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Protein contact prediction

Khalid Shahin, Kim D Thompson, Neil F Inglis, Kevin Mclean, Jose Gustavo Ramirez-Paredes, Sean J Monaghan, Rowena Hoare, Michael Fontaine, Matthijs Metselaar, Alexandra Adams
AIMS: The aims of the current study were to characterise the outer membrane proteins (OMPs) of Francisella noatunensis subsp. orientalis (Fno) STIR-GUS-F2f7, and identify proteins recognised by sera from tilapia, Oreochromis niloticus, (L) that survived experimental challenge with Fno. METHODS AND RESULTS: The composition of the OMPs of a virulent strain of Fno (STIR-GUS- F2f7), isolated from diseased red Nile tilapia in UK, was examined. The sarcosine-insoluble OMP fraction was screened with tilapia hyper-immune sera by western blot analysis following separation of the proteins by 1D SDS-PAGE...
May 19, 2018: Journal of Applied Microbiology
Sirikul Kulanuwat, Watip Tangjittipokin, Prapaporn Jungtrakoon, Chutima Chanprasert, Jatuporn Sujjitjoon, Ninareeman Binnima, Pa-Thai Yenchitsomanus, Nattachet Plengvidhya
Type 2 diabetes mellitus (T2D) is a heterogeneous disease, with certain cases presenting an autosomal dominant type. The rare coding variants of disease‑causing genes in T2D remain mostly unclear. The present study aimed to identify the disease‑causing gene conducting whole exome sequencing in a Thai T2D family with an autosomal dominant transmission of T2D with no evidence of mutations in known maturity‑onset diabetes of the young (MODY) genes. Candidate variants were selected according to certain criteria of mutation prediction programs, followed by segregation analysis with diabetes in the family...
May 14, 2018: International Journal of Molecular Medicine
Aleksander Kuriata, Aleksandra Maria Gierut, Tymoteusz Oleniecki, Maciej Pawel Ciemny, Andrzej Kolinski, Mateusz Kurcinski, Sebastian Kmiecik
Classical simulations of protein flexibility remain computationally expensive, especially for large proteins. A few years ago, we developed a fast method for predicting protein structure fluctuations that uses a single protein model as the input. The method has been made available as the CABS-flex web server and applied in numerous studies of protein structure-function relationships. Here, we present a major update of the CABS-flex web server to version 2.0. The new features include: extension of the method to significantly larger and multimeric proteins, customizable distance restraints and simulation parameters, contact maps and a new, enhanced web server interface...
May 14, 2018: Nucleic Acids Research
Sandra Käppel, Rainer Melzer, Florian Rümpler, Christian Gafert, Günter Theißen
SEPALLATA3 of Arabidopsis thaliana is a MADS-domain transcription factor and a key regulator of flower development. MADS-domain proteins bind to sequences termed 'CArG-boxes' (consensus 5'-CC(A/T)6 GG-3'). Since only a fraction of the CArG-boxes in the Arabidopsis genome are bound by SEPALLATA3, more elaborate principles have to be discovered to better understand which features turn CArG-boxes into genuine recognition sites. Here, we investigate to which extent the shape of the DNA is involved in a 'shape readout' that contributes to the binding of SEPALLATA3...
May 9, 2018: Plant Journal: for Cell and Molecular Biology
Song-Ho Chong, Sihyun Ham
Dimensionality reduction with a suitable choice of order parameters or reaction coordinates is commonly used for analyzing high-dimensional time-series data generated by atomistic biomolecular simulations. So far, geometric order parameters, such as the root mean square deviation, fraction of native amino acid contacts, and collective coordinates that best characterize rare or large conformational transitions, have been prevailing in protein folding studies. Here, we show that the solvent-averaged effective energy, which is a thermodynamic quantity but unambiguously defined for individual protein conformations, serves as a good order parameter of protein folding...
May 8, 2018: Scientific Reports
Jacopo Marino, Reto Walser, Martin Poms, Oliver Zerbe
Cotranslational protein folding is a vectorial process, and for membrane proteins, N-terminal helical segments are the first that become available for membrane insertion. While structures of many G-protein coupled receptors (GPCRs) in various states have been determined, the details of their folding pathways are largely unknown. The seven transmembrane (TM) helices of GPCRs often contain polar residues within the hydrophobic core, and some of the helices in isolation are predicted to be only marginally stable in a membrane environment...
2018: RSC Advances
Ognen Pop-Georgievski, Ralf Zimmermann, Ilya Kotelnikov, Vladimir Proks, Dirk Romeis, Jan Kucka, Anja Caspari, Frantisek Rypacek, Carsten Werner
Polymer layers capable of suppressing protein adsorption from biological media while presenting extracellular matrix derived peptide motifs offer valuable new options for biomimetic surface engineering. Herein, we provide detailed insights into physico-chemical changes induced in a non-fouling poly(ethylene oxide) (PEO) brush/polydopamine (PDA) system by incorporation of adhesion ligand (RGD) peptides. Brushes with high surface chain densities (σ ≥ 0.5 chains·nm-2 ) and pronounced hydrophilicity (water contact angles ≤ 10°) were prepared by end-tethering of hetero-bifunctional PEOs (Mn ~ 20000 g∙mol-1 ) to PDA-modified surfaces from a reactive melt...
May 4, 2018: Langmuir: the ACS Journal of Surfaces and Colloids
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
Spencer Bliven, Aleix Lafita, Althea Parker, Guido Capitani, Jose M Duarte
A correct assessment of the quaternary structure of proteins is a fundamental prerequisite to understanding their function, physico-chemical properties and mode of interaction with other proteins. Currently about 90% of structures in the Protein Data Bank are crystal structures, in which the correct quaternary structure is embedded in the crystal lattice among a number of crystal contacts. Computational methods are required to 1) classify all protein-protein contacts in crystal lattices as biologically relevant or crystal contacts and 2) provide an assessment of how the biologically relevant interfaces combine into a biological assembly...
April 30, 2018: PLoS Computational Biology
Sarah A Roberts, Mark C Prescott, Amanda J Davidson, Lynn McLean, Robert J Beynon, Jane L Hurst
BACKGROUND: Reliable recognition of individuals requires phenotypic identity signatures that are both individually distinctive and appropriately stable over time. Individual-specific vocalisations or visual patterning are well documented among birds and some mammals, whilst odours play a key role in social recognition across many vertebrates and invertebrates. Less well understood, though, is whether individuals are recognised through variation in cues that arise incidentally from a wide variety of genetic and non-genetic differences between individuals, or whether animals evolve distinctive polymorphic signals to advertise identity reliably...
April 27, 2018: BMC Biology
Ivan V Antonov, Evgeny Mazurov, Mark Borodovsky, Yulia A Medvedeva
The genomes of mammalian species are pervasively transcribed producing as many noncoding as protein-coding RNAs. There is a growing body of evidence supporting their functional role. Long noncoding RNA (lncRNA) can bind both nucleic acids and proteins through several mechanisms. A reliable computational prediction of the most probable mechanism of lncRNA interaction can facilitate experimental validation of its function. In this study, we benchmarked computational tools capable to discriminate lncRNA from mRNA and predict lncRNA interactions with other nucleic acids...
April 24, 2018: Briefings in Bioinformatics
A O Bragin, V S Sokolov, P S Demenkov, T V Ivanisenko, E Yu Bragina, Yu G Matushkin, V A Ivanisenko
Nowadays, allergic disorders have become one of the most important social problems in the world. This can be related to the advent of new allergenic agents in the environment, as well as an increasing density of human contact with known allergens, including various proteins. Thus, the development of computer programs designed for the prediction of allergenic properties of proteins becomes one of the urgent tasks of mo dern bioinformatics. Previously we developed a web accessible Allpred Program (http://www-bionet...
March 2018: Molekuliarnaia Biologiia
Wenzhi Mao, Tong Wang, Wenxuan Zhang, Haipeng Gong
BACKGROUND: Despite the rapid progress of protein residue contact prediction, predicted residue contact maps frequently contain many errors. However, information of residue pairing in β strands could be extracted from a noisy contact map, due to the presence of characteristic contact patterns in β-β interactions. This information may benefit the tertiary structure prediction of mainly β proteins. In this work, we propose a novel ridge-detection-based β-β contact predictor to identify residue pairing in β strands from any predicted residue contact map...
April 19, 2018: BMC Bioinformatics
Renate Richardus, Anouk van Hooij, Susan J F van den Eeden, Louis Wilson, Korshed Alam, Jan Hendrik Richardus, Annemieke Geluk
Background: Notwithstanding its beneficial immunoprophylactic outcomes regarding leprosy and childhood TB, BCG vaccination may cause adverse events, particularly of the skin. However, this local hyper-immune reactivity cannot be predicted before vaccination, nor is its association with protection against leprosy known. In this study we investigated the occurrence of adverse events after BCG (re)vaccination in contacts of leprosy patients and analyzed whether the concomitant systemic anti-mycobacterial immunity was associated with these skin manifestations...
2018: Frontiers in Immunology
Sandra Lara, André Perez-Potti, Luciana M Herda, Laurent Adumeau, Kenneth A Dawson, Yan Yan
Key practical challenges such as to understand the immunological processes at the nanoscale, and to control the targeting and accumulation of nano-objects in vivo now further stimulate efforts to underpin phenomenological knowledge of the nanoscale with more mechanistic and molecular insight. Thus, the question as to what constitutes nanoscale biological identity continues to evolve. Certainly nanoparticles in contact with complex biological milieu develop a biological identity, differing from the original nanomaