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Frontiers in Molecular Biosciences

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https://read.qxmd.com/read/30729112/editorial-weak-interactions-in-molecular-machinery
#1
EDITORIAL
Rivka L Isaacson, Irene Díaz-Moreno
No abstract text is available yet for this article.
2018: Frontiers in Molecular Biosciences
https://read.qxmd.com/read/30723719/metabolic-alterations-in-cardiopulmonary-vascular-dysfunction
#2
REVIEW
Valérie Françoise Smolders, Erika Zodda, Paul H A Quax, Marina Carini, Joan Albert Barberà, Timothy M Thomson, Olga Tura-Ceide, Marta Cascante
Cardiovascular diseases (CVD) are the leading cause of death worldwide. CVD comprise a range of diseases affecting the functionality of the heart and blood vessels, including acute myocardial infarction (AMI) and pulmonary hypertension (PH). Despite their different causative mechanisms, both AMI and PH involve narrowed or blocked blood vessels, hypoxia, and tissue infarction. The endothelium plays a pivotal role in the development of CVD. Disruption of the normal homeostasis of endothelia, alterations in the blood vessel structure, and abnormal functionality are essential factors in the onset and progression of both AMI and PH...
2018: Frontiers in Molecular Biosciences
https://read.qxmd.com/read/30713843/the-origin-of-unpleasant-aftertastes-in-synthetic-sweeteners-a-hypothesis
#3
Waldo Acevedo, Piero A Temussi
Most sweeteners are plagued with unwanted unpleasant aftertastes. Here we examined the possibility that one of the main reasons for this is the similarity of sweet and umami receptors. We performed docking calculations on models of sweet and umami receptors using as template the recently determined solid state structure of the first taste receptor, the medaka fish T1R2-T1R3 receptor. Our results show convincingly that sweeteners can be recognized also by the T1R1-T1R3 umami receptor, owing to the similarity of its architecture to that of the sweet receptor...
2018: Frontiers in Molecular Biosciences
https://read.qxmd.com/read/30713842/troubleshooting-guide-to-expressing-intrinsically-disordered-proteins-for-use-in-nmr-experiments
#4
REVIEW
Steffen P Graether
Intrinsically disordered proteins (IDPs) represent a structural class of proteins that do not have a well-defined, 3D fold in solution, and often have little secondary structure. To characterize their function and molecular mechanism, it is helpful to examine their structure using nuclear magnetic resonance (NMR), which can report on properties, such as residual structure (at both the secondary and tertiary levels), ligand binding affinity, and the effect of ligand binding on IDP structure, all on a per residue basis...
2018: Frontiers in Molecular Biosciences
https://read.qxmd.com/read/30687716/the-energy-landscape-of-human-serine-racemase
#5
REVIEW
Samanta Raboni, Marialaura Marchetti, Serena Faggiano, Barbara Campanini, Stefano Bruno, Francesco Marchesani, Marilena Margiotta, Andrea Mozzarelli
Human serine racemase is a pyridoxal 5'-phosphate (PLP)-dependent dimeric enzyme that catalyzes the reversible racemization of L-serine and D-serine and their dehydration to pyruvate and ammonia. As D-serine is the co-agonist of the N-methyl-D-aspartate receptors for glutamate, the most abundant excitatory neurotransmitter in the brain, the structure, dynamics, function, regulation and cellular localization of serine racemase have been investigated in detail. Serine racemase belongs to the fold-type II of the PLP-dependent enzyme family and structural models from several orthologs are available...
2018: Frontiers in Molecular Biosciences
https://read.qxmd.com/read/30662898/hidden-gems-in-the-transcriptome-maps-of-competent-streptococci
#6
Roger Junges, Gabriela Salvadori, Tsute Chen, Donald A Morrison, Fernanda C Petersen
Natural transformation is regarded as an important mechanism in bacteria that allows for adaptation to different environmental stressors by ensuring genome plasticity. Since the discovery of this phenomenon in Streptococcus pneumoniae , remarkable progress has been made in the understanding of the molecular mechanisms and pathways coordinating this process. Recently, the advent of high-throughput sequencing allows the posing of questions that address the system at a larger scale but also allow for the creation of high-resolution maps of transcription...
2018: Frontiers in Molecular Biosciences
https://read.qxmd.com/read/30619881/why-the-energy-landscape-of-barnase-is-hierarchical
#7
Maya J Pandya, Stefanie Schiffers, Andrea M Hounslow, Nicola J Baxter, Mike P Williamson
We have used NMR and computational methods to characterize the dynamics of the ribonuclease barnase over a wide range of timescales in free and inhibitor-bound states. Using temperature- and denaturant-dependent measurements of chemical shift, we show that barnase undergoes frequent and highly populated hinge bending. Using relaxation dispersion, we characterize a slower and less populated motion with a rate of 750 ± 200 s-1 , involving residues around the lip of the active site, which occurs in both free and bound states and therefore suggests conformational selection...
