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Protein structure alignment

Fang-Chi Hsieh, Yu-Fen Lu, Ian Liau, Chien-Chang Chen, Chao-Min Cheng, Chung-Der Hsiao, Sheng-Ping L Hwang
Sarcomeric signaling complexes are important to sustain proper sarcomere structure and function, however, the mechanisms underlying these processes are not fully elucidated. In a gene trap experiment, we found that vascular cell adhesion protein 1 isoform X2 (VCAP1X2) mutant embryos displayed a dilated cardiomyopathy phenotype, including reduced cardiac contractility, enlarged ventricular chamber and thinned ventricular compact layer. Cardiomyocyte and epicardial cell proliferation was decreased in the mutant heart ventricle, as was the expression of pAKT and pERK...
May 18, 2018: Scientific Reports
Cornelius M Kyalo, Andrew W Gichira, Zhi-Zhong Li, Josphat K Saina, Itambo Malombe, Guang-Wan Hu, Qing-Feng Wang
Streptocarpus teitensis (Gesneriaceae) is an endemic species listed as critically endangered in the International Union for Conservation of Nature (IUCN) red list of threatened species. However, the sequence and genome information of this species remains to be limited. In this article, we present the complete chloroplast genome structure of Streptocarpus teitensis and its evolution inferred through comparative studies with other related species. S. teitensis displayed a chloroplast genome size of 153,207 bp, sheltering a pair of inverted repeats (IR) of 25,402 bp each split by small and large single-copy (SSC and LSC) regions of 18,300 and 84,103 bp, respectively...
2018: BioMed Research International
J-T Jiang, Y-J Jiang
OBJECTIVE: We established an animal model of diet-induced obesity pregnant rats and their offsprings, and explored the effect of high-energy feeding on oxidative stress in filial rat liver, as well as the underlying mechanism. MATERIALS AND METHODS: Pregnant female Sprague-Dawley (SD) rats were randomly assigned into two groups: control group and palatable high-energy diet (PHED) group. Liver tissues were obtained 12 days after offspring rats were born for further study...
April 2018: European Review for Medical and Pharmacological Sciences
Zhiyuan Yang, Stephen Kwok-Wing Tsui
In synthetic biology, one of key focuses is building a minimal artificial cell which can provide basic chassis for functional study. Recently, the J. Craig Venter Institute published the latest version of the minimal bacterial genome JCVI-syn3.0, which only encoded 438 essential proteins. However, among them functions of 149 proteins remain unknown because of the lack of effective annotation method. Here, we report a secondary structure element alignment method called SSEalign based on an effective training dataset extracting from various bacterial genomes...
May 14, 2018: Journal of Proteome Research
Hye Young Oh, Chan-Hee Kim, Hye-Jin Go, Nam Gyu Park
Invertebrates, unlike vertebrates which have adaptive immune system, rely heavily on the innate immune system for the defense against pathogenic bacteria. Lysozymes, along with other immune effectors, are regarded as an important group in this defense. An invertebrate-type (i-type) lysozyme, designated Urechis unicinctus invertebrate-type lysozyme, Uu-ilys, has been isolated from nephridia of Urechis unicinctus using a series of high performance liquid chromatography (HPLC), and ultrasensitive radial diffusion assay (URDA) as a bioassay system...
May 9, 2018: Fish & Shellfish Immunology
Jingsi Yang, Fei Wang, Dan Yang, Ke Zhou, Min Liu, Zengqiang Gao, Peng Liu, Yuhui Dong, Jianjun Zhang, Quansheng Liu
HD-domain is a conserved domain, with the signature of histidine and aspartic (HD) residues doublets. HD-domain proteins may possess nucleotidase and phosphodiesterase activities, and they play important roles in signaling and nucleotide metabolism. In yeast, HD-domain proteins with nucleotidase activity remained unexplored. Here, we biochemically and structurally characterized two HD domain proteins YGK1 (YGL101W) and YB92 (YBR242W) from Saccharomyces cerevisiae as nucleoside 5'-monophosphatases, with substrate preference for deoxyribonucleoside 5'-monophosphatase over ribonucleoside 5'-monophosphatase...
May 9, 2018: Biochemical and Biophysical Research Communications
Giuseppe Ciossani, Katharina Overlack, Arsen Petrovic, Pim J Huis In 't Veld, Carolin Koerner, Sabine Wohlgemuth, Stefano Maffini, Andrea Musacchio
The segregation of chromosomes during cell division relies on the function of the kinetochores, protein complexes that physically connect chromosomes with microtubules of the spindle. The metazoan proteins, centromere protein E (CENP-E) and CENP-F, are components of a fibrous layer of mitotic kinetochores named the corona. Several of their features suggest that CENP-E and CENP-F are paralogs: they are very large (comprising approximately 2700 and 3200 residues, respectively), contain abundant predicted coiled-coil structures, are C-terminally prenylated, and are endowed with microtubule-binding sites at their termini...
