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Structural bioinformatics

Lauriane Lecoq, Shishan Wang, Thomas Wiegand, Stéphane Bressanelli, Michael Nassal, Beat H Meier, Anja Böckmann
The hepatitis B virus (HBV) icosahedral nucleocapsid is assembled from 240 chemically identical core protein molecules and, structurally, comprises four groups of symmetrically nonequivalent subunits. We show here that this asymmetry is reflected in solid-state NMR spectra of the capsids in which peak splitting is observed for a subset of residues. We compare this information to dihedral angle variations from available 3D structures, and also to computational predictions of dynamic domains and molecular hinges...
March 15, 2018: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
Michelle N Goettge, Joel P Cioni, Kou-San Ju, Katharina Pallitsch, William W Metcalf
Several oxime-containing small molecules have useful properties, including antimicrobial, insecticidal, anticancer, and immunosuppressive activities. Phosphonocystoximate and its hydroxylated congener, hydroxyphosphonocystoximate, are recently discovered oxime-containing natural products produced by Streptomyces sp. NRRL S-481 and Streptomyces regensis NRRL WC-3744, respectively. The biosynthetic pathways for these two compounds are proposed to diverge at an early step in which 2-aminoethylphosphonate (2AEPn) is converted to (S)-1-hydroxy-2- aminoethylphosphonate ((S)-1H2AEPn) in S...
March 14, 2018: Journal of Biological Chemistry
Leila M Lopes-Bezerra, Hector M Mora-Montes, Yu Zhang, Gustavo Nino-Vega, Anderson Messias Rodrigues, Zoilo Pires de Camargo, Sybren de Hoog
The description of cryptic species with different pathogenic potentials has changed the perspectives on sporotrichosis. Sporothrix schenckii causes a benign chronic subcutaneous mycosis, Sporothrix brasiliensis is highly virulent, and Sporothrix globosa mainly causes fixed cutaneous lesions. Furthermore, S. brasiliensis is the prevalent species related to cat-transmitted sporotrichosis. Sources of infection, transmission, and distribution patterns also differ between species, and variability differs between species because of different degrees of clonality...
April 1, 2018: Medical Mycology: Official Publication of the International Society for Human and Animal Mycology
Chin-Yuan Chang, Jeremy R Lohman, Tingting Huang, Karolina Michalska, Lance Bigelow, Jeffrey D Rudolf, Robert Jedrzejczak, Xiaohui Yan, Ming Ma, Gyorgy Babnigg, Andrzej Joachimiak, George N Phillips, Ben Shen
C-1027 is a chromoprotein enediyne antitumor antibiotic, consisting of the CagA apo-protein and the C-1027 chromophore. The C-1027 chromophore features a nine-membered enediyne core appended with three peripheral moieties, including an (S)-3-chloro-5-hydroxy--tyrosine. In a convergent biosynthesis of the C-1027 chromophore, the (S)-3-chloro-5-hydroxy--tyrosine moiety is appended to the enediyne core by the free-standing condensation enzyme SgcC5. Unlike canonical condensation domains from the modular nonribosomal peptide synthetases that catalyze amide bond formation, SgcC5 catalyzes ester bond formation, as demonstrated in vitro, between SgcC2-tethered (S)-3-chloro-5-hydroxy-β-tyrosine and (R)-1-phenyl-1,2-ethanediol, a mimic of the enediyne core as an acceptor substrate...
March 13, 2018: Biochemistry
Ronan M Keegan, Stuart J McNicholas, Jens M H Thomas, Adam J Simpkin, Felix Simkovic, Ville Uski, Charles C Ballard, Martyn D Winn, Keith S Wilson, Daniel J Rigden
Increasing sophistication in molecular-replacement (MR) software and the rapid expansion of the PDB in recent years have allowed the technique to become the dominant method for determining the phases of a target structure in macromolecular X-ray crystallography. In addition, improvements in bioinformatic techniques for finding suitable homologous structures for use as MR search models, combined with developments in refinement and model-building techniques, have pushed the applicability of MR to lower sequence identities and made weak MR solutions more amenable to refinement and improvement...
March 1, 2018: Acta Crystallographica. Section D, Structural Biology
Anh Nhi Tran, Fulya Taylan, Vasilios Zachariadis, Ingegerd Ivanov Öfverholm, Anna Lindstrand, Francesco Vezzi, Britta Lötstedt, Magnus Nordenskjöld, Ann Nordgren, Daniel Nilsson, Gisela Barbany
The detection of recurrent somatic chromosomal rearrangements is standard of care for most leukemia types. Even though karyotype analysis-a low-resolution genome-wide chromosome analysis-is still the gold standard, it often needs to be complemented with other methods to increase resolution. To evaluate the feasibility and applicability of mate pair whole genome sequencing (MP-WGS) to detect structural chromosomal rearrangements in the diagnostic setting, we sequenced ten bone marrow samples from leukemia patients with recurrent rearrangements...
