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Frontiers in Molecular Biosciences

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https://www.readbyqxmd.com/read/28232911/structural-basis-of-the-substrate-specificity-and-enzyme-catalysis-of-a-papaver-somniferum-tyrosine-decarboxylase
#1
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
#2
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
#3
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
#4
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
#5
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
#6
COMMENT
Derek Caetano-Anollés, Gustavo Caetano-Anollés
No abstract text is available yet for this article.
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28119916/prokaryotic-chaperonins-as-experimental-models-for-elucidating-structure-function-abnormalities-of-human-pathogenic-mutant-counterparts
#7
REVIEW
Everly Conway de Macario, Frank T Robb, Alberto J L Macario
All archaea have a chaperonin of Group II (thermosome) in their cytoplasm and some have also a chaperonin of Group I (GroEL; Cpn60; Hsp60). Conversely, all bacteria have GroEL, some in various copies, but only a few have, in addition, a chaperonin (tentatively designated Group III chaperonin) very similar to that occurring in all archaea, i.e., the thermosome subunit, and in the cytosol of eukaryotic cells, named CCT. Thus, nature offers a range of prokaryotic organisms that are potentially useful as experimental models to study the human CCT and its abnormalities...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28111626/editorial-modulating-prokaryotic-lifestyle-by-dna-binding-proteins-learning-from-apparently-simple-systems
#8
EDITORIAL
Tatiana Venkova, Antonio Juárez, Manuel Espinosa
No abstract text is available yet for this article.
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28083537/comparative-normal-mode-analysis-of-the-dynamics-of-denv-and-zikv-capsids
#9
Yin-Chen Hsieh, Frédéric Poitevin, Marc Delarue, Patrice Koehl
Key steps in the life cycle of a virus, such as the fusion event as the virus infects a host cell and its maturation process, relate to an intricate interplay between the structure and the dynamics of its constituent proteins, especially those that define its capsid, much akin to an envelope that protects its genomic material. We present a comprehensive, comparative analysis of such interplay for the capsids of two viruses from the flaviviridae family, Dengue (DENV) and Zika (ZIKV). We use for that purpose our own software suite, DD-NMA, which is based on normal mode analysis...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28083536/conformational-rigidity-within-plasticity-promotes-differential-target-recognition-of-nerve-growth-factor
#10
Francesca Paoletti, Cesira de Chiara, Geoff Kelly, Sonia Covaceuszach, Francesca Malerba, Robert Yan, Doriano Lamba, Antonino Cattaneo, Annalisa Pastore
Nerve Growth Factor (NGF), the prototype of the neurotrophin family, is essential for maintenance and growth of different neuronal populations. The X-ray crystal structure of NGF has been known since the early '90s and shows a β-sandwich fold with extensive loops that are involved in the interaction with its binding partners. Understanding the dynamical properties of these loops is thus important for molecular recognition. We present here a combined solution NMR/molecular dynamics study which addresses the question of whether and how much the long loops of NGF are flexible and describes the N-terminal intrinsic conformational tendency of the unbound NGF molecule...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28066774/pipe-chipsad-a-pipeline-for-the-analysis-of-high-density-arrays-of-bacterial-transcriptomes
#11
Silvia Bottini, Elena Del Tordello, Luca Fagnocchi, Claudio Donati, Alessandro Muzzi
PIPE-chipSAD is a pipeline for bacterial transcriptome studies based on high-density microarray experiments. The main algorithm chipSAD, integrates the analysis of the hybridization signal with the genomic position of probes and identifies portions of the genome transcribing for mRNAs. The pipeline includes a procedure, align-chipSAD, to build a multiple alignment of transcripts originating in the same locus in multiple experiments and provides a method to compare mRNA expression across different conditions...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28018906/chaperonopathies-spotlight-on-hereditary-motor-neuropathies
#12
REVIEW
Vincenzo Lupo, Carmen Aguado, Erwin Knecht, Carmen Espinós
Distal hereditary motor neuropathies (dHMN) are a group of rare hereditary neuromuscular disorders characterized by an atrophy that affects peroneal muscles in the absence of sensory symptoms. To date, 23 genes are thought to be responsible for dHMN, four of which encode chaperones: DNAJB2, which encodes a member of the HSP40/DNAJ co-chaperone family; and HSPB1, HSPB3, and HSPB8, encoding three members of the small heat shock protein family. While around 30 different mutations in HSPB1 have been identified, the remaining three genes are altered in many fewer cases...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28018905/the-mutational-landscape-of-the-oncogenic-mzf1-scan-domain-in-cancer
#13
Mads Nygaard, Thilde Terkelsen, André Vidas Olsen, Valentina Sora, Juan Salamanca Viloria, Fabio Rizza, Sanne Bergstrand-Poulsen, Miriam Di Marco, Mette Vistesen, Matteo Tiberti, Matteo Lambrughi, Marja Jäättelä, Tuula Kallunki, Elena Papaleo
SCAN domains in zinc-finger transcription factors are crucial mediators of protein-protein interactions. Up to 240 SCAN-domain encoding genes have been identified throughout the human genome. These include cancer-related genes, such as the myeloid zinc finger 1 (MZF1), an oncogenic transcription factor involved in the progression of many solid cancers. The mechanisms by which SCAN homo- and heterodimers assemble and how they alter the transcriptional activity of zinc-finger transcription factors in cancer and other diseases remain to be investigated...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28008398/dynamic-complexes-in-the-chaperonin-mediated-protein-folding-cycle
