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Frontiers in Molecular Biosciences

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https://www.readbyqxmd.com/read/28443288/rubisco-activases-aaa-chaperones-adapted-to-enzyme-repair
#1
REVIEW
Javaid Y Bhat, Gabriel Thieulin-Pardo, F Ulrich Hartl, Manajit Hayer-Hartl
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), the key enzyme of the Calvin-Benson-Bassham cycle of photosynthesis, requires conformational repair by Rubisco activase for efficient function. Rubisco mediates the fixation of atmospheric CO2 by catalyzing the carboxylation of the five-carbon sugar ribulose-1,5-bisphosphate (RuBP). It is a remarkably inefficient enzyme, and efforts to increase crop yields by bioengineering Rubisco remain unsuccessful. This is due in part to the complex cellular machinery required for Rubisco biogenesis and metabolic maintenance...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28428956/physiological-functions-of-the-cellular-prion-protein
#2
REVIEW
Andrew R Castle, Andrew C Gill
The prion protein, PrP(C), is a small, cell-surface glycoprotein notable primarily for its critical role in pathogenesis of the neurodegenerative disorders known as prion diseases. A hallmark of prion diseases is the conversion of PrP(C) into an abnormally folded isoform, which provides a template for further pathogenic conversion of PrP(C), allowing disease to spread from cell to cell and, in some circumstances, to transfer to a new host. In addition to the putative neurotoxicity caused by the misfolded form(s), loss of normal PrP(C) function could be an integral part of the neurodegenerative processes and, consequently, significant research efforts have been directed toward determining the physiological functions of PrP(C)...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28421184/the-proteasomal-atpases-use-a-slow-but-highly-processive-strategy-to-unfold-proteins
#3
Aaron Snoberger, Raymond T Anderson, David M Smith
All domains of life have ATP-dependent compartmentalized proteases that sequester their peptidase sites on their interior. ATPase complexes will often associate with these compartmentalized proteases in order to unfold and inject substrates into the protease for degradation. Significant effort has been put into understanding how ATP hydrolysis is used to apply force to proteins and cause them to unfold. The unfolding kinetics of the bacterial ATPase, ClpX, have been shown to resemble a fast motor that traps unfolded intermediates as a strategy to unfold proteins...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28396859/electron-microscopy-structural-insights-into-cpap-oligomeric-behavior-a-plausible-assembly-process-of-a-supramolecular-scaffold-of-the-centrosome
#4
Ana L Alvarez-Cabrera, Sandra Delgado, David Gil-Carton, Gulnahar B Mortuza, Guillermo Montoya, Carlos O S Sorzano, Tang K Tang, Jose M Carazo
Centrosomal P4.1-associated protein (CPAP) is a cell cycle regulated protein fundamental for centrosome assembly and centriole elongation. In humans, the region between residues 897-1338 of CPAP mediates interactions with other proteins and includes a homodimerization domain. CPAP mutations cause primary autosomal recessive microcephaly and Seckel syndrome. Despite of the biological/clinical relevance of CPAP, its mechanistic behavior remains unclear and its C-terminus (the G-box/TCP domain) is the only part whose structure has been solved...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28393069/commentary-synthetic-ubiquinones-specifically-bind-to-mitochondrial-voltage-dependent-anion-channel-1-vdac1-in-saccharomyces-cerevisiae-mitochondria
#5
COMMENT
Manuel Gutiérrez-Aguilar
No abstract text is available yet for this article.
