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Protein structure alignment

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https://www.readbyqxmd.com/read/28538144/probing-the-potential-role-of-non-b-dna-structures-at-yeast-meiosis-specific-dna-double-strand-breaks
#1
Rucha Kshirsagar, Krishnendu Khan, Mamata V Joshi, Ramakrishna V Hosur, K Muniyappa
A plethora of evidence suggests that different types of DNA quadruplexes are widely present in the genome of all organisms. The existence of a growing number of proteins that selectively bind and/or process these structures underscores their biological relevance. Moreover, G-quadruplex DNA has been implicated in the alignment of four sister chromatids by forming parallel guanine quadruplexes during meiosis; however, the underlying mechanism is not well defined. Here we show that a G/C-rich motif associated with a meiosis-specific DNA double-strand break (DSB) in Saccharomyces cerevisiae folds into G-quadruplex, and the C-rich sequence complementary to the G-rich sequence forms an i-motif...
May 23, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28535189/predicting-accurate-contacts-in-thousands-of-pfam-domain-families-using-pconsc3
#2
Mirco Michel, Marcin J Skwark, David Menéndez Hurtado, Magnus Ekeberg, Arne Elofsson
Motivation: A fewyears ago it was shown that by using amaximumentropy approach to describe couplings between columns in a multiple sequence alignment it is possible to significantly increase the accuracy of residue contact predictions. For very large protein families with more than 1000 effective sequences the accuracy is sufficient to produce accurate models of proteins as well as complexes. Today, for about half of all Pfam domain families no structure is known, but unfortunately most of these families have at most a few hundred members, i...
May 23, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28534849/evaluation-and-comparison-of-the-pathogenicity-and-host-immune-responses-induced-by-a-g2b-taiwan-porcine-epidemic-diarrhea-virus-strain-pintung-52-and-its-highly-cell-culture-passaged-strain-in-conventional-5-week-old-pigs
#3
Yen-Chen Chang, Chi-Fei Kao, Chia-Yu Chang, Chian-Ren Jeng, Pei-Shiue Tsai, Victor Fei Pang, Hue-Ying Chiou, Ju-Yi Peng, Ivan-Chen Cheng, Hui-Wen Chang
A genogroup 2b (G2b) porcine epidemic diarrhea virus (PEDV) Taiwan Pintung 52 (PEDVPT) strain was isolated in 2014. The pathogenicity and host antibody responses elicited by low-passage (passage 5; PEDVPT-P5) and high-passage (passage 96; PEDVPT-P96) PEDVPT strains were compared in post-weaning PEDV-seronegative pigs by oral inoculation. PEDVPT-P5-inoculation induced typical diarrhea during 1-9 days post inoculation with fecal viral shedding persisting for 26 days. Compared to PEDVPT-P5, PEDVPT-P96 inoculation induced none-to-mild diarrhea and lower, delayed fecal viral shedding...
May 19, 2017: Viruses
https://www.readbyqxmd.com/read/28534783/nahal-flex-a-numerical-and-alphabetical-hinge-detection-algorithm-for-flexible-protein-structure-alignment
#4
Samira Fotoohifiroozabadi, Mohd Saberi Mohamad, Safaai Deris
Flexible proteins are proteins that have conformational changes in their structures. Protein flexibility analysis is critical for classifying and understanding protein functionality. For that analysis, the hinge areas where proteins show flexibility must be detected. To detect the location of the hinges, previous methods have utilized the three-dimensional (3D) structure of proteins, which is highly computational. To reduce the computational complexity, this study proposes a novel text-based method using structural alphabets (SAs) for detecting the hinge position, called NAHAL-Flex...
May 17, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28534082/conformational-dynamics-and-alignment-properties-of-loop-lanthanide-binding-tags-lbts-studied-in-interleukin-1%C3%AE
#5
Dominic Barthelmes, Katja Barthelmes, Kai Schnorr, Hendrik R A Jonker, Bianca Bodmer, Karen N Allen, Barbara Imperiali, Harald Schwalbe
Encodable lanthanide binding tags (LBTs) have become an attractive tool in modern structural biology as they can be expressed as fusion proteins of targets of choice. Previously, we have demonstrated the feasibility of inserting encodable LBTs into loop positions of interleukin-1β (Barthelmes et al. in J Am Chem Soc 133:808-819, 2011). Here, we investigate the differences in fast dynamics of selected loop-LBT interleukin-1β constructs by measuring (15)N nuclear spin relaxation experiments. We show that the loop-LBT does not significantly alter the dynamic motions of the host protein in the sub-τc-timescale and that the loop-LBT adopts a rigid conformation with significantly reduced dynamics compared to the terminally attached encodable LBT leading to increased paramagnetic alignment strength...
