative funded by the VI National R&D&i Plan 2008–2011, Iniciativa Ingenio 2010, Consolider Program, CIBER Actions, and the Instituto de Salud Carlos III, with the support of the European Regional Development Fund. This work was financially supported by the Commission for Universities and Research of the Department of Innovation, Universities, and Enterprise of the Generalitat de Catalunya (2017 SGR 1442, 2014 SGR 1442, and 2017 SGR 1189), by the Andalusian Government (BIO198), and the projects CTQ2016–80066-R, CTQ2015-66194-R, CTQ2017-85496-P and Spanish Structures of Excellence Maria de Maeztu, MDM2017-0767, and BFU2015-71017-P/BMC awarded by the Spanish Ministry of Economy and Competitiveness. A.N.-H. thanks the Generalitat de Catalunya-AGAUR for a FI scholarship. MINECO/ICTI2013-2016/CTQ2015-66194-R MINECO/ICTI2013-2016/BFU2015-71017-P MICIU/ICTI2017-2020/CTQ2017-85496-P MICIU/ICTI2017-2020/MDM2017-0767 ; Peer reviewed

5 páginas, 5 figuras ; The metal cofactor determines the thermal stability in cupredoxins, but how the redox state of copper modulates their melting points remains unknown. The metal coordination environment is highly conserved in cyanobacterial plastocyanins. However, the oxidised form is more stable than the reduced one in thermophilic Phormidium, but the opposite occurs in mesophilic Synechocystis. We have performed neutral amino-acid substitutions at loops of Phormidium plastocyanin far from the copper site. Notably, mutation P49G/G50P confers a redox-dependent thermal stability similar to that of the mesophilic plastocyanin. Moreover, X-ray absorption spectroscopy reveals that P49G/G50P mutation makes the electron density distribution at the oxidised copper site shift towards that of Synechocystis plastocyanin. ; This work was supported by the Spanish Ministry of Science and Innovation (MICINN, BFU2006-01361, BFU2009-07190, FIS2008-03951), the Andalusian Government (BIO-198 and P06-CVI-01713), the ESRF (SC-2486). F.J.M.L. is the recipient of a FPI fellowship (BES-2005-10404) from MICINN. ; Peer reviewed

mRNA metabolism is tightly orchestrated by highly-regulated RNA Binding Proteins (RBPs) that determine mRNA fate, thereby influencing multiple cellular functions across biological contexts. Here, we review the interplay between six well-known RBPs (TTP, AUF-1, KSRP, HuR, TIA-1, and TIAR) that recognize AU-rich elements (AREs) at the 3' untranslated regions of mRNAs, namely ARE-RBPs. Examples of the links between their cross-regulations and modulation of their targets are analyzed during mRNA processing, turnover, localization, and translational control. Furthermore, ARE recognition can be self-regulated by several factors that lead to the prevalence of one RBP over another. Consequently, we examine the factors that modulate the dynamics of those protein-RNA transient interactions to better understand the final consequences of the regulation mediated by ARE-RBPs. For instance, factors controlling the RBP isoforms, their conformational state or their post-translational modifications (PTMs) can strongly determine the fate of the protein-RNA complexes. Moreover, mRNA specific sequence and secondary structure or subtle environmental changes are also key determinants to take into account. To sum up, the whole understanding of such a fine tuned regulation is a challenge for future research and requires the integration of all the available structural and functional data by in vivo, in vitro and in silico approaches. ; Financial support was provided by the Andalusian Government (P11-CVI-7216, BIO198); the Spanish Ministry of Economy, Industry and Competitiveness (BFU2015-71017-P); the Spanish Ministry of Education, Culture and Sports (FPU013/04373, FPU016/01513) and the Ramón Areces Foundation. ; Peer reviewed

Respiratory cytochrome c has been found to be phosphorylated at tyrosine 97 in the postischemic brain upon neuroprotective insulin treatment, but how such posttranslational modification affects mitochondrial metabolism is unclear. Here, we report the structural features and functional behavior of a phosphomimetic cytochrome c mutant, which was generated by site-specific incorporation at position 97 of p-carboxymethyl-l-phenylalanine using the evolved tRNA synthetase method. We found that the point mutation does not alter the overall folding and heme environment of cytochrome c, but significantly affects the entire oxidative phosphorylation process. In fact, the electron donation rate of the mutant heme protein to cytochrome c oxidase, or complex IV, within respiratory supercomplexes was higher than that of the wild-type species, in agreement with the observed decrease in reactive oxygen species production. Direct contact of cytochrome c with the respiratory supercomplex factor HIGD1A (hypoxia-inducible domain family member 1A) is reported here, with the mutant heme protein exhibiting a lower affinity than the wild-type species. Interestingly, phosphomimetic cytochrome c also exhibited a lower caspase-3 activation activity. Altogether, these findings yield a better understanding of the molecular basis for mitochondrial metabolism in acute diseases, such as brain ischemia, and thus could allow the use of phosphomimetic cytochrome c as a neuroprotector with therapeutic applications. ; This work was supported by Ministry of Economy and Competitiveness and European Regional Development Fund (MINECO/FEDER) Grant BFU2015-71017/BMC, European Union; the Ramón Areces Foundation, European Social Fund, Andalusian Government (BIO-198); Consejo Superior de Investigaciones Científicas Fellowship JaePre_2011_01248 (to A.G.-C.); a Fundación Cámara PhD Fellowship (to C.A.E.-R.); Biointeractomics Platform (cicCartuja, Seville); and TA Instruments. ; Peer reviewed

