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Protein structure alignment

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https://www.readbyqxmd.com/read/28435440/core-column-prediction-for-protein-multiple-sequence-alignments
#1
Dan DeBlasio, John Kececioglu
BACKGROUND: In a computed protein multiple sequence alignment, the coreness of a column is the fraction of its substitutions that are in so-called core columns of the gold-standard reference alignment of its proteins. In benchmark suites of protein reference alignments, the core columns of the reference alignment are those that can be confidently labeled as correct, usually due to all residues in the column being sufficiently close in the spatial superposition of the known three-dimensional structures of the proteins...
2017: Algorithms for Molecular Biology: AMB
https://www.readbyqxmd.com/read/28434103/structure-restraints-from-heteronuclear-pseudocontact-shifts-generated-by-lanthanide-tags-at-two-different-sites
#2
Benjamin J G Pearce, Shereen Jabar, Choy-Theng Loh, Monika Szabo, Bim Graham, Gottfried Otting
Pseudocontact shifts (PCS) encode long-range information on 3D structures of protein backbones and side-chains. The level of structural detail that can be obtained increases with the number of different sites tagged with a paramagnetic metal ion to generate PCSs. Here we show that PCSs from two different sites can suffice to determine the structure of polypeptide chains and their location and orientation relative to the magnetic susceptibility tensor χ, provided that PCSs are available for (1)H as well as heteronuclear spins...
April 22, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28432363/joint-based-description-of-protein-structure-its-application-to-the-geometric-characterization-of-membrane-proteins
#3
Jayaraman Thangappan, Sangwook Wu, Sun-Gu Lee
A macroscopic description of a protein structure allows an understanding of the protein conformations in a more simplistic manner. Here, a new macroscopic approach that utilizes the joints of the protein secondary structures as a basic descriptor for the protein structure is proposed and applied to study the arrangement of secondary structures in helical membrane proteins. Two types of dihedral angle, Ω and λ, were defined based on the joint points of the transmembrane (TM) helices and loops, and employed to analyze 103 non-homologous membrane proteins with 3 to 14 TM helices...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28431137/trapp-webserver-predicting-protein-binding-site-flexibility-and-detecting-transient-binding-pockets
#4
Antonia Stank, Daria B Kokh, Max Horn, Elena Sizikova, Rebecca Neil, Joanna Panecka, Stefan Richter, Rebecca C Wade
The TRAnsient Pockets in Proteins (TRAPP) webserver provides an automated workflow that allows users to explore the dynamics of a protein binding site and to detect pockets or sub-pockets that may transiently open due to protein internal motion. These transient or cryptic sub-pockets may be of interest in the design and optimization of small molecular inhibitors for a protein target of interest. The TRAPP workflow consists of the following three modules: (i) TRAPP structure- generation of an ensemble of structures using one or more of four possible molecular simulation methods; (ii) TRAPP analysis-superposition and clustering of the binding site conformations either in an ensemble of structures generated in step (i) or in PDB structures or trajectories uploaded by the user; and (iii) TRAPP pocket-detection, analysis, and visualization of the binding pocket dynamics and characteristics, such as volume, solvent-exposed area or properties of surrounding residues...
April 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28430779/a-coevolution-analysis-for-identifying-protein-protein-interactions-by-fourier-transform
#5
Changchuan Yin, Stephen S-T Yau
Protein-protein interactions (PPIs) play key roles in life processes, such as signal transduction, transcription regulations, and immune response, etc. Identification of PPIs enables better understanding of the functional networks within a cell. Common experimental methods for identifying PPIs are time consuming and expensive. However, recent developments in computational approaches for inferring PPIs from protein sequences based on coevolution theory avoid these problems. In the coevolution theory model, interacted proteins may show coevolutionary mutations and have similar phylogenetic trees...
2017: PloS One
https://www.readbyqxmd.com/read/28428870/gene-expression-profiling-during-the-embryo-to-larva-transition-in-the-giant-red-sea-urchin-mesocentrotus-franciscanus
#6
Juan Diego Gaitán-Espitia, Gretchen E Hofmann
In echinoderms, major morphological transitions during early development are attributed to different genetic interactions and changes in global expression patterns that shape the regulatory program for the specification of embryonic territories. In order more thoroughly to understand these biological and molecular processes, we examined the transcriptome structure and expression profiles during the embryo-to-larva transition of a keystone species, the giant red sea urchin Mesocentrotus franciscanus. Using a de novo assembly approach, we obtained 176,885 transcripts from which 60,439 (34%) had significant alignments to known proteins...
April 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28419258/eigenthreader-analogous-protein-fold-recognition-by-efficient-contact-map-threading
#7
Daniel Wa Buchan, David T Jones
Motivation: Protein fold recognition when appropriate, evolutionarily-related, structural templates can be identified is often trivial and may even be viewed as a solved problem. However in cases where no homologous structural templates can be detected, fold recognition is a notoriously difficult problem (Moult, Fidelis et al. 2014). Here we present EigenTHREADER, a novel fold recognition method capable of identifying folds where no homologous structures can be identified. EigenTHREADER takes a query amino acid sequence, generates a map of intra-residue contacts, and then searches a library of contact maps of known structures...
April 13, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28417193/genome-wide-analysis-of-vq-motif-containing-proteins-in-moso-bamboo-phyllostachys-edulis
#8
Yujiao Wang, Huanlong Liu, Dongyue Zhu, Yameng Gao, Hanwei Yan, Yan Xiang
29 Moso bamboo VQ proteins were genome-wide identified for the first time, and bioinformatics analysis was performed to investigate phylogenetic relationships and evolutionary divergence. The qRT-PCR data show that PeVQ genes response to different stress treatments. Accumulating evidence suggests that VQ motif-containing proteins in rice (Oryza sativa), Arabidopsis (Arabidopsis thaliana), and maize (Zea mays) play fundamental roles in response to various biotic and abiotic stresses. However, little is known about the functions of VQ family proteins in Moso bamboo (Phyllostachys edulis)...
April 17, 2017: Planta
https://www.readbyqxmd.com/read/28415220/multistage-modeling-of-protein-dynamics-with-monomeric-myc-oncoprotein-as-an-example
#9
Jiaojiao Liu, Jin Dai, Jianfeng He, Antti J Niemi, Nevena Ilieva
We propose to combine a mean-field approach with all-atom molecular dynamics (MD) into a multistage algorithm that can model protein folding and dynamics over very long time periods yet with atomic-level precision. As an example, we investigate an isolated monomeric Myc oncoprotein that has been implicated in carcinomas including those in colon, breast, and lungs. Under physiological conditions a monomeric Myc is presumed to be an example of intrinsically disordered proteins that pose a serious challenge to existing modeling techniques...
March 2017: Physical Review. E
https://www.readbyqxmd.com/read/28411543/the-disorder-metabolic-profiling-in-kidney-and-spleen-of-mice-induced-by-mycotoxins-deoxynivalenol-through-gas-chromatography-mass-spectrometry
#10
Jian Ji, Pei Zhu, Fangchao Cui, Fuwei Pi, Yinzhi Zhang, Xiulan Sun
Gas chromatography mass spectrometry (GC-MS) based metabolomics strategy was implemented for the metabolites detection in kidney and spleen samples of mice, which were treated with 2 mg kg(-1) deoxynivalenol (DON), through intragastric administration for three weeks, for studying the toxicity of DON on the metabolic profiling in kidney and spleen. The spectrum was deconvoluted, aligned and identified with MS DIAL, equipped with Fiehn library. And the data matrix was processed with univariate analysis and multivariate analysis for selection of metabolites with VIP >1, t-test p value < 0...
March 31, 2017: Chemosphere
https://www.readbyqxmd.com/read/28407117/nnalign-a-platform-to-construct-and-evaluate-artificial-neural-network-models-of-receptor-ligand-interactions
#11
Morten Nielsen, Massimo Andreatta
Peptides are extensively used to characterize functional or (linear) structural aspects of receptor-ligand interactions in biological systems, e.g. SH2, SH3, PDZ peptide-recognition domains, the MHC membrane receptors and enzymes such as kinases and phosphatases. NNAlign is a method for the identification of such linear motifs in biological sequences. The algorithm aligns the amino acid or nucleotide sequences provided as training set, and generates a model of the sequence motif detected in the data. The webserver allows setting up cross-validation experiments to estimate the performance of the model, as well as evaluations on independent data...