May 22, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28528958/investigation-of-calcium-dependent-activity-and-conformational-dynamics-of-zebra-fish-12-lipoxygenase
#6
Monica Mittal, Mahmudul Hasan, Navisraj Balagunaseelan, Alexander Fauland, Craig Wheelock, Olof Rådmark, Jesper Z Haeggström, Agnes Rinaldo-Matthis
BACKGROUND: A 12-lipoxygenase in zebra fish (zf12-LOX) was found to be required for normal embryonic development and LOXs are of great interest for targeted drug designing. In this study, we investigate the structural-functional aspects of zf12-LOX in response to calcium. METHODS: A soluble version of zf12-LOX was created by mutagenesis. Based on multiple sequence alignment, we mutated the putative calcium-responsive amino acids in N-PLAT domain of soluble zf12-LOX...
May 18, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28524861/an-apicobasal-gradient-of-rac-activity-determines-protrusion-form-and-position
#7
Africa Couto, Natalie Ann Mack, Lucrezia Favia, Marios Georgiou
Each cell within a polarized epithelial sheet must align and correctly position a wide range of subcellular structures, including actin-based dynamic protrusions. Using in vivo inducible transgenes that can sense or modify Rac activity, we demonstrate an apicobasal gradient of Rac activity that is required to correctly form and position distinct classes of dynamic protrusion along the apicobasal axis of the cell. We show that we can modify the Rac activity gradient in genetic mutants for specific polarity proteins, with consequent changes in protrusion form and position and additionally show, using photoactivatable Rac transgenes, that it is the level of Rac activity that determines protrusion form...
May 19, 2017: Nature Communications
https://www.readbyqxmd.com/read/28513982/plasmon-enhanced-fluorescence-based-on-porphyrin-peptoid-hybridized-gold-nanoparticle-platform
#8
Younghye Kim, Boyeong Kang, Hyo-Yong Ahn, Jiwon Seo, Ki Tae Nam
A porphyrin-peptoid-hybridized silica-coated gold nanoparticle is developed, which is inspired by the protein-chlorophyll ensemble found in photosynthetic antenna. In the natural antenna, chlorophylls are integrated into dense assemblies that are supported by frameworks of proteins, which ensure optimal pigment arrangement for effective light harvesting. In the subject platform, porphyrins are conjugated to the peptoid helix scaffold in a structurally well-defined alignments and subsequently immobilized on the surface of nanoparticles...
May 17, 2017: Small
https://www.readbyqxmd.com/read/28510698/xsult-a-web-server-for-structural-annotation-and-representation-of-sequence-structure-alignments
#9
Bernardo Ochoa-Montaño, Tom L Blundell
The web server XSuLT, an enhanced version of the protein alignment annotation program JoY, formats a submitted multiple-sequence alignment using three-dimensional (3D) structural information in order to assist in the comparative analysis of protein evolution and in the optimization of alignments for comparative modelling and construct design. In addition to the features analysed by JoY, which include secondary structure, solvent accessibility and sidechain hydrogen bonds, XSuLT annotates each amino acid residue with residue depth, chain and ligand interactions, inter-residue contacts, sequence entropy, root mean square deviation and secondary structure and disorder prediction...
May 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28503857/recent-developments-in-structural-studies-on-acetylcholinesterase
#10
REVIEW
Israel Silman, Joel L Sussman
This review focuses on several recent developments concerning structure-function relationships in vertebrate acetylcholinesterase. These include studies on high-resolution structures of human acetylcholinesterase and its complexes; the first crystal structure of a snake venom acetylcholinesterase, in which open and closed states of the 'back door' are visualized; a powerful algorithm for redesigning proteins for enhanced expression in prokaryotic systems, as applied to human acetylcholinesterase, which has hitherto been an intractable target; in situ implementation of 'click chemistry' in crystalline acetylcholinesterase, which yields novel insights into the steric and dynamic changes involved in the reaction within the active-site gorge; and a study that demonstrates the effect of crystallization conditions on ligand alignment within a protein complex, in this case the methylene blue-Torpedo californica acetylcholinesterase complex, which highlights the relevance of the precipitant employed to structure-based drug design...
