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The Light Conduction in an Antenna of a Phycobilisome

Jose R. Sepulveda-Ugarte, Maximiliano Figueroa, José Martínez-Oyanedel, Marta C. Bunster
2010 Biophysical Journal  
Sepulveda-Ugarte, Maximiliano Figueroa, José Martínez-Oyanedel, Marta C. Bunster. Universidad de Concepcion, Concepción, Chile.  ...  This mechanism should be operative in proteins. 3016-Pos 3017-Pos The Light Conduction in an Antenna of a Phycobilisome Jose R.  ... 
doi:10.1016/j.bpj.2009.12.3169 fatcat:n7iadzgku5d3thiycvwg4p6qgi

Structural Studies of a Phycobilisome

Marta C. Bunster, Carola E. Bruna, Jose A. Martinez-Oyanedel, Maximiliano Figueroa, Carolina Meza, Jose R. Sepulveda, Adelio Matamala
2009 Biophysical Journal  
Bruna, Jose A. Martinez-Oyanedel, Maximiliano Figueroa, Carolina Meza, Jose R. Sepulveda, Adelio Matamala. Universidad de Concepcion, Concepción, Chile.  ... 
doi:10.1016/j.bpj.2008.12.297 fatcat:xgeiy6vgrbecxlofmmmid7knry

Teaching Biochemistry Using New Strategies in the Universidad de Concepción (Symposium)

José Martínez Oyanedel, Carola Bruna, Marta Bunster
2012 Journal of Biochemistry Education  
doi:10.16923/reb.v10i2.112 fatcat:mybx23mbsrfkjlg6n4ninxfknq

Impact of white wine macromolecules on fractionation performance of ultrafiltration membranes

Johannes De Bruijn, José Martínez-Oyanedel, Cristina Loyola, Francisco Lobos, Javier Seiter, Ricardo Pérez
2011 OENO One  
<p style="text-align: justify;"><strong>Aim</strong>: The aim of this study was to investigate the performance of ultrafiltration (UF) membranes to achieve a selective separation of macromolecules from Sauvignon blanc wine into stable and unstable fractions and to characterize the main compounds separated.</p><p style="text-align: justify;"><strong>Methods and results</strong>: The macromolecules from two Sauvignon blanc wines (Curicó Valley and Casablanca Valley, Chile) were separated by a
more » ... ade of UF membranes into three nominal fractions (10-30, 30-100 and 100-300 kDa). These fractions were characterized by native and SDS electrophoresis and membrane performance was evaluated by protein rejection and transmission. Separation by UF allowed the concentration of thermally unstable proteins in the 10-30 kDa retentate fraction, increasing heat induced haze by 8.9 fold, while heat stable glycoproteins were concentrated into the 100-300 kDa retentate fraction, reducing heat induced haze by 5.3 fold compared to unfiltered wine. The retention of high macromolecular species by the UF membrane with a 100 kDa molecular weight cut-off contributed to increased protein aggregation in the filtered wines.</p><p style="text-align: justify;"><strong>Conclusion</strong>: The concentration and purification of anti-hazing compounds by membrane filtration seem to be a new technology to improve the protein stability of white wines.</p><p style="text-align: justify;"><strong>Significance and impact of the study</strong>: Specific wine proteins are responsible for wine instability, resulting in haze formation in white wines. On the other hand, glycoproteins prevent protein aggregation and precipitation, thereby improving wine stability. Fractionation of wine macromolecules by UF membranes may help us to improve our knowledge about the contribution of specific proteins and glycoproteins to the haze stability of white wines.</p>
doi:10.20870/oeno-one.2011.45.3.1493 fatcat:zqclna5dund45pgmhl5uooa6jy

Crystal Structure of Escherichia coli Agmatinase: Catalytic Mechanism and Residues Relevant for Substrate Specificity

