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Protein structure alignment

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https://www.readbyqxmd.com/read/29327814/systematic-evaluation-of-protein-sequence-filtering-algorithms-for-proteoform-identification-using-top-down-mass-spectrometry
#1
Qiang Kou, Si Wu, Xiaowen Liu
Complex proteoforms contain various primary structural alterations resulting from variations in genes, RNA, and proteins. Top-down mass spectrometry is commonly used for analyzing complex proteoforms because it provides whole sequence information of the proteoforms. Proteoform identification by top-down mass spectral database search is a challenging computational problem because the types and/or locations of some alterations in target proteoforms are in general unknown. Although spectral alignment and mass graph alignment algorithms have been proposed for identifying proteoforms with unknown alterations, they are extremely slow to align millions of spectra against tens of thousand protein sequences in high throughput proteome level analyses...
January 12, 2018: Proteomics
https://www.readbyqxmd.com/read/29327436/effect-of-patterned-electrospun-hierarchical-structures-on-alignment-and-differentiation-of-mesenchymal-stem-cells-biomimicking-bone
#2
Sharanya Sankar, Manohar Kakunuri, Sindhuja D E, Chandra S Sharma, Subha N Rath
Considering the complex hierarchical structure of bone, biomimicking the micro and nano level features should be an integral part of scaffold fabrication for successful bone regeneration. We aim to biomimic the micro- and nano-structure of bone and study the effect of physical cues on cell alignment, proliferation and differentiation. To achieve this, we have divided the scaffolds into groups: electrospun SU-8 nanofibers, electrospun SU-8 nanofibers with UV treatment and micropatterned (20 μm sized ridges and grooves) SU-8 nanofibers by photolithography with UV treatment...
January 11, 2018: Journal of Tissue Engineering and Regenerative Medicine
https://www.readbyqxmd.com/read/29321316/two-residues-in-nsp9-contribute-to-the-enhanced-replication-and-pathogenicity-of-highly-pathogenic-porcine-reproductive-and-respiratory-syndrome-virus
#3
Kuan Zhao, Jia-Cong Gao, Jun-Yao Xiong, Jin-Chao Guo, Yong-Bo Yang, Cheng-Gang Jiang, Yan-Dong Tang, Zhi-Jun Tian, Xue-Hui Cai, Guang-Zhi Tong, Tong-Qing An
Highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) possesses greater replicative capacity and pathogenicity than classical PRRSV. However, the factors that lead to enhanced replication and pathogenicity remain unclear. In our study, an alignment of all available full-length sequences of North-American type PRRSVs (n = 204) revealed two consistent amino acid mutations that differed between HP-PRRSV and classical PRRSV and were located at positions 519 and 544 in non-structural protein 9...
January 10, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29319811/identification-of-a-consensus-motif-in-erg28p-required-for-c-4-demethylation-in-yeast-ergosterol-biosynthesis-based-on-mutation-analysis
#4
Xia Ke, Xiao-Yuan Xia, Ren-Chao Zheng, Yu-Guo Zheng
The Erg28p protein is localized to the endoplasmic reticulum (ER), where it acts as a scaffold to tether the C-4 demethylase complex involved in the sterol biosynthesis pathway of Saccharomyces cerevisiae. However, due to the challenges involved in characterizing the interactions of membrane proteins, the precise region of Erg28p that is responsible for the assembly of this enzyme complex remains unknown. To address this question, mutants with serial truncations in the C-terminus of Erg28p were constructed based on a topology prediction of its transmembrane domain...
January 8, 2018: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/29317308/molecular-characterization-of-caspase-members-and-expression-response-to-nervous-necrosis-virus-outbreak-in-pacific-cod
#5
Ming-Guang Mao, Jie-Lan Jiang, Zhi-Qiang Jiang, Rui-Ting Liu, Qi-Ya Zhang, Jian-Fang Gui
Multiple functions of caspases include normal cell turnover, proper development and function of the immune system, hormone-dependent atrophy, embryonic development and chemical-induced cell injury. During artificial propagation of Pacific cod, Gadus macrocephalus, high mortality occurred during early development stages. Here, we performed various analyses on the cDNA and protein sequences of six different G. macrocephalus caspases namely GmCasp3, 6, 7, 8, 9 and 10, and tried to investigate the contributions of caspase family to the development and Nervous Necrosis Virus (NNV) resistance...