2018: PloS One
Zhen Chen, Pei Zhao, Fuyi Li, André Leier, Tatiana T Marquez-Lago, Yanan Wang, Geoffrey I Webb, A Ian Smith, Roger J Daly, Kuo-Chen Chou, Jiangning Song
Summary: Structural and physiochemical descriptors extracted from sequence data have been widely used to represent sequences and predict structural, functional, expression and interaction profiles of proteins and peptides as well as DNAs/RNAs. Here, we present iFeature, a versatile Python-based toolkit for generating various numerical feature representation schemes for both protein and peptide sequences. iFeature is capable of calculating and extracting a comprehensive spectrum of 18 major sequence encoding schemes that encompass 53 different types of feature descriptors...
March 8, 2018: Bioinformatics
Fiona Newberry, Shen-Yuan Hsieh, Tom Wileman, Simon R Carding
Myalgic encephalomyelitis (ME)/chronic fatigue syndrome (CFS) (ME/CFS) is a disabling and debilitating disease of unknown aetiology. It is a heterogeneous disease characterized by various inflammatory, immune, viral, neurological and endocrine symptoms. Several microbiome studies have described alterations in the bacterial component of the microbiome (dysbiosis) consistent with a possible role in disease development. However, in focusing on the bacterial components of the microbiome, these studies have neglected the viral constituent known as the virome...
March 15, 2018: Clinical Science (1979-)
Gunnar von Heijne
My scientific career has taken me from chemistry, via theoretical physics and bioinformatics, to molecular biology and even structural biology. Along the way, serendipity led me to work on problems such as the identification of signal peptides that direct protein trafficking, membrane protein biogenesis, and cotranslational protein folding. I've had some great collaborations that came about because of a stray conversation or from following up on an interesting paper. And I've had the good fortune to be asked to sit on the Nobel Committee for Chemistry, where I am constantly reminded of the amazing pace and often intricate history of scientific discovery...
March 9, 2018: Journal of Biological Chemistry
Alberto Ramírez Mata, César Millán Pacheco, José F Cruz Pérez, Martha Minjárez Sáenz, Beatriz E Baca
BACKGROUND: The cyclic-di-GMP (c-di-GMP) second messenger exemplifies a signaling system that regulates many bacterial behaviors of key importance; among them, c-di-GMP controls the transition between motile and sessile life-styles in bacteria. Cellular c-di-GMP levels in bacteria are regulated by the opposite enzymatic activities of diguanylate cyclases and phosphodiesterases, which are proteins that have GGDEF and EAL domains, respectively. Azospirillum is a genus of plant-growth-promoting bacteria, and members of this genus have beneficial effects in many agronomically and ecologically essential plants...
March 9, 2018: BMC Microbiology
Michele Berselli, Enrico Lavezzo, Stefano Toppo
Motivation: Non-B DNA conformations play an important role in genomic rearrangements, structural three-dimensional organization and gene regulation. Many non-B DNA structures show symmetrical properties as palindromes and mirrors that can form hairpins, cruciform structures or triplexes. A comprehensive tool, capable to perform a fast genome wide search for exact and degenerate symmetrical patterns, is needed for further investigating nucleotide tracts potentially forming non-B DNA structures...
March 7, 2018: Bioinformatics
Guang Xu, Jacek Stupak, Li Yang, Luokai Hu, Bo Guo, Jianjun Li
Mass spectrometry (MS) has played a vital role across a broad range of fields and applications in proteomics. The development of high-resolution MS for the past decades has significantly advanced biology, such as protein structure, function, post translational modification and global protein dynamics. In MS, two ionization techniques are often used-electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI). ESI mass spectra are generally crowded by signals of multiple charge values for each molecular mass and an isotopic cluster for each nominal mass-to-charge (m/z) value...
March 8, 2018: Rapid Communications in Mass Spectrometry: RCM
Ning Yang, Krishna D P Anapindi, Stanislav S Rubakhin, Pingli Wei, Qing Yu, Lingjun Li, Paul J Kenny, Jonathan V Sweedler
Conserved across vertebrates, the habenular nuclei are a pair of small symmetrical structures in the epithalamus. The nuclei functionally link the forebrain and midbrain by receiving input from and projecting to several brain regions. Each habenular nucleus comprises two major asymmetrical subnuclei, the medial and lateral habenula. These subnuclei are associated with different physiological processes and disorders, such as depression, nicotine addiction, and encoding aversive stimuli or omitting expected rewarding stimuli...
March 8, 2018: Journal of Proteome Research
Dominic Agyei, Apollinaire Tsopmo, Chibuike C Udenigwe
There are emerging advancements in the strategies used for the discovery and development of food-derived bioactive peptides because of their multiple food and health applications. Bioinformatics and peptidomics are two computational and analytical techniques that have the potential to speed up the development of bioactive peptides from bench to market. Structure-activity relationships observed in peptides form the basis for bioinformatics and in silico prediction of bioactive sequences encrypted in food proteins...
March 7, 2018: Analytical and Bioanalytical Chemistry
Rafael R C Cuadrat, Danny Ionescu, Alberto M R Dávila, Hans-Peter Grossart
Metagenomic approaches became increasingly popular in the past decades due to decreasing costs of DNA sequencing and bioinformatics development. So far, however, the recovery of long genes coding for secondary metabolites still represents a big challenge. Often, the quality of metagenome assemblies is poor, especially in environments with a high microbial diversity where sequence coverage is low and complexity of natural communities high. Recently, new and improved algorithms for binning environmental reads and contigs have been developed to overcome such limitations...
2018: Frontiers in Microbiology
Sheng Tao Bo, Zi Fei Xu, Li Yang, Ping Cheng, Ren Xiang Tan, Rui Hua Jiao, Hui Ming Ge
Mayamycin B, a new antibacterial type II polyketide, together with its known congener mayamycin A, were isolated from Streptomyces sp. 120454. The structure of new compound was elucidated by extensive spectroscopic analysis and comparison with literature data. Sequencing and bioinformatics analysis revealed the biosynthetic gene cluster for mayamycins A and B.
March 7, 2018: Journal of Antibiotics
Donhyun Shin, Jae-Don Oh, Kyung-Hye Won, Ki-Duk Song
Objective: Non-synonymous single nucleotide polymorphisms (nsSNPs) were identified nsSNPs in Berkshire selective sweep regions and investigated Berkshire-specific nsSNPs to discover genetic nsSNP mechanisms that were potentially associated with Berkshire domestication and meat quality. We further used bioinformatics tools to predict damaging amino-acid substitutions in Berkshire-related nsSNPs. Methods: NsSNPs were examined in whole genome resequencing data of 110 pigs, including 14 Berkshire pigs, generated using the Illumina Hiseq2000 platform to identify variations that might affect meat quality in Berkshire pigs...
March 2, 2018: Asian-Australasian Journal of Animal Sciences
Simona Arena, Andrea Scaloni
Hen egg is a raw material widely used for preparation of food, pharmaceutical and cosmetoceutical products. Dedicated proteomic studies on egg fractions identified most abundant proteins. No similar studies have been performed at the peptidomic level so far. This study fills this gap and provides a comprehensive picture of the peptides present in the yolk plasma of different hen egg types after 24 and 264 h of laying, using a two-step fractionation followed by combined MALDI-TOF-TOF-MS and nanoLC-ESI-Q-Orbitrap-MS/MS analysis...
March 7, 2018: Journal of Agricultural and Food Chemistry
T S Tikhomirova, R S Ievlev, M Yu Suvorina, L G Bobyleva, I M Vikhlyantsev, A K Surin, O V Galzitskaya
The scientific interest to the structural and functional properties of actin is determined by its abundance in cells. Being an important component of the cytoskeleton, actin is involved in many protein-protein interactions. Using crystal structures and molecular models, we have mapped the amino acid residues that are involved in these interactions and form the ATP-binding site of the actin monomer. Moreover, using mass spectrometry and high-performance liquid chromatography methods, we have discovered the regions of the amino acid sequence of actin that form the core of the actin fibril...
January 2018: Molekuliarnaia Biologiia
Saeideh Jalali, Amir Zarrinhaghighi, Saman Sadraei, Younes Ghasemi, Amirhossein Sakhteman, Pouya Faridi
Background The plant Nardostachys jatamansi from Valerianaceae family is a well known antidepressant plant and has historically been used in traditional medicine. As N. jatamansi contains many different compounds, to identify its mechanisms of action, we need a network-based study. Network-based studies are becoming an increasingly important tool in understanding the mechanisms of actions of drugs. Systems pharmacology (SP) and bioinformatics are two emerging tools that use computation to develop an understanding of drug actions in molecular and cellular levels...
March 5, 2018: Current Drug Metabolism
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