17 pags., 9 figs., 1 tab. ; Repair of injured DNA relies on nucleosome dismantling by histone chaperones and de-phosphorylation events carried out by Protein Phosphatase 2A (PP2A). Typical histone chaperones are the Acidic leucine-rich Nuclear Phosphoprotein 32 family (ANP32) members, e.g. ANP32A, which is also a well-known PP2A inhibitor (a.k.a. IPP2A). Here we report the novel interaction between the endogenous family member B—so-called ANP32B—and endogenous cytochrome c in cells undergoing camptothecin-induced DNA damage. Soon after DNA lesions but prior to caspase cascade activation, the hemeprotein translocates to the nucleus to target the Low Complexity Acidic Region (LCAR) of ANP32B; in a similar way, our group recently reported that the hemeprotein targets the acidic domain of SET/Template Activating Factor-Iβ (SET/TAF-Iβ), which is another histone chaperone and PP2A inhibitor (a.k.a. IPP2A). The nucleosome assembly activity of ANP32B is indeed unaffected by cytochrome c binding. Like ANP32A, ANP32B inhibits PP2A activity and is thus herein referred to as IPP2A. Our data demonstrates that ANP32B-dependent inhibition of PP2A is regulated by respiratory cytochrome c, which induces long-distance allosteric changes in the structured N-terminal domain of ANP32B upon binding to the C-terminal LCAR. In agreement with the reported role of PP2A in the DNA damage response, we propose a model wherein cytochrome c is translocated from the mitochondria into the nucleus upon DNA damage to modulate PP2A activity via its interaction with ANP32B. ; This work was supported by the Spanish Ministry of Science, Innovation and Universities (BFU2012-31670, BFU2015-71017, PGC2018-096049- BI00), Spanish Ministry of Education and Professional Training (FPU013/04373 to FRR, FPU016/01513 to AVC), Regional Government of Andalusia (BIO198, US-1254317 US/JUNTA/FEDER,UE, US- 1257019 US/JUNTA/FEDER,UE, P18-FR-3487 and P18–HO-4091), Ramon Areces Foundation, Biointeractomics Platform (cicCartuja, Seville) and the Microscopy and NMR Services at CITIUS (University of Seville). MPG is funded by a postdoctoral grant from the Spanish Association Against Cancer Scientific Foundation (FC AECC)

8 pages, 4 figures, 1 table.-- PMID: 11786337 [PubMed].-- Available online Nov 29, 2001. ; Photosystem I reduction by the soluble metalloproteins cytochrome c6 and plastocyanin, which are alternatively synthesized by some photosynthetic organisms depending on the relative availability of copper and iron, has been investigated in cyanobacteria, green algae and plants. The reaction mechanism is classified in three different types on the basis of the affinity of the membrane complex towards its electron donor protein. The role of electrostatic interactions in forming an intermediate transient complex, as well as the structural and functional similarities of cytochrome c6 and plastocyanin are analysed from an evolutionary point of view. The proposal made is that the heme protein was first "discovered" by nature, when iron was much more abundant on the Earth's surface, and replaced by plastocyanin when copper became available because of the oxidizing conditions of the new atmosphere. ; The research was supported by the European Union (Networks ERB-FMRX-CT98-0218 and HPRN-CT1999-00095), Spanish Ministry of Science and Technology (MCYT, Grant BMC2000-0444), and Andalusian Government (PAI, CVI-0198). ; Peer reviewed

Regulation of mitochondrial activity allows cells to adapt to changing conditions and to control oxidative stress, and its dysfunction can lead to hypoxia-dependent pathologies such as ischemia and cancer. Although cytochrome c phosphorylation—in particular, at tyrosine 48—is a key modulator of mitochondrial signaling, its action and molecular basis remain unknown. Here we mimic phosphorylation of cytochrome c by replacing tyrosine 48 with p-carboxy-methyl-L-phenylalanine (pCMF). The NMR structure of the resulting mutant reveals significant conformational shifts and enhanced dynamics around pCMF that could explain changes observed in its functionality: The phosphomimetic mutation impairs cytochrome c diffusion between respiratory complexes, enhances hemeprotein peroxidase and reactive oxygen species scavenging activities, and hinders caspase-dependent apoptosis. Our findings provide a framework to further investigate the modulation of mitochondrial activity by phosphorylated cytochrome c and to develop novel therapeutic approaches based on its prosurvival effects. ; Financial support was provided by the Spanish Ministry of Economy and Competitiveness (Grants BFU2015-71017-P/BMC and BFU2015-19451/BMC, cofounded by FEDER EU), European Union (Bio-MR-00130 and CALIPSO-312284), Ramon Areces Foundation, and Andalusian Government (BIO198). B.M.-B. was awarded a PhD fellowship from the Spanish Ministry of Education (AP2009-4092) and a short-term traveling fellowship from the European Bio-NMR Project. A.G.-C. was awarded a PhD fellowship from the CSIC (JaePre-2011-01248). ; Peer reviewed