#14
REVIEW
Celeste Weiss, Fady Jebara, Shahar Nisemblat, Abdussalam Azem
The GroEL-GroES chaperonin system is probably one of the most studied chaperone systems at the level of the molecular mechanism. Since the first reports of a bacterial gene involved in phage morphogenesis in 1972, these proteins have stimulated intensive research for over 40 years. During this time, detailed structural and functional studies have yielded constantly evolving concepts of the chaperonin mechanism of action. Despite of almost three decades of research on this oligomeric protein, certain aspects of its function remain controversial...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/27990419/mutations-in-the-human-aaa-chaperone-p97-and-related-diseases
#15
REVIEW
Wai Kwan Tang, Di Xia
A number of neurodegenerative diseases have been linked to mutations in the human protein p97, an abundant cytosolic AAA(+) (ATPase associated with various cellular activities) ATPase, that functions in a large number of cellular pathways. With the assistance of a variety of cofactors and adaptor proteins, p97 couples the energy of ATP hydrolysis to conformational changes that are necessary for its function. Disease-linked mutations, which are found at the interface between two main domains of p97, have been shown to alter the function of the protein, although the pathogenic mutations do not appear to alter the structure of individual subunit of p97 or the formation of the hexameric biological unit...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/27933298/non-targeted-plasma-metabolome-of-early-and-late-lactation-gilts
#16
Lea A Rempel, Jeremy R Miles, William T Oliver, Corey D Broeckling
Female pigs nursing their first litter (first-parity gilts) have increased energy requirements not only to support their piglets, but they themselves are still maturing. Non-targeted plasma metabolomics were used to investigate the differences between (1) post-farrowing and weaning (early or late lactation), (2) degree of body condition loss after lactation (extreme or minimal), and (3) interactions; to potentially identify compounds or pathways that could aide in alleviating energetic demands of lactation in gilts...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/27900322/patterns-of-transposable-element-expression-and-insertion-in-cancer
#17
Evan A Clayton, Lu Wang, Lavanya Rishishwar, Jianrong Wang, John F McDonald, I King Jordan
Human transposable element (TE) activity in somatic tissues causes mutations that can contribute to tumorigenesis. Indeed, TE insertion mutations have been implicated in the etiology of a number of different cancer types. Nevertheless, the full extent of somatic TE activity, along with its relationship to tumorigenesis, have yet to be fully explored. Recent developments in bioinformatics software make it possible to analyze TE expression levels and TE insertional activity directly from transcriptome (RNA-seq) and whole genome (DNA-seq) next-generation sequence data...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/27900321/genome-wide-transcriptional-regulation-and-chromosome-structural-arrangement-by-galr-in-e-coli
#18
Zhong Qian, Andrei Trostel, Dale E A Lewis, Sang Jun Lee, Ximiao He, Anne M Stringer, Joseph T Wade, Thomas D Schneider, Tim Durfee, Sankar Adhya
The regulatory protein, GalR, is known for controlling transcription of genes related to D-galactose metabolism in Escherichia coli. Here, using a combination of experimental and bioinformatic approaches, we identify novel GalR binding sites upstream of several genes whose function is not directly related to D-galactose metabolism. Moreover, we do not observe regulation of these genes by GalR under standard growth conditions. Thus, our data indicate a broader regulatory role for GalR, and suggest that regulation by GalR is modulated by other factors...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/27891505/comparative-genomics-of-the-conjugation-region-of-f-like-plasmids-five-shades-of-f
#19
Raul Fernandez-Lopez, Maria de Toro, Gabriel Moncalian, M Pilar Garcillan-Barcia, Fernando de la Cruz
The F plasmid is the foremost representative of a large group of conjugative plasmids, prevalent in Escherichia coli, and widely distributed among the Enterobacteriaceae. These plasmids are of clinical relevance, given their frequent association with virulence determinants, colicins, and antibiotic resistance genes. Originally defined by their sensitivity to certain male-specific phages, IncF plasmids share a conserved conjugative system and regulatory circuits. In order to determine whether the genetic architecture and regulation circuits are preserved among these plasmids, we analyzed the natural diversity of F-like plasmids...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/27882317/bacterial-rna-polymerase-dna-interaction-the-driving-force-of-gene-expression-and-the-target-for-drug-action
#20
REVIEW
Jookyung Lee, Sergei Borukhov
DNA-dependent multisubunit RNA polymerase (RNAP) is the key enzyme of gene expression and a target of regulation in all kingdoms of life. It is a complex multifunctional molecular machine which, unlike other DNA-binding proteins, engages in extensive and dynamic interactions (both specific and nonspecific) with DNA, and maintains them over a distance. These interactions are controlled by DNA sequences, DNA topology, and a host of regulatory factors. Here, we summarize key recent structural and biochemical studies that elucidate the fine details of RNAP-DNA interactions during initiation...
2016: Frontiers in Molecular Biosciences
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