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Frontiers in Molecular Biosciences

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https://www.readbyqxmd.com/read/28536693/the-essential-role-of-clpxp-in-caulobacter-crescentus-requires-species-constrained-substrate-specificity
#1
Robert H Vass, Jacob Nascembeni, Peter Chien
The ClpXP protease is a highly conserved AAA+ degradation machine that is present throughout bacteria and in eukaryotic organelles. ClpXP is essential in some bacteria, such as Caulobacter crescentus, but dispensible in others, such as Escherichia coli. In Caulobacter, ClpXP normally degrades the SocB toxin and increased levels of SocB result in cell death. ClpX can be deleted in cells lacking this toxin, but these ΔclpX strains are still profoundly deficient in morphology and growth supporting the existence of additional important functions for ClpXP...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28523272/structural-elements-regulating-aaa-protein-quality-control-machines
#2
REVIEW
Chiung-Wen Chang, Sukyeong Lee, Francis T F Tsai
Members of the ATPases Associated with various cellular Activities (AAA+) superfamily participate in essential and diverse cellular pathways in all kingdoms of life by harnessing the energy of ATP binding and hydrolysis to drive their biological functions. Although most AAA+ proteins share a ring-shaped architecture, AAA+ proteins have evolved distinct structural elements that are fine-tuned to their specific functions. A central question in the field is how ATP binding and hydrolysis are coupled to substrate translocation through the central channel of ring-forming AAA+ proteins...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28523271/the-protein-chaperone-clpx-targets-native-and-non-native-aggregated-substrates-for-remodeling-disassembly-and-degradation-with-clpp
#3
Christopher J LaBreck, Shannon May, Marissa G Viola, Joseph Conti, Jodi L Camberg
ClpX is a member of the Clp/Hsp100 family of ATP-dependent chaperones and partners with ClpP, a compartmentalized protease, to degrade protein substrates bearing specific recognition signals. ClpX targets specific proteins for degradation directly or with substrate-specific adaptor proteins. Native substrates of ClpXP include proteins that form large oligomeric assemblies, such as MuA, FtsZ, and Dps in Escherichia coli. To remodel large oligomeric substrates, ClpX utilizes multivalent targeting strategies and discriminates between assembled and unassembled substrate conformations...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28516087/dna-sequence-analysis-in-clinical-medicine-proceeding-cautiously
#4
REVIEW
Moyra Smith
Delineation of underlying genomic and genetic factors in a specific disease may be valuable in establishing a definitive diagnosis and may guide patient management and counseling. In addition, genetic information may be useful in identification of at risk family members. Gene mapping and initial genome sequencing data enabled the development of microarrays to analyze genomic variants. The goal of this review is to consider different generations of sequencing techniques and their application to exome sequencing and whole genome sequencing and their clinical applications...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28487858/a-balanced-approach-to-adaptive-probability-density-estimation
#5
Julio A Kovacs, Cailee Helmick, Willy Wriggers
Our development of a Fast (Mutual) Information Matching (FIM) of molecular dynamics time series data led us to the general problem of how to accurately estimate the probability density function of a random variable, especially in cases of very uneven samples. Here, we propose a novel Balanced Adaptive Density Estimation (BADE) method that effectively optimizes the amount of smoothing at each point. To do this, BADE relies on an efficient nearest-neighbor search which results in good scaling for large data sizes...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28487857/determining-complex-structures-using-docking-method-with-single-particle-scattering-data
#6
Hongxiao Wang, Haiguang Liu
Protein complexes are critical for many molecular functions. Due to intrinsic flexibility and dynamics of complexes, their structures are more difficult to determine using conventional experimental methods, in contrast to individual subunits. One of the major challenges is the crystallization of protein complexes. Using X-ray free electron lasers (XFELs), it is possible to collect scattering signals from non-crystalline protein complexes, but data interpretation is more difficult because of unknown orientations...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28487856/computing-spatiotemporal-heat-maps-of-lipid-electropore-formation-a-statistical-approach
#7
Willy Wriggers, Federica Castellani, Julio A Kovacs, P Thomas Vernier
We extend the multiscale spatiotemporal heat map strategies originally developed for interpreting molecular dynamics simulations of well-structured proteins to liquids such as lipid bilayers and solvents. Our analysis informs the experimental and theoretical investigation of electroporation, that is, the externally imposed breaching of the cell membrane under the influence of an electric field of sufficient magnitude. To understand the nanoscale architecture of electroporation, we transform time domain data of the coarse-grained interaction networks of lipids and solvents into spatial heat maps of the most relevant constituent molecules...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28451587/the-interplay-of-cofactor-interactions-and-post-translational-modifications-in-the-regulation-of-the-aaa-atpase-p97
#8
REVIEW
Petra Hänzelmann, Hermann Schindelin
The hexameric type II AAA ATPase (ATPase associated with various activities) p97 (also referred to as VCP, Cdc48, and Ter94) is critically involved in a variety of cellular activities including pathways such as DNA replication and repair which both involve chromatin remodeling, and is a key player in various protein quality control pathways mediated by the ubiquitin proteasome system as well as autophagy. Correspondingly, p97 has been linked to various pathophysiological states including cancer, neurodegeneration, and premature aging...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28443288/rubisco-activases-aaa-chaperones-adapted-to-enzyme-repair
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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