January 6, 2018: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/29311320/power-law-tails-in-phylogenetic-systems
#6
Chongli Qin, Lucy J Colwell
Covariance analysis of protein sequence alignments uses coevolving pairs of sequence positions to predict features of protein structure and function. However, current methods ignore the phylogenetic relationships between sequences, potentially corrupting the identification of covarying positions. Here, we use random matrix theory to demonstrate the existence of a power law tail that distinguishes the spectrum of covariance caused by phylogeny from that caused by structural interactions. The power law is essentially independent of the phylogenetic tree topology, depending on just two parameters-the sequence length and the average branch length...
January 8, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29310857/a-conserved-residue-of-l-alanine-dehydrogenase-from-bacillus-pseudofirmus-lys-73-participates-in-the-catalytic-reaction-through-hydrogen-bonding
#7
Guangzheng He, Shujing Xu, Shanshan Wang, Qing Zhang, Dong Liu, Yuling Chen, Jiansong Ju, Baohua Zhao
A multiple protein sequence alignment of l-alanine dehydrogenases from different bacterial species revealed that five highly conserved amino acid residues Arg-15, Lys-73, Lys-75, His-96 and Asp-269 are potential catalytic residues of l-alanine dehydrogenase from Bacillus pseudofirmus OF4. In this study, recombinant OF4Ald and its mutants of five conserved residues were constructed, expressed in Escherichia coli, purified by His6-tag affinity column and gel filtration chromatography, structure homology modeling, and characterized...
March 2018: Enzyme and Microbial Technology
https://www.readbyqxmd.com/read/29304483/genome-wide-identification-of-phd-finger-genes-and-expression-pattern-analysis-under-various-treatments-in-moso-bamboo-phyllostachys-edulis
#8
Yameng Gao, Huanlong Liu, Yujiao Wang, Fei Li, Yan Xiang
Plant homeodomain (PHD)-finger proteins are a class of important zinc-finger transcription factors responsible for regulating transcription and the chromatin state and responsive to various stresses. The family genes have been reported in many plants, but there is little information about PHD-finger genes in moso bamboo. In this study, 60 PHD-finger genes (PePHD1-60) were identified in moso bamboo and classified into 11 subfamilies (A-K) based on phylogenetic analysis. Gene structure and conserved motif analysis showed that these genes contained different numbers of introns but had similar motif organizations within each subfamily...
December 26, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/29304092/dipeptidyl-peptidase-3-a-novel-protease-from-leishmania-braziliensis
#9
Jenny R Diaz, Cesar A Ramírez, Paola A Nocua, Fanny Guzman, José M Requena, Concepción J Puerta
The increase of leishmaniasis cases worldwide and the emergence of Leishmania strains resistant to current treatments make necessary to find new therapeutic targets. Proteases are appealing drug targets because they play pivotal roles in facilitating parasite survival and promoting pathogenesis. Enzymes belonging to the dipeptidyl peptidase 3 (DPP3) group have been described in different organisms such as mammals, insects and yeast, in which these enzymes have been involved in both protein turnover and protection against oxidative damage...
2018: PloS One
https://www.readbyqxmd.com/read/29297284/automated-classification-and-characterization-of-the-mitotic-spindle-following-knockdown-of-a-mitosis-related-protein
#10
Matloob Khushi, Imraan M Dean, Erdahl T Teber, Megan Chircop, Jonathan W Arthur, Neftali Flores-Rodriguez
BACKGROUND: Cell division (mitosis) results in the equal segregation of chromosomes between two daughter cells. The mitotic spindle plays a pivotal role in chromosome alignment and segregation during metaphase and anaphase. Structural or functional errors of this spindle can cause aneuploidy, a hallmark of many cancers. To investigate if a given protein associates with the mitotic spindle and regulates its assembly, stability, or function, fluorescence microscopy can be performed to determine if disruption of that protein induces phenotypes indicative of spindle dysfunction...
December 28, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29288354/functional-characterization-and-substrate-specificity-analysis-of-%C3%AE-6-desaturase-from-marine-microalga-isochrysis-sp
#11
S Thiyagarajan, M Arumugam, N Senthil, S Vellaikumar, S Kathiresan
OBJECTIVES: To express a Δ6-desaturase gene and produce gamma-linolenic acid (GLA) and stearidonic acid (SDA) in prokaryotic expression system (Escherichia coli), and analyze its substrate specificity in the omega-3 fatty acid biosynthetic pathway. RESULTS: Full-length ORF (1448 bp) of Δ6Des-Iso was isolated from Isochrysis sp. and characterized using multiple sequence alignment, phylogenetic analysis, transmembrane domain, and protein tertiary structure. Δ6Des-Iso is a front-end desaturase consisting of three conserved histidine domains and a cytochrome b5 domain...
December 29, 2017: Biotechnology Letters
https://www.readbyqxmd.com/read/29288125/functional-characterization-of-isolated-rna-binding-domains-of-the-grsf1-protein
#12
Sajad Sofi, Sabine Stehling, Agathe Niewienda, Katharina Janek, Hartmut Kuhn, Christoph Ufer
The Guanine-rich RNA sequence binding factor 1 (GRSF1) is a member of the heterogeneous nuclear ribonucleoprotein F/H family and has been implicated in RNA processing, RNA transport and translational regulation. Amino acid alignments and homology modeling suggested the existence of three distinct RNA-binding domains and two auxiliary domains. Unfortunately, little is known about the molecular details of GRSF1/RNA interactions. To explore the RNA-binding mechanisms we first expressed full-length human GRSF1 and several truncation mutants, which include the three separated qRRM domains in E...
December 26, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29287778/structural-evidence-for-a-fatty-acid-independent-myotoxic-mechanism-for-a-phospholipase-a2-like-toxin
#13
Guilherme H M Salvador, Juliana I Dos Santos, Rafael J Borges, Marcos R M Fontes
The myotoxic mechanism for PLA2-like toxins has been proposed recently to be initiated by an allosteric change induced by a fatty acid binding to the protein, leading to the alignment of the membrane docking site (MDoS) and membrane disrupting site (MDiS). Previous structural studies performed by us demonstrated that MjTX-II, a PLA2-like toxin isolated from Bothrops moojeni, presents a different mode of ligand-interaction, with its hydrophobic channels caused by natural amino acid substitutions and an insertion...
December 26, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29282316/silk-based-multilayered-angle-ply-annulus-fibrosus-construct-to-recapitulate-form-and-function-of-the-intervertebral-disc
#14
Bibhas K Bhunia, David L Kaplan, Biman B Mandal
Recapitulation of the form and function of complex tissue organization using appropriate biomaterials impacts success in tissue engineering endeavors. The annulus fibrosus (AF) represents a complex, multilamellar, hierarchical structure consisting of collagen, proteoglycans, and elastic fibers. To mimic the intricacy of AF anatomy, a silk protein-based multilayered, disc-like angle-ply construct was fabricated, consisting of concentric layers of lamellar sheets. Scanning electron microscopy and fluorescence image analysis revealed cross-aligned and lamellar characteristics of the construct, mimicking the native hierarchical architecture of the AF...
December 27, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29281674/convergent-evolution-and-topologically-disruptive-polymorphisms-among-multidrug-resistant-tuberculosis-in-peru
#15
Louis Grandjean, Robert H Gilman, Tomatada Iwamoto, Claudio U Köser, Jorge Coronel, Mirko Zimic, M Estee Török, Diepreye Ayabina, Michelle Kendall, Christophe Fraser, Simon Harris, Julian Parkhill, Sharon J Peacock, David A J Moore, Caroline Colijn
BACKGROUND: Multidrug-resistant tuberculosis poses a major threat to the success of tuberculosis control programs worldwide. Understanding how drug-resistant tuberculosis evolves can inform the development of new therapeutic and preventive strategies. METHODS: Here, we use novel genome-wide analysis techniques to identify polymorphisms that are associated with drug resistance, adaptive evolution and the structure of the phylogenetic tree. A total of 471 samples from different patients collected between 2009 and 2013 in the Lima suburbs of Callao and Lima South were sequenced on the Illumina MiSeq platform with 150bp paired-end reads...
2017: PloS One
https://www.readbyqxmd.com/read/29281009/mtm-align-an-algorithm-for-fast-and-accurate-multiple-protein-structure-alignment
#16
Runze Dong, Zhenling Peng, Yang Zhang, Jianyi Yang
Motivation: As protein structure is more conserved than sequence during evolution, multiple structure alignment can be more informative than multiple sequence alignment, especially for distantly related proteins. With the rapid increase of the number of protein structures in the Protein Data Bank, it becomes urgent to develop efficient algorithms for multiple structure alignment. Results: A new multiple structure alignment algorithm (mTM-align) was proposed, which is an extension of the highly efficient pairwise structure alignment program TM-align...
December 21, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29278693/crustacean-cardioactive-peptides-expression-localization-structure-and-a-possible-involvement-in-regulation-of-egg-laying-in-the-cuttlefish-sepia-officinalis
#17
Maxime Endress, Céline Zatylny-Gaudin, Erwan Corre, Gildas Le Corguillé, Louis Benoist, Jérôme Leprince, Benjamin Lefranc, Benoît Bernay, Alexandre Leduc, Jimmy Rangama, Anne-Gaëlle Lafont, Arnaud Bondon, Joël Henry
The cuttlefish (Sepia officinalis) is a cephalopod mollusk distributed on the western European coast, in the West African Ocean and in the Mediterranean Sea. On the Normandy coast (France), cuttlefish is a target species of professional fishermen, so its reproduction strategy is of particular interest in the context of stock management. Egg-laying, which is coastal, is controlled by several types of regulators among which neuropeptides. The cuttlefish neuropeptidome was recently identified by Zatylny-Gaudin et al...
December 23, 2017: General and Comparative Endocrinology
https://www.readbyqxmd.com/read/29277995/tilted-uninterrupted-monomeric-hiv-1-gp41-transmembrane-helix-from-residual-dipolar-couplings
#18
Sai Chaitanya Chiliveri, John M Louis, Rodolfo Ghirlando, James L Baber, Ad Bax
Cryo-electron microscopy and X-ray crystallography have shown that the pre- and post-fusion states of the HIV-1 gp41 viral coat protein, although very different from one another, each adopt C3 symmetric structures. A stable homotrimeric structure for the transmembrane domain (TM) also was modeled and supported by experimental data. For a C3 symmetric structure, alignment in an anisotropic medium must be axially symmetric, with the unique axis of the alignment tensor coinciding with the C3 axis. However, NMR residual dipolar couplings (RDCs) measured under three different alignment conditions were found to be incompatible with C3 symmetry...
December 26, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29277866/comparative-genome-annotation
#19
Stefanie König, Lars Romoth, Mario Stanke
Newly sequenced genomes are being added to the tree of life at an unprecedented fast pace. Increasingly, such new genomes are phylogenetically close to previously sequenced and annotated genomes. In other cases, whole clades of closely related species or strains ought to be annotated simultaneously. Often, in subsequent studies differences between the closely related species or strains are in the focus of research when the shared gene structures prevail. We here review methods for comparative structural genome annotation...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29275190/molecular-characterization-of-genomic-dna-in-mycoplasma-pneumoniae-strains-isolated-from-serious-mycoplasma-pneumonia-cases-in-2016-yunnan-china
#20
Lijuan Qiu, Lin Wang, Li Tan, Ming Li, Chengqing Wu, Li Li, Zhen Zhang, Hongchao Jiang, Qiangming Sun, Tiesong Zhang
Mycoplasma pneumoniae (MP) is particularly prevalent in low-immunity school-age children. Few data have been reported on MP prevalence in Yunnan, China. This study was designed to investigate the prevalence and characterize genomic DNA of MP in a small outbreak in 2016, Southwest China. RepMP4 and RepMP2/3 genes of MP positive samples were amplified for molecular typing through sequence alignment and PCR-RFLP assay. Phylogenetic trees were constructed by MEGA5.0. The results showed that two distinct P1 types (type I and type II) were prevalent in this MP outbreak...
December 22, 2017: Infection, Genetics and Evolution
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