2018: Frontiers in Molecular Biosciences
https://read.qxmd.com/read/30619880/the-evolution-and-the-advantages-of-microed
#8
REVIEW
Brent L Nannenga, Guanhong Bu, Dan Shi
MicroED is a method which combines cryo-EM sample preparation and instrumentation, with electron and X-ray crystallography data analysis, and it has been employed to solve many protein crystal structures at high resolution. Initially, the main doubts of this method for structure determination were the dynamic scattering of electrons, which would cause severe inaccuracies in the measured intensities. In this paper, we will review the evolution of MicroED data collection and processing, the major differences of multiple scattering effects in protein crystals and inorganic material, and the advantages of continuous rotation data collection...
2018: Frontiers in Molecular Biosciences
https://read.qxmd.com/read/30619879/fragile-x-mental-retardation-protein-to-be-or-not-to-be-a-translational-enhancer
#9
Thomas Maurin, Barbara Bardoni
No abstract text is available yet for this article.
2018: Frontiers in Molecular Biosciences
https://read.qxmd.com/read/30619878/d-3-phosphoglycerate-dehydrogenase
#10
REVIEW
Gregory A Grant
l-Serine is the immediate precursor of d-serine, a major agonist of the N-methyl-d-aspartate (NMDA) receptor. l-Serine is a pivotal amino acid since it serves as a precursor to a large number of essential metabolites besides d-serine. In all non-photosynthetic organisms, including mammals, a major source of l-serine is the phosphorylated pathway of l-serine biosynthesis. The pathway consists of three enzymes, d-3-phosphoglycerate dehydrogenase (PGDH), phosphoserine amino transferase (PSAT), and l-phosphoserine phosphatase (PSP)...
2018: Frontiers in Molecular Biosciences
https://read.qxmd.com/read/30560136/a-method-for-rna-structure-prediction-shows-evidence-for-structure-in-lncrnas
#11
Riccardo Delli Ponti, Alexandros Armaos, Stefanie Marti, Gian Gaetano Tartaglia
To compare the secondary structure profiles of RNA molecules we developed the CROSSalign method. CROSSalign is based on the combination of the Computational Recognition Of Secondary Structure (CROSS) algorithm to predict the RNA secondary structure profile at single-nucleotide resolution and the Dynamic Time Warping (DTW) method to align profiles of different lengths. We applied CROSSalign to investigate the structural conservation of long non-coding RNAs such as XIST and HOTAIR as well as ssRNA viruses including HIV ...
2018: Frontiers in Molecular Biosciences
https://read.qxmd.com/read/30560135/the-reproduction-rate-of-peptide-transporter-pept-1-deficient-c-elegans-is-dependent-on-dietary-glutamate-supply
#12
Britta Spanier, Jacqueline Wallwitz, Despoina Zapoglou, Bio Maria Ghéo Idrissou, Christine Fischer, Martina Troll, Katrin Petzold, Hannelore Daniel
Intestinal absorption of dietary amino acids is mediated via two routes. Free amino acids released by hydrolysis of dietary proteins are taken up by a multitude of amino acid transporters while di- and tripeptides released are taken up by the peptide transporter PEPT-1. Loss of PEPT-1 impairs growth, post-embryonic development and reproduction in Caenorhabditis elegans , and supplementation with a mixture of all L-amino acids only partially rescues fertility. In the present study, we demonstrate that dietary L-glutamate is the responsible amino acid that can increase fertility in hermaphrodite pept-1 worms...
2018: Frontiers in Molecular Biosciences
https://read.qxmd.com/read/30555832/changes-in-serine-racemase-dependent-modulation-of-nmda-receptor-impact-on-physiological-and-pathological-brain-aging
#13
REVIEW
Jean-Marie Billard
The N-methyl-D-Aspartate glutamate receptors (NMDARs) are pivotal for the functional and morphological plasticity that are required in neuronal networks for efficient brain activities and notably for cognitive-related abilities. Because NMDARs are heterogeneous in subunit composition and associated with multiple functional regulatory sites, their efficacy is under the tonic influence of numerous allosteric modulations, whose dysfunction generally represents the first step generating pathological states. Among the enzymatic candidates, serine racemase (SR) has recently gathered an increasing interest considering that it tightly regulates the production of d-serine, an amino acid now viewed as the main endogenous co-agonist necessary for NMDAR activation...
2018: Frontiers in Molecular Biosciences
https://read.qxmd.com/read/30555831/analysis-of-the-effect-of-intestinal-ischemia-and-reperfusion-on-the-rat-neutrophils-proteome
#14
Muhammad Tahir, Samina Arshid, Belchor Fontes, Mariana S Castro, Isabelle S Luz, Katyelle L R Botelho, Simone Sidoli, Veit Schwämmle, Peter Roepstorff, Wagner Fontes
Intestinal ischemia and reperfusion injury is a model system of possible consequences of severe trauma and surgery, which might result into tissue dysfunction and organ failure. Neutrophils contribute to the injuries preceded by ischemia and reperfusion. However, the mechanisms by which intestinal ischemia and reperfusion stimulate and activate circulating neutrophils is still not clear. In this work, we used proteomics approach to explore the underlying regulated mechanisms in Wistar rat neutrophils after ischemia and reperfusion...
2018: Frontiers in Molecular Biosciences
https://read.qxmd.com/read/30547038/editorial-bioscience-of-d-amino-acid-oxidase-from-biochemistry-to-pathophysiology
#15
EDITORIAL
Loredano Pollegioni, Jumpei Sasabe
No abstract text is available yet for this article.
2018: Frontiers in Molecular Biosciences
https://read.qxmd.com/read/30547037/human-d-amino-acid-oxidase-structure-function-and-regulation
#16
REVIEW
Loredano Pollegioni, Silvia Sacchi, Giulia Murtas
D-Amino acid oxidase (DAAO) is an FAD-containing flavoenzyme that catalyzes with absolute stereoselectivity the oxidative deamination of all natural D-amino acids, the only exception being the acidic ones. This flavoenzyme plays different roles during evolution and in different tissues in humans. Its three-dimensional structure is well conserved during evolution: minute changes are responsible for the functional differences between enzymes from microorganism sources and those from humans. In recent years several investigations focused on human DAAO, mainly because of its role in degrading the neuromodulator D-serine in the central nervous system...
2018: Frontiers in Molecular Biosciences
https://read.qxmd.com/read/30547036/alternative-splicing-regulator-rbm20-and-cardiomyopathy
#17
REVIEW
Takeshi Watanabe, Akinori Kimura, Hidehito Kuroyanagi
RBM20 is a vertebrate-specific RNA-binding protein with two zinc finger (ZnF) domains, one RNA-recognition motif (RRM)-type RNA-binding domain and an arginine/serine (RS)-rich region. RBM20 has initially been identified as one of dilated cardiomyopathy (DCM)-linked genes. RBM20 is a regulator of heart-specific alternative splicing and Rbm20 Δ RRM mice lacking the RRM domain are defective in the splicing regulation. The Rbm20 Δ RRM mice, however, do not exhibit a characteristic DCM-like phenotype such as dilatation of left ventricles or systolic dysfunction...
2018: Frontiers in Molecular Biosciences
https://read.qxmd.com/read/30547035/biochemical-characterization-of-aspergillus-fumigatus-aroh-a-putative-aromatic-amino-acid-aminotransferase
#18
Mirco Dindo, Egidia Costanzi, Marco Pieroni, Claudio Costantini, Giannamaria Annunziato, Agostino Bruno, Nancy P Keller, Luigina Romani, Teresa Zelante, Barbara Cellini
The rise in the frequency of nosocomial infections is becoming a major problem for public health, in particular in immunocompromised patients. Aspergillus fumigatus is an opportunistic fungus normally present in the environment directly responsible for lethal invasive infections. Recent results suggest that the metabolic pathways related to amino acid metabolism can regulate the fungus-host interaction and that an important role is played by enzymes involved in the catabolism of L-tryptophan. In particular, in A...
2018: Frontiers in Molecular Biosciences
https://read.qxmd.com/read/30542652/expanded-insights-into-mechanisms-of-gene-expression-and-disease-related-disruptions
#19
REVIEW
Moyra Smith, Pamela L Flodman
Definitive molecular diagnoses in disorders apparently due to genetic or genomic defects are still lacking in a significant number of investigated cases, despite use of studies designed to discover defects in the protein coding regions of the genome. Increasingly studies are being designed to search for defects in the non-protein coding genome, and for alterations in gene expression. Here we review new insights into genomic elements involved in control of gene expression, including methods to analyze chromatin that is accessible for transcription factor binding, enhancers, chromatin looping, transcription, RNA binding proteins, and alternative splicing...
2018: Frontiers in Molecular Biosciences
https://read.qxmd.com/read/30538993/structural-basis-for-the-limited-response-to-oxidative-and-thiol-conjugating-agents-by-triosephosphate-isomerase-from-the-photosynthetic-bacteria-synechocystis
#20
Eduardo Castro-Torres, Pedro Jimenez-Sandoval, Eli Fernández-de Gortari, Margarita López-Castillo, Noe Baruch-Torres, Marisol López-Hidalgo, Antolín Peralta-Castro, Corina Díaz-Quezada, Rogerio R Sotelo-Mundo, Claudia G Benitez-Cardoza, L Michel Espinoza-Fonseca, Adrian Ochoa-Leyva, Luis G Brieba
In plants, the ancestral cyanobacterial triosephosphate isomerase (TPI) was replaced by a duplicated version of the cytosolic TPI. This isoform acquired a transit peptide for chloroplast localization and functions in the Calvin-Benson cycle. To gain insight into the reasons for this gene replacement in plants, we characterized the TPI from the photosynthetic bacteria Synechocystis (SyTPI). SyTPI presents typical TPI enzyme kinetics profiles and assembles as a homodimer composed of two subunits that arrange in a (β-α)8 fold...
2018: Frontiers in Molecular Biosciences
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