May 10, 2018: Journal of Biological Chemistry
Arnaud Kress, Odile Lecompte, Olivier Poch, Julie D Thompson
Summary: Comparative studies of protein sequences are widely used in evolutionary and comparative genomics studies, but there is a lack of efficient tools to identify conserved regions ab initio within a protein multiple alignment. PROBE provides a fully automatic analysis of protein family conservation, to identify conserved regions, or 'blocks', that may correspond to structural / functional domains or motifs. Conserved blocks are identified at two different levels: (i) family level blocks indicate sites that are probably of central importance to the protein's structure or function, and (ii) sub-family level blocks highlight regions that may signify functional specialization, such as binding partners, etc...
May 7, 2018: Bioinformatics
Anderson Rici Amorim, Leandro Alves Neves, Carlos Roberto Valêncio, Guilherme Freire Roberto, Geraldo Francisco Donegá Zafalon
Multiple sequence alignment (MSA) is one of the most important tasks in bioinformatics and it can be used to prediction of structures or functions of unknown proteins and to phylogenetic tree reconstruction. There are many heuristics to perform multiple sequence alignment, as Progressive Alignment, Ant Colony, Genetic Algorithms, among others. Along the years, some tools were proposed to perform MSA and MSA-GA is one of them. The MSA-GA is a tool based on Genetic Algorithm to perform multiple sequence alignment and its results are generally better than other well-known tools in bioinformatics, as Clustal W...
April 25, 2018: Computational Biology and Chemistry
Jia Chen, Xiaoxin Li, Yuchen Niu, Zhihong Wu, Guixing Qiu
BACKGROUND The present study aimed to evaluate the pathogenicity of 5 [i]GDF3[/i] gene variations using functional and [i]in silico[/i] assessment approaches in a Chinese congenital scoliosis population. MATERIAL AND METHODS We selected 13 patients carrying 5 variants from a congenital scoliosis cohort. The PCR products of samples were verified by Sanger sequencing. The data and sequence alignment were analyzed using Chromas and ClustalW. SIFT and PolyPhen-2 were used to predict the functional effects of each missense and amino acid substitutions...
May 8, 2018: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
Wenya Wang, Hui Shi, Jianhua Zhu, Chunlei Li, Liyan Song, Rongmin Yu
A novel protein (J2-C4) with antioxidant and antibacterial activities was purified from the edible portion of Arca inflata. The purity of J2-C4 was measured to be 97.62% by RP-HPLC analysis, and the molecular weight was 20,537.0 Da by ESI-MS/MS. The isoelectric point of J2-C4 was determined to be 5.18 by IEF-PAGE. Secondary structure analysis of J2-C4 showed that it contained 34.9% α-helix, 15.0% β-sheet, 16.3% β-turn and 34.0% random coil by CD spectroscopy. The complete amino acid sequence of J2-C4 was identified by gel electrophoresis and LC-MS/MS together with transcriptome database analysis...
May 4, 2018: International Journal of Biological Macromolecules
Shintaro Minami, Kengo Sawada, Motonori Ota, George Chikenji
Motivation: Protein structure alignment is a significant tool to understand evolutionary processes and physicochemical properties of proteins. Important targets of structure alignment are not only monomeric but also oligomeric proteins that sometimes include domain swapping or fusions. Although various protein structural alignment programs have been developed, no method is applicable to any protein pair regardless of the number of chain components and oligomeric states with retaining sequential restrictions: structurally equivalent regions must be aligned in the same order along protein sequences...
May 3, 2018: Bioinformatics
Qi Cui, Xiao Yan, Xue Gao, Dong-Mei Zhang, Heng-Bin He, Gui-Xia Jia
A major constraint in producing lilies is gray mold caused by Botrytis elliptica and B. cinerea. WRKY transcription factors play important roles in plant immune responses. However, limited information is available about the WRKY gene family in lily plants. In this study, 23 LrWRKY genes with complete WRKY domains were identified from the Botrytis-resistant species Lilium regale. The putative WRKY genes were divided into seven subgroups (Group I, IIa-e, and III) according to their structural features. Sequence alignment revealed that LrWRKY proteins have a highly conserved WRKYGQK domain and a variant, the WRKYGKK domain, and these proteins generally contained similar motif compositions throughout the same subgroup...
April 24, 2018: Plant Physiology and Biochemistry: PPB
Richard M Walsh, Soung-Hun Roh, Anant Gharpure, Claudio L Morales-Perez, Jinfeng Teng, Ryan E Hibbs
Fast chemical communication in the nervous system is mediated by neurotransmitter-gated ion channels. The prototypical member of this class of cell surface receptors is the cation-selective nicotinic acetylcholine receptor. As with most ligand-gated ion channels, nicotinic receptors assemble as oligomers of subunits, usually as hetero-oligomers and often with variable stoichiometries 1 . This intrinsic heterogeneity in protein composition provides fine tunability in channel properties, which is essential to brain function, but frustrates structural and biophysical characterization...
May 2, 2018: Nature
Xiaoman Sun, Dandi Li, Jianxun Qi, Wengang Chai, Luyao Wang, Lihong Wang, Ruchao Peng, Han Wang, Qing Zhang, Lili Pang, Xiangyu Kong, Hong Wang, Miao Jin, George F Gao, Zhaojun Duan
Rotaviruses (RVs), which cause severe gastroenteritis in infants and children, recognize glycan ligands in a genotype-dependent manner via the distal VP8* head of the spike protein VP4. However, the glycan binding mechanisms remain elusive for the P[II] genogroup RVs, including the widely prevalent human RVs (P[8], P[4], and P[6]) and a rare P[19] RV. In this study, we characterized the glycan binding specificity of human and porcine P[6]/P[19] RV VP8* and found that the P[II] genogroup RV VP8*s could commonly interact with mucin core 2 which may play an important role in the RV evolution and cross-species transmission...
May 2, 2018: Journal of Virology
Priyankar Panwar, A K Verma, Ashutosh Dubey
Barnyard ( Echinochloa frumentacea ) and finger ( Eleusine coracana ) millet growing at northwestern Himalaya were explored for the α-amylase inhibitor (α-AI). The mature seeds of barnyard millet variety PRJ1 had maximum α-AI activity which increases in different developmental stage. α-AI was purified up to 22.25-fold from barnyard millet variety PRJ1. Semi-quantitative PCR of different developmental stages of barnyard millet seeds showed increased levels of the transcript from 7 to 28 days. Sequence analysis revealed that it contained 315 bp nucleotide which encodes 104 amino acid sequence with molecular weight 10...
May 2018: 3 Biotech
Abigail R Moye, Ratnesh Singh, Victoria A Kimler, Tanya L Dilan, Daniella Munezero, Thamaraiselvi Saravanan, Andrew F X Goldberg, Visvanathan Ramamurthy
The outer segment (OS) of photoreceptor cells is an elaboration of a primary cilium with organized stacks of membranous discs that contain the proteins needed for phototransduction and vision. Though cilia formation and function has been well characterized, little is known about the role of cilia in the development of photoreceptor OS. Nevertheless, progress has been made by studying mutations in ciliary proteins which often result in malformed outer segments and lead to blinding diseases. To investigate how ciliary proteins contribute to outer segment formation, we generated a knockout mouse model for ARL2BP, a ciliary protein linked to Retinitis Pigmentosa...
May 2, 2018: Molecular Biology of the Cell
Dongxu Shen, Lei Wang, Jiayue Ji, Qizhi Liu, Chunju An
C-type lectins (CTLs) are a large family of calcium-dependent carbohydrate-binding proteins. They function primarily in cell adhesion and immunity by recognizing various glycoconjugates. We identified 14 transcripts encoding proteins with one or two CTL domains from the transcriptome from Asian corn borer, Ostrinia furnacalis (Guenée; Lepidoptera: Pyralidae). Among them, five (OfCTL-S1 through S5) only contain one CTL domain, the remaining nine (OfIML-1 through 9) have two tandem CTL domains. Five CTL-Ss and six OfIMLs have a signal peptide are likely extracellular while another two OfIMLs might be cytoplasmic...
March 1, 2018: Journal of Insect Science
David T Jones, Shaun M Kandathil
Motivation: In addition to substitution frequency data from protein sequence alignments, many state-of-the-art methods for contact prediction rely on additional sources of information, or features, of protein sequences in order to predict residue-residue contacts, such as solvent accessibility, predicted secondary structure, and scores from other contact prediction methods. It is unclear how much of this information is needed to achieve state-of-the-art results. Here, we show that using deep neural network models, simple alignment statistics contain sufficient information to achieve state-of-the-art precision...
April 26, 2018: Bioinformatics
Tatiana Zaitseva, Cynthia Alcazar, Maedeh Zamani, Luqia Hou, Steve Sawamura, Eduard Yakubov, Michael Hopkins, Y Joseph Woo, Michael Paukshto, Ngan F Huang
RNA-based vector delivery is a promising gene therapy approach. Recent advances in chemical modification of mRNA structure to form modified mRNA (mmRNA or cmRNA or modRNA) have substantially improved their stability and translational efficiency within cells. However, mmRNA conventionally delivered in solution can be taken up non-specifically or become cleared away prematurely, which markedly limits the potential benefit of mmRNA therapy. To address this limitation, we developed mmRNA-incorporated nanofibrillar scaffolds that could target spatially localized delivery and temporally controlled release of the mmRNA both in vitro and in vivo...
May 2, 2018: Tissue Engineering. Part A
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