May 15, 2017: Journal of Neurochemistry
https://www.readbyqxmd.com/read/28498888/cardiomyocyte-specific-loss-of-mitochondrial-p32-c1qbp-causes-cardiomyopathy-and-activates-stress-responses
#11
Toshiro Saito, Takeshi Uchiumi, Mikako Yagi, Rie Amamoto, Daiki Setoyama, Yuichi Matsushima, Dongchon Kang
Aims: Mitochondria are important organelles, dedicated to energy production. Mitochondrial p32/C1qbp, which functions as an RNA and protein chaperone, interacts with mitochondrial mRNA and is indispensable for mitochondrial function through its regulation of mitochondrial translation in cultured cell lines. However, the precise role of p32/C1qbp in vivo is poorly understood because of embryonic lethality in the systemic p32-deficient mouse. The goal of this study was to examine the physiological function of mitochondrial p32/C1qbp in the heart...
May 11, 2017: Cardiovascular Research
https://www.readbyqxmd.com/read/28498662/sub-molecular-gates-self-assemble-for-hot-electron-transfer-in-proteins
#12
Neta Filip-Granit, Eran Goldberg, Ilan Samish, Idan Ashur, Milko E van der Boom, Hagai Cohen, Avigdor Scherz
Redox reactions play key roles in fundamental biological processes. The related spatial organization of donors and acceptors is assumed to undergo evolutionary optimization facilitating charge mobilization within the relevant biological context. Experimental information from sub-molecular functional sites is needed to understand the organization strategies and driving forces involved in the self-development of structure-function relationships. Here we exploit chemically resolved electrical measurements (CREM) to probe the atom-specific electrostatic potentials (ESPs) in artificial arrays of bacteriochlorophyll (BChl) derivatives that provide model systems for photoexcited (hot) electron donation and withdrawal...
May 12, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28488468/functional-characterization-of-key-residues-in-regulatory-proteins-hrpg-and-hrpv-of-pseudomonas-syringae-pv-tomato-dc3000
#13
Milija Jovanovic, Christopher Waite, Ellen James, Nicholas Synn, Timothy Simpson, Ioly Kotta-Loizou, Martin Buck
The plant pathogen Pseudomonas syringae pv. tomato DC3000, uses a Type III secretion system (T3SS) to transfer effector proteins into the host. The expression of T3SS proteins is controlled by the HrpL sigma factor. Transcription of hrpL is sigma54-dependent and bacterial enhancer binding proteins HrpR and HrpS co-activate the hrpL promoter. The HrpV protein imposes negative control upon HrpRS through direct interaction with HrpS. HrpG interacts with HrpV and relieves such negative control. The sequence alignments across Hrp Group I-type plant pathogens revealed conserved HrpV and HrpG amino acids...
May 10, 2017: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/28487280/the-identification-and-functional-annotation-of-rna-structures-conserved-in-vertebrates
#14
Stefan E Seemann, Aashiq H Mirza, Claus Hansen, Claus H Bang-Berthelsen, Christian Garde, Mikkel Christensen-Dalsgaard, Elfar Torarinsson, Zizhen Yao, Christopher T Workman, Flemming Pociot, Henrik Nielsen, Niels Tommerup, Walter L Ruzzo, Jan Gorodkin
Structured elements of RNA molecules are essential in, e.g., RNA stabilization, localization and protein interaction, and their conservation across species suggests a common functional role. We computationally screened vertebrate genomes for Conserved RNA Structures (CRSs), leveraging structure-based, rather than sequence-based, alignments. After careful correction for sequence identity and GC content, we predict ~516k human genomic regions containing CRSs. We find that a substantial fraction of human-mouse CRS regions (i) co-localize consistently with binding sites of the same RNA binding proteins (RBPs) or (ii) are transcribed in corresponding tissues...