April 12, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28402104/hydrogen-deuterium-exchange-mass-spectrometry-of-human-green-opsin-reveals-a-conserved-pro-pro-motif-in-extracellular-loop-2-of-monostable-visual-g-protein-coupled-receptors
#12
Lukas Hofmann, Nathan S Alexander, Wenyu Sun, Jianye Zhang, Tivadar Orban, Krzysztof Palczewski
Opsins comprise the protein component of light sensitive G protein-coupled receptors (GPCRs) in the retina of the eye that are responsible for the transduction of light into a biochemical signal. Here, we used hydrogen/deuterium (H/D) exchange coupled with mass spectrometry to map conformational changes in green cone opsin upon light activation. We then compared these findings with those reported for rhodopsin. The extent of H/D exchange in green cone opsin was greater than in rhodopsin in the dark and bleached states, suggesting a higher structural heterogeneity for green cone opsin...
April 21, 2017: Biochemistry
https://www.readbyqxmd.com/read/28401457/comparative-studies-of-vertebrate-iduronate-2-sulfatase-ids-genes-and-proteins-evolution-of-a-mammalian-x-linked-gene
#13
REVIEW
Roger S Holmes
IDS is responsible for the lysosomal degradation of heparan sulfate and dermatan sulfate and linked to an X-linked lysosomal storage disease, mucopolysaccharidosis 2 (MPS2), resulting in neurological damage and early death. Comparative IDS amino acid sequences and structures and IDS gene locations were examined using data from several vertebrate genome projects. Vertebrate IDS sequences shared 60-99% identities with each other. Human IDS showed 47% sequence identity with fruit fly (Drosophila melanogaster) IDS...
May 2017: 3 Biotech
https://www.readbyqxmd.com/read/28398555/biophysical-and-functional-characterization-of-hippocalcin-mutants-responsible-for-human-dystonia
#14
Nordine Helassa, Svetlana V Antonyuk, Lu-Yun Lian, Lee P Haynes, Robert D Burgoyne
Dystonia is a neurological movement disorder that forces the body into twisting, repetitive movements or sometimes painful abnormal postures. With the advent of next-generation sequencing technologies, the homozygous mutations T71N and A190T in the neuronal calcium sensor (NCS) hippocalcin were identified as the genetic cause of primary isolated dystonia (DYT2 dystonia). However, the effect of these mutations on the physiological role of hippocalcin has not yet been elucidated. Using a multidisciplinary approach, we demonstrated that hippocalcin oligomerises in a calcium-dependent manner and binds to voltage-gated calcium channels...
April 7, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28397099/maturation-of-human-pluripotent-stem-cell-derived-cardiomyocytes-is-improved-in-cardiovascular-construct
#15
Hanna Vuorenpää, Kirsi Penttinen, Tuula Heinonen, Mari Pekkanen-Mattila, Jertta-Riina Sarkanen, Timo Ylikomi, Katriina Aalto-Setälä
In order to translate preclinical data into the clinical studies, relevant in vitro models with structure and key functional properties similar to native human tissue should be used. In vitro cardiac models with vascular structures mimic the highly vascularized myocardium and provide interactions between endothelial cells, stromal cells and cardiomyocytes. Currently, human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) have been shown to present immature morphology and fetal-like electrophysiological properties that may limit their use as physiological test platform...
April 10, 2017: Cytotechnology
https://www.readbyqxmd.com/read/28394942/evidence-for-the-evolutionary-steps-leading-to-meca-mediated-%C3%AE-lactam-resistance-in-staphylococci
#16
Joana Rolo, Peder Worning, Jesper Boye Nielsen, Rita Sobral, Rory Bowden, Ons Bouchami, Peter Damborg, Luca Guardabassi, Vincent Perreten, Henrik Westh, Alexander Tomasz, Hermínia de Lencastre, Maria Miragaia
The epidemiologically most important mechanism of antibiotic resistance in Staphylococcus aureus is associated with mecA-an acquired gene encoding an extra penicillin-binding protein (PBP2a) with low affinity to virtually all β-lactams. The introduction of mecA into the S. aureus chromosome has led to the emergence of methicillin-resistant S. aureus (MRSA) pandemics, responsible for high rates of mortality worldwide. Nonetheless, little is known regarding the origin and evolution of mecA. Different mecA homologues have been identified in species belonging to the Staphylococcus sciuri group representing the most primitive staphylococci...