Pablo Maturana, María S Orellana, Sixto M Herrera, Ignacio Martínez, Maximiliano Figueroa, José Martínez-Oyanedel, Victor Castro-Fernandez, Elena Uribe
2021 International Journal of Molecular Sciences  
Agmatine is the product of the decarboxylation of L-arginine by the enzyme arginine decarboxylase. This amine has been attributed to neurotransmitter functions, anticonvulsant, anti-neurotoxic, and antidepressant in mammals and is a potential therapeutic agent for diseases such as Alzheimer's, Parkinson's, and cancer. Agmatinase enzyme hydrolyze agmatine into urea and putrescine, which belong to one of the pathways producing polyamines, essential for cell proliferation. Agmatinase from
more » ... ia coli (EcAGM) has been widely studied and kinetically characterized, described as highly specific for agmatine. In this study, we analyze the amino acids involved in the high specificity of EcAGM, performing a series of mutations in two loops critical to the active-site entrance. Two structures in different space groups were solved by X-ray crystallography, one at low resolution (3.2 Å), including a guanidine group; and other at high resolution (1.8 Å) which presents urea and agmatine in the active site. These structures made it possible to understand the interface interactions between subunits that allow the hexameric state and postulate a catalytic mechanism according to the Mn2+ and urea/guanidine binding site. Molecular dynamics simulations evaluated the conformational dynamics of EcAGM and residues participating in non-binding interactions. Simulations showed the high dynamics of loops of the active site entrance and evidenced the relevance of Trp68, located in the adjacent subunit, to stabilize the amino group of agmatine by cation-pi interaction. These results allow to have a structural view of the best-kinetic characterized agmatinase in literature up to now.
doi:10.3390/ijms22094769 pmid:33946272 fatcat:7v7gl32menanjb37ivao4ooevm

Comparative analyses and structural insights of new class glutathione transferases in Cryptosporidium species

Mbalenhle Sizamile Mfeka, José Martínez-Oyanedel, Wanping Chen, Ikechukwu Achilonu, Khajamohiddin Syed, Thandeka Khoza
2020 Scientific Reports  
AbstractCryptosporidiosis, caused by protozoan parasites of the genus Cryptosporidium, is estimated to rank as a leading cause in the global burden of neglected zoonotic parasitic diseases. This diarrheal disease is the second leading cause of death in children under 5 years of age. Based on the C. parvum transcriptome data, glutathione transferase (GST) has been suggested as a drug target against this pathogen. GSTs are diverse multifunctional proteins involved in cellular defense and
more » ... ation in organisms and help pathogens to alleviate chemical and environmental stress. In this study, we performed genome-wide data mining, identification, classification and in silico structural analysis of GSTs in fifteen Cryptosporidium species. The study revealed the presence three GSTs in each of the Cryptosporidium species analyzed in the study. Based on the percentage identity and comprehensive comparative phylogenetic analysis, we assigned Cryptosporidium species GSTs to three new GST classes, named Vega (ϑ), Gamma (γ) and Psi (ψ). The study also revealed an atypical thioredoxin-like fold in the C. parvum GST1 of the Vega class, whereas C. parvum GST2 of the Gamma class and C. melagridis GST3 of the Psi class has a typical thioredoxin-like fold in the N-terminal region. This study reports the first comparative analysis of GSTs in Cryptosporidium species.
doi:10.1038/s41598-020-77233-5 pmid:33230237 fatcat:5fvkqvjl25hjbbfly6zccbesba

Biophysical studies support a predicted superhelical structure with armadillo repeats for Ric-8

Maximiliano Figueroa, María Victoria Hinrichs, Marta Bunster, Patricia Babbitt, José Martinez-Oyanedel, Juan Olate
2009 Protein Science  
Ric-8 is a highly conserved cytosolic protein (MW 63 KDa) initially identified in C. elegans as an essential factor in neurotransmitter release and asymmetric cell division. Two different isoforms have been described in mammals, Ric-8A and Ric-8B; each possess guanine nucleotide exchange activity (GEF) on heterotrimeric G-proteins, but with different Ga subunits specificities. To gain insight on the mechanisms involved in Ric-8 cellular functions it is essential to obtain some information about
more » ... its structure. Therefore, the aim of this work was to create a structural model for Ric-8. In this case, it was not possible to construct a model based on comparison with a template structure because Ric-8 does not present sequence similarity with any other protein. Consequently, different bioinformatics approaches that include protein folding and structure prediction were used. The Ric-8 structural model is composed of 10 armadillo folding motifs, organized in a right-twisted a-alpha super helix. In order to validate the structural model, a His-tag fusion construct of Ric-8 was expressed in E. coli, purified by affinity and anion exchange chromatography and subjected to circular dichroism analysis (CD) and thermostability studies. Ric-8 is approximately 80% alpha helix, with a Tm of 43.1°C, consistent with an armadillo-type structure such as a-importin, a protein composed of 10 armadillo repeats. The proposed structural model for Ric-8 is intriguing because armadillo proteins are known to interact with multiple partners and participate in diverse cellular functions. These results open the possibility of finding new protein partners for Ric-8 with new cellular functions.
doi:10.1002/pro.124 pmid:19472323 pmcid:PMC2774424 fatcat:fprpjten2rernpjhh5mrqcrcxi

Electrophoretic protein profiles of mid-sized copepod Calanoides patagoniensis steadily fed bloom-forming diatoms

Victor M Aguilera, Rubén Escribano, José Martínez-Oyanedel
2015 Latin American Journal of Aquatic Research  
Aguilera 1,2, Rubén Escribano3 & José Martínez-Oyanedel3 1 Instituto de Ciencias Naturales Alexander von Humboldt, Universidad de Antofagasta P.O.  ...  ACKNOWLEDGEMENTS Authors are very grateful to the staff of Marine Biology Station of Dichato: Jose Marileo, Gisela Letelier, Claudia Pérez, Katty Donoso, Marcelo Fuentes, and Jose Caamaño  ... 
doi:10.3856/vol43-issue4-fulltext-20 doaj:78ecc56ce0794f25ae0fde6888b3341b fatcat:etk6pzmolrc4ramfgasudtnpeu

In silicomodel of an antenna of a phycobilisome and energy transfer rates determination by theoretical Förster approach

Maximiliano Figueroa, José Martínez-Oyanedel, Adelio R. Matamala, Jorge Dagnino-Leone, Claudia Mella, Rubén Fritz, José Sepúlveda-Ugarte, Marta Bunster
2012 Protein Science  
Energy transfer (ET) in phycobilisomes, a macrocomplex of phycobiliproteins and linker proteins, is a process that is difficult to understand completely. A model for a rod composed of two hexamers of Phycocyanin and two hexamers of Phycoerythrin was built using an in silico approach and the three-dimensional structures of both phycobiliproteins from Gracilaria chilensis. The model was characterized and showed 125 Å wide and 230 Å high, which agree with the dimensions of a piling of four
more » ... as observed in the images of subcomplexes of phycobilisomes obtained by transmission electron microscopy. ET rates between every pair of chromophores in the model were calculated using the F€ orster approach, and the fastest rates were selected to draw preferential ET pathways along the rod. Every path indicates that the ET is funneled toward the chromophores located at Cysteines 82 in Phycoerythrin and 84 in Phycocyanin. The chromophores that face the exterior of the rod are phycoerythrobilins, and they also show a preferential ET toward the chromophores located at the center of the rod. The values calculated, in general, agree with the experimental data reported previously, which validates the use of this experimental approach.
doi:10.1002/pro.2176 pmid:23047609 pmcid:PMC3575921 fatcat:bku2g3t3fretrbsr5rcq537nea

The γ33 subunit of R-phycoerythrin from Gracilaria chilensis has a typical double linked phycourobilin similar to γ subunit

Aleikar Vásquez-Suárez, Francisco Lobos-González, Andrew Cronshaw, José Sepúlveda-Ugarte, Maximiliano Figueroa, Jorge Dagnino-Leone, Marta Bunster, José Martínez-Oyanedel, Peter Butko
2018 PLoS ONE  
Phycobilisomes (PBS) are accessory light harvesting protein complexes formed mainly by phycobiliproteins (PBPs). The PBPs absorb light that is efficiently transferred to Photosystems due to chromophores covalently bound to specific cysteine residues. Besides phycobiliproteins (PE), the PBS contains linker proteins responsible for assembly and stabilization of the whole complex and the tuning of energy transfer steps between chromophores. The linker (γ 33 ) from Gracilaria chilensis, is a
more » ... horylated rod linker associated to (αβ) 6 hexamers of R-phycoerythrin (R-PE). Its role in the energy transfer process is not clear yet. Structural studies as well as the composition and location of the chromophores are essential to understand their involvement in the energy transfer process in PBS. To achieve this, the coding gene of γ 33 was cloned and sequenced. The sequence was analyzed by informatics tools, to obtain preliminary information which leaded the next experiments. The protein was purified from R-phycoerythrin, and the sequence confirmed by mass spectrometry. The coding sequence analysis revealed a protein of 318 aminoacid residues containing a chloroplastidial transit peptide (cTP) of 39 aminoacids at the N-terminus. The conservation of cysteines revealed possible chromophorylation sites. Using α and β R-PE subunits as spectroscopic probes in denaturation assays, we deduced a double bonded phycourobilin (PUB) on γ 33 subunit that were confirmed between Cys62 and Cys73 (DL-PUB 62/73 ) by mass spectrometry. The cysteines involved in the double link are located in a helical region, in a conformation that reminds the position of the DL-PUB 50/61 in the β subunit of R-PE. The position of single linked PUB at Cys 95 and a single linked PEB at Cys 172 were also confirmed. Spectroscopic studies show the presence of both types of chromophores and that there are not energy transfer by FRET among them.
doi:10.1371/journal.pone.0195656 pmid:29634783 pmcid:PMC5892909 fatcat:3mwbr6cyhvh2vh7cooqwthayom

The First Crystal Structure of Phosphofructokinase from a Eukaryote: Trypanosoma brucei

José Martinez-Oyanedel, Iain W. McNae, Matthew W. Nowicki, Jeffrey W. Keillor, Paul A.M. Michels, Linda A. Fothergill-Gilmore, Malcolm D. Walkinshaw
2007 Journal of Molecular Biology  
The crystal structure of the ATP-dependent phosphofructokinase (PFK) from Trypanosoma brucei provides the first detailed description of a eukaryotic PFK, and enables comparisons to be made with the crystal structures of bacterial ATP-dependent and PPi-dependent PFKs. The structure reveals that two insertions (the 17-20 and 329-348 loops) that are characteristic of trypanosomatid PFKs, but absent from bacterial and mammalian ATP-dependent PFKs, are located within and adjacent to the active site,
more » ... and are in positions to play important roles in the enzyme's mechanism. The 90 residue N-terminal extension forms a novel domain that includes an "embracing arm" across the subunit boundary to the symmetryrelated subunit in the tetrameric enzyme. Comparisons with the PPidependent PFK from Borrelia burgdorferi show that several features thought to be characteristic of PPi-dependent PFKs are present in the trypanosome ATP-dependent PFK. These two enzymes are generally more similar to each other than to the bacterial or mammalian ATP-dependent PFKs. However, there are critical differences at the active site of PPi-dependent PFKs that are sufficient to prevent the binding of ATP. This crystal structure of a eukaryotic PFK has enabled us to propose a detailed model of human muscle PFK that shows active site and other differences that offer opportunities for structure-based drug discovery for the treatment of sleeping sickness and other diseases caused by the trypanosomatid family of protozoan parasites.
doi:10.1016/j.jmb.2006.10.019 pmid:17207816 fatcat:vqy6sjpm7bf6lcv6nyfc7j2suy

Correction: The γ33 subunit of R-phycoerythrin from Gracilaria chilensis has a typical double linked phycourobilin similar to β subunit

Aleikar Vásquez-Suárez, Francisco Lobos-González, Andrew Cronshaw, José Sepúlveda-Ugarte, Maximiliano Figueroa, Jorge Dagnino-Leone, Marta Bunster, José Martínez-Oyanedel
2018 PLoS ONE  
doi:10.1371/journal.pone.0200867 pmid:30005087 pmcid:PMC6044531 fatcat:s54xtfwnjvb77fl4wqeozbptta

Molecular and functional characterization of ferredoxin NADP(H) oxidoreductase from Gracilaria chilensis and its complex with ferredoxin

María Alejandra Vorphal, Carola Bruna, Traudy Wandersleben, Jorge Dagnino-Leone, Francisco Lobos-González, Elena Uribe, José Martínez-Oyanedel, Marta Bunster
2017 Biological Research  
Backgroud: Ferredoxin NADP(H) oxidoreductases (EC 1.18.1.2) (FNR) are flavoenzymes present in photosynthetic organisms; they are relevant for the production of reduced donors to redox reactions, i.e. in photosynthesis, the reduction of NADP + to NADPH using the electrons provided by Ferredoxin (Fd), a small FeS soluble protein acceptor of electrons from PSI in chloroplasts. In rhodophyta no information about this system has been reported, this work is a contribution to the molecular and
more » ... al characterization of FNR from Gracilaria chilensis, also providing a structural analysis of the complex FNR/Fd. Methods: The biochemical and kinetic characterization of FNR was performed from the enzyme purified from phycobilisomes enriched fractions. The sequence of the gene that codifies for the enzyme, was obtained using primers designed by comparison with sequences of Synechocystis and EST from Gracilaria. 5′RACE was used to confirm the absence of a CpcD domain in FNRPBS of Gracilaria chilensis. A three dimensional model for FNR and Fd, was built by comparative modeling and a model for the complex FNR: Fd by docking. Results: The kinetic analysis shows K M NADPH of 12.5 M and a k cat of 86 s −1 , data consistent with the parameters determined for the enzyme purified from a soluble extract. The sequence for FNR was obtained and translated to a protein of 33646 Da. A FAD and a NADP+ binding domain were clearly identified by sequence analysis as well as a chloroplast signal sequence. Phycobilisome binding domain, present in some cyanobacteria was absent. Transcriptome analysis of Gch revealed the presence of two Fd; FdL and FdS , sharing the motif CX5CX2CX29X. The analysis indicated that the most probable partner for FNR is FdS. Conclusion: The interaction model produced, was consistent with functional properties reported for FNR in plants leaves, and opens the possibilities for research in other rhodophyta of commercial interest.
doi:10.1186/s40659-017-0144-5 pmid:29221464 pmcid:PMC5723097 fatcat:jaevspzmorcehfyl4grmymwfqu

Structural models of the different trimers present in the core of phycobilisomes from Gracilaria chilensis based on crystal structures and sequences

Jorge Dagnino-Leone, Maximiliano Figueroa, Claudia Mella, María Alejandra Vorphal, Frédéric Kerff, Aleikar José Vásquez, Marta Bunster, José Martínez-Oyanedel, Jiajie Diao
2017 PLoS ONE  
Phycobilisomes (PBS) are accessory light harvesting protein complexes that directionally transfer energy towards photosystems. Phycobilisomes are organized in a central core and rods radiating from it. Components of phycobilisomes in Gracilaria chilensis (Gch) are Phycobiliproteins (PBPs), Phycoerythrin (PE), and Phycocyanin (PC) in the rods, while Allophycocyanin (APC) is found in the core, and linker proteins (L). The function of such complexes depends on the structure of each component and
more » ... eir interaction. The core of PBS from cyanobacteria is mainly composed by cylinders of trimers of α and β subunits forming heterodimers of Allophycocyanin, and other components of the core including subunits α II and PLOS ONE | https://doi.
doi:10.1371/journal.pone.0177540 pmid:28542288 pmcid:PMC5436742 fatcat:73g5ko4lpfal3ck7z2svc5x5oi

A semiempirical approach to the intra-phycocyanin and inter-phycocyanin fluorescence resonance energy-transfer pathways in phycobilisomes

Adelio R. Matamala, Daniel E. Almonacid, Maximiliano F. Figueroa, JosÉ Martínez-oyanedel, Marta C. Bunster
2007 Journal of Computational Chemistry  
A semiempirical methodology to model the intra-phycocyanin and inter-phycocyanin fluorescence resonance energy-transfer (FRET) pathways in the rods of the phycobilisomes (PBSs) from Fremyella diplosiphon is presented. Using the Förster formulation of FRET and combining experimental data and PM3 calculation of the dipole moments of the aromatic portions of the chromophores, transfer constants between pairs of chromophores in the phycocyanin (PC) structure were obtained. Protein docking of two PC
more » ... hexamers was used to predict the optimal distance and axial rotation angle for the staked PCs in the PBSs' rods. Using the distance obtained by the docking process, transfer constants between pairs of chromophores belonging to different PC hexamers were calculated as a function of the angle of rotation. We show that six preferential FRET pathways within the PC hexameric ring and 15 pathways between hexamers exist, with transfer constants consistent with experimental results. Protein docking predicted the quaternary structure for PCs in rods with inter-phycocyanin distance of 55.6 Å and rotation angle of 20.58. The inter-phycocyanin FRET constant between chromophores at positions 155 is maximized at the rotation angle predicted by docking revealing the crucial role of this specific inter-phycocyanin channel in defining the complete set of FRET pathways in the system. q
doi:10.1002/jcc.20628 pmid:17299727 fatcat:7bd3vivpv5e23jrzilxlpxn4im
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