May 9, 2017: Genome Research
https://www.readbyqxmd.com/read/28486913/pharmacophore-3d-qsar-models-and-dynamic-simulation-of-1-4-benzothiazines-for-colorectal-cancer-treatment
#15
Amit Rai, Vinit Raj, Mohamed Hodhod Aboumanei, Ashok K Singh, Amit K Keshari, Suraj P Verma, Sudipta Saha
Interleukin-6 has become an attractive protein target. This is found in the progression of colon cancer. It performs various functions in the colon cancer cells such as inflammation, activates various cell types signaling and also promotes proliferation in colon cancer cells. It is a valid target to develop of anticolon cancer drug. The purpose of our study is to develop the Three-dimensional Quantitative Structure-Activity Relationship (3D-QSAR) models, pharmacophore modeling and docking study as well as MD simulation to find out the novel potent inhibitors that bind with Interleukin-6 in colon cancer treatment...
May 9, 2017: Combinatorial Chemistry & High Throughput Screening
https://www.readbyqxmd.com/read/28482255/molecular-cloning-characterization-and-expression-analysis-of-metallothionein-in-the-liver-of-the-teleost-acrossocheilus-fasciatus-exposed-to-cadmium-chloride
#16
Guo-Di Liu, Zhang Sheng, Cong-Cong Hou, Jie Ni, Ying-Li Han, You-Fa Wang, Yang Zhou, Su-Yan Fu, Jun-Quan Zhu
Metallothionein (MT) has a characteristic molecular structure with a cysteine-rich content. This unique structure provides metal-binding and redox capabilities and promoting metal homeostasis and detoxification in living animals. In order to evaluate the effects of cadmium (Cd) on hepatic MT expression in the liver of Acrossocheilus fasciatus, we obtained the complete cDNA of the A. fasciatus liver MT for the first time. The MT cDNA contains a 605-bp sequence, which codes for 60 amino acids. Protein alignment showed that the similarity between MT protein sequences of A...
March 29, 2017: Environmental Toxicology and Pharmacology
https://www.readbyqxmd.com/read/28481970/foldit-standalone-a-video-game-derived-protein-structure-manipulation-interface-using-rosetta
#17
Robert Kleffner, Jeff Flatten, Andrew Leaver-Fay, David Baker, Justin B Siegel, Firas Khatib, Seth Cooper
Summary: Foldit Standalone is an interactive graphical interface to the Rosetta molecular modeling package. In contrast to most command-line or batch interactions with Rosetta, Foldit Standalone is designed to allow easy, real-time, direct manipulation of protein structures, while also giving access to the extensive power of Rosetta computations. Derived from the user interface of the scientific discovery game Foldit (itself based on Rosetta), Foldit Standalone has added more advanced features and removed the competitive game elements...
May 8, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28473706/molecular-mechanisms-underlying-the-evolution-of-the-slp76-signalosome
#18
Xuemei Qu, Xin Lan, Chong Deng, Jiatao Zhou, Jingjing Du, Shengfeng Huang, Yingqiu Li
The well-defined mammalian slp76-signalosome is crucial for T-cell immune response, yet whether slp76-signalosome exists in invertebrates and how it evolved remain unknown. Here we investigated slp76-signalosome from an evolutionary perspective in amphioxus Branchiostoma belcheri (bb). We proved slp76-signalosome components bbslp76, bbGADS and bbItk are present in amphioxus and bbslp76 interacts with bbGADS and bbItk, but differences exist between the interaction manners within slp76-signalosome components of amphioxus and human (h)...
May 4, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28472402/cofactor-improved-protein-function-prediction-by-combining-structure-sequence-and-protein-protein-interaction-information
#19
Chengxin Zhang, Peter L Freddolino, Yang Zhang
The COFACTOR web server is a unified platform for structure-based multiple-level protein function predictions. By structurally threading low-resolution structural models through the BioLiP library, the COFACTOR server infers three categories of protein functions including gene ontology, enzyme commission and ligand-binding sites from various analogous and homologous function templates. Here, we report recent improvements of the COFACTOR server in the development of new pipelines to infer functional insights from sequence profile alignments and protein-protein interaction networks...
May 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28470598/esprit-a-method-for-defining-soluble-expression-constructs-in-poorly-understood-gene-sequences
#20
Philippe J Mas, Darren J Hart
Production of soluble, purifiable domains or multi-domain fragments of proteins is a prerequisite for structural biology and other applications. When target sequences are poorly annotated, or when there are few similar sequences available for alignments, identification of domains can be problematic. A method called expression of soluble proteins by random incremental truncation (ESPRIT) addresses this problem by high-throughput automated screening of tens of thousands of enzymatically truncated gene fragments...
2017: Methods in Molecular Biology
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