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28382301/bayesian-modeling-of-biomolecular-assemblies-with-cryo-em-maps
#6
Michael Habeck
A growing array of experimental techniques allows us to characterize the three-dimensional structure of large biological assemblies at increasingly higher resolution. In addition to X-ray crystallography and nuclear magnetic resonance in solution, new structure determination methods such cryo-electron microscopy (cryo-EM), crosslinking/mass spectrometry and solid-state NMR have emerged. Often it is not sufficient to use a single experimental method, but complementary data need to be collected by using multiple techniques...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28367437/antimicrobial-antioxidant-and-cytotoxic-activity-of-silver-nanoparticles-synthesized-by-leaf-extract-of-erythrina-suberosa-roxb
#7
Yugal K Mohanta, Sujogya K Panda, Rasu Jayabalan, Nanaocha Sharma, Akshaya K Bastia, Tapan K Mohanta
In this experiment, biosynthesized silver nanoparticles (AgNPs) were synthesized using aqueous leaf extract of Erythrina suberosa (Roxb.). The biosynthesis of silver nanoparticle was continuously followed by UV-vis spectrophotometric analysis. The response of the phytoconstituents resides in E. suberusa during synthesis of stable AgNPs were analyzed by ATR- fourier-transform infrared spectroscopy. Further, the size, charge, and polydispersity nature of AgNPs were studied using dynamic light scattering spectroscopy...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28349052/hybrid-methods-in-iron-sulfur-cluster-biogenesis
#8
REVIEW
Filippo Prischi, Annalisa Pastore
Hybrid methods, which combine and integrate several biochemical and biophysical techniques, have rapidly caught up in the last twenty years to provide a way to obtain a fuller description of proteins and molecular complexes with sizes and complexity otherwise not easily affordable. Here, we review the use of a robust hybrid methodology based on a mixture of NMR, SAXS, site directed mutagenesis and molecular docking which we have developed to determine the structure of weakly interacting molecular complexes...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28344973/coarse-grained-conformational-sampling-of-protein-structure-improves-the-fit-to-experimental-hydrogen-exchange-data
#9
Didier Devaurs, Dinler A Antunes, Malvina Papanastasiou, Mark Moll, Daniel Ricklin, John D Lambris, Lydia E Kavraki
Monitoring hydrogen/deuterium exchange (HDX) undergone by a protein in solution produces experimental data that translates into valuable information about the protein's structure. Data produced by HDX experiments is often interpreted using a crystal structure of the protein, when available. However, it has been shown that the correspondence between experimental HDX data and crystal structures is often not satisfactory. This creates difficulties when trying to perform a structural analysis of the HDX data. In this paper, we evaluate several strategies to obtain a conformation providing a good fit to the experimental HDX data, which is a premise of an accurate structural analysis...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28321398/unveiling-the-metabolic-changes-on-muscle-cell-metabolism-underlying-p-phenylenediamine-toxicity
#10
Igor Marín de Mas, Silvia Marín, Gisela Pachón, Juan C Rodríguez-Prados, Pedro Vizán, Josep J Centelles, Romà Tauler, Amaya Azqueta, Vitaly Selivanov, Adela López de Ceraín, Marta Cascante
Rhabdomyolysis is a disorder characterized by acute damage of the sarcolemma of the skeletal muscle leading to release of potentially toxic muscle cell components into the circulation, most notably creatine phosphokinase (CK) and myoglobulin, and is frequently accompanied by myoglobinuria. In the present work, we evaluated the toxicity of p-phenylenediamine (PPD), a main component of hair dyes which is reported to induce rhabdomyolysis. We studied the metabolic effect of this compound in vivo with Wistar rats and in vitro with C2C12 muscle cells...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28303242/editorial-molecular-diagnostics-in-the-detection-of-neurodegenerative-disorders
#11
EDITORIAL
Megha Agrawal, William C Cho
No abstract text is available yet for this article.
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28293558/the-copper-efflux-regulator-cuer-is-subject-to-atp-dependent-proteolysis-in-escherichia-coli
#12
Lisa-Marie Bittner, Alexander Kraus, Sina Schäkermann, Franz Narberhaus
The trace element copper serves as cofactor for many enzymes but is toxic at elevated concentrations. In bacteria, the intracellular copper level is maintained by copper efflux systems including the Cue system controlled by the transcription factor CueR. CueR, a member of the MerR family, forms homodimers, and binds monovalent copper ions with high affinity. It activates transcription of the copper tolerance genes copA and cueO via a conserved DNA-distortion mechanism. The mechanism how CueR-induced transcription is turned off is not fully understood...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28286750/cellular-pathology-of-pelizaeus-merzbacher-disease-involving-chaperones-associated-with-endoplasmic-reticulum-stress
#13
REVIEW
Ken Inoue
Disease-causing mutations in genes encoding membrane proteins may lead to the production of aberrant polypeptides that accumulate in the endoplasmic reticulum (ER). These mutant proteins have detrimental conformational changes or misfolding events, which result in the triggering of the unfolded protein response (UPR). UPR is a cellular pathway that reduces ER stress by generally inhibiting translation, increasing ER chaperones levels, or inducing cell apoptosis in severe ER stress. This process has been implicated in the cellular pathology of many neurological disorders, including Pelizaeus-Merzbacher disease (PMD)...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28275610/mutant-analysis-reveals-allosteric-regulation-of-clpb-disaggregase
#14
Kamila B Franke, Bernd Bukau, Axel Mogk
The members of the hexameric AAA+ disaggregase of E. coli and S. cerevisiae, ClpB, and Hsp104, cooperate with the Hsp70 chaperone system in the solubilization of aggregated proteins. Aggregate solubilization relies on a substrate threading activity of ClpB/Hsp104 fueled by ATP hydrolysis in both ATPase rings (AAA-1, AAA-2). ClpB/Hsp104 ATPase activity is controlled by the M-domains, which associate to the AAA-1 ring to downregulate ATP hydrolysis. Keeping M-domains displaced from the AAA-1 ring by association with Hsp70 increases ATPase activity due to enhanced communication between protomers...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28232911/structural-basis-of-the-substrate-specificity-and-enzyme-catalysis-of-a-papaver-somniferum-tyrosine-decarboxylase
#15
Huai Guan, Shuaibao Song, Howard Robinson, Jing Liang, Haizhen Ding, Jianyong Li, Qian Han
Tyrosine decarboxylase (TyDC), a type II pyridoxal 5'-phosphate decarboxylase, catalyzes the decarboxylation of tyrosine. Due to a generally high sequence identity to other aromatic amino acid decarboxylases (AAADs), primary sequence information is not enough to understand substrate specificities with structural information. In this study, we selected a typical TyDC from Papaver somniferum as a model to study the structural basis of AAAD substrate specificities. Analysis of the native P. somniferum TyDC crystal structure and subsequent molecular docking and dynamics simulation provide some structural bases that explain substrate specificity for tyrosine...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28210618/an-optimized-procedure-for-the-site-directed-labeling-of-ngf-and-prongf-for-imaging-purposes
#16
Pierluigi Di Matteo, Mariantonietta Calvello, Stefano Luin, Laura Marchetti, Antonino Cattaneo
Neurotrophins are growth factors of fundamental importance for the development, survival and maintenance of different neuronal and non-neuronal populations. Over the years, the use of labeled neurotrophins has helped in the study of their biological functions, leading to a better understanding of the processes that regulate their transport, traffic, and signaling. However, the diverse and heterogeneous neurotrophin labeling strategies adopted so far have often led to poorly reproducible protocols and sometimes conflicting conclusions...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28197405/on-the-helix-propensity-in-generalized-born-solvent-descriptions-of-modeling-the-dark-proteome
#17
Mark A Olson
Intrinsically disordered proteins that populate the so-called "Dark Proteome" offer challenging benchmarks of atomistic simulation methods to accurately model conformational transitions on a multidimensional energy landscape. This work explores the application of parallel tempering with implicit solvent models as a computational framework to capture the conformational ensemble of an intrinsically disordered peptide derived from the Ebola virus protein VP35. A recent X-ray crystallographic study reported a protein-peptide interface where the VP35 peptide underwent a folding transition from a disordered form to a helix-β-turn-helix topological fold upon molecular association with the Ebola protein NP...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28197404/using-global-analysis-to-extend-the-accuracy-and-precision-of-binding-measurements-with-t-cell-receptors-and-their-peptide-mhc-ligands
#18
Sydney J Blevins, Brian M Baker
In cellular immunity, clonally distributed T cell receptors (TCRs) engage complexes of peptides bound to major histocompatibility complex proteins (pMHCs). In the interactions of TCRs with pMHCs, regions of restricted and variable diversity align in a structurally complex fashion. Many studies have used mutagenesis to attempt to understand the "roles" played by various interface components in determining TCR recognition properties such as specificity and cross-reactivity. However, these measurements are often complicated or even compromised by the weak affinities TCRs maintain toward pMHC...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28174697/editorial-the-hsp70-molecular-chaperone-machines
#19
EDITORIAL
Pierre Goloubinoff
No abstract text is available yet for this article.
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28119917/commentary-history-of-the-ribosome-and-the-origin-of-translation
#20
COMMENT
Derek Caetano-Anollés, Gustavo Caetano-Anollés
No abstract text is available yet for this article.
2016: Frontiers in Molecular Biosciences
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