April 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28388355/in-silico-analysis-of-l1-l2-sequences-of-human-papillomaviruses-implication-for-universal-vaccine-design
#17
Nazila Ghorban Hosseini, Majid Tebianian, Ayoub Farhadi, Ali Hossein Khani, Arian Rahimi, Mojtaba Mortazavi, Seyed Younes Hosseini, Morteza Taghizadeh, Mahsa Rezaei, Mehdi Mahdavi
The aim of this study was to design a multiepitope universal vaccine for major human papillomavirus (HPV) structural proteins, L1/L2, by bioinformatics models. For this purpose, we predicted the most probable immunogenic epitopes of L1 and L2 from common high-risk HPV 16, 18, 31, and 45 beside high prevalent type 6 and 11 based on BCPREDS defaulted model, while solvent accessibility of structure was extrapolated. The three-dimensional molecular model of L1 protein was constructed by Swiss Model server, whereas sequence alignment provided model for prediction of L2 protein epitopes...
April 2017: Viral Immunology
https://www.readbyqxmd.com/read/28387730/mimilook-a-phylogenetic-workflow-for-detection-of-gene-acquisition-in-major-orthologous-groups-of-megavirales
#18
Sourabh Jain, Arup Panda, Philippe Colson, Didier Raoult, Pierre Pontarotti
With the inclusion of new members, understanding about evolutionary mechanisms and processes by which members of the proposed order, Megavirales, have evolved has become a key area of interest. The central role of gene acquisition has been shown in previous studies. However, the major drawback in gene acquisition studies is the focus on few MV families or putative families with large variation in their genetic structure. Thus, here we have tried to develop a methodology by which we can detect horizontal gene transfers (HGTs), taking into consideration orthologous groups of distantly related Megavirale families...
April 7, 2017: Viruses
https://www.readbyqxmd.com/read/28384713/forkhead-box-protein-p1-is-dispensable-for-retina-but-essential-for-lens-development
#19
Haruna Suzuki-Kerr, Yukihiro Baba, Asano Tsuhako, Hideto Koso, Joseph D Dekker, Haley O Tucker, Hiroshi Kuribayashi, Sumiko Watanabe
Purpose: Forkhead box protein P1 (Foxp1) is a transcriptional repressor expressed in many tissues. We identified Foxp1 as a highly expressed gene in retinal progenitor cells and investigated its roles during eye development. Methods: Mouse eyes with Foxp1 gain- or loss-of-function were established in vitro and in vivo. Results: Foxp1 overexpression in retinal progenitor cells resulted in reduced rod and increased cone photoreceptors. However, retina-specific knockout of Foxp1 was not associated with retinal differentiation abnormalities...
April 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28384226/inhibition-of-prenylated-kras-in-a-lipid-environment
#20
Johanna M Jansen, Charles Wartchow, Wolfgang Jahnke, Susan Fong, Tiffany Tsang, Keith Pfister, Tatiana Zavorotinskaya, Dirksen Bussiere, Jan Marie Cheng, Kenneth Crawford, Yumin Dai, Jeffrey Dove, Eric Fang, Yun Feng, Jean-Michel Florent, John Fuller, Alvar D Gossert, Mohammad Hekmat-Nejad, Chrystèle Henry, Julia Klopp, William P Lenahan, Andreas Lingel, Sylvia Ma, Arndt Meyer, Yuji Mishina, Jamie Narberes, Gwynn Pardee, Savithri Ramurthy, Sebastien Rieffel, Darrin Stuart, Sharadha Subramanian, Laura Tandeske, Stephania Widger, Armin Widmer, Aurelie Winterhalter, Isabel Zaror, Stephen Hardy
RAS mutations lead to a constitutively active oncogenic protein that signals through multiple effector pathways. In this chemical biology study, we describe a novel coupled biochemical assay that measures activation of the effector BRAF by prenylated KRASG12V in a lipid-dependent manner. Using this assay, we discovered compounds that block biochemical and cellular functions of KRASG12V with low single-digit micromolar potency. We characterized the structural basis for inhibition using NMR methods and showed that the compounds stabilized the inactive conformation of KRASG12V...
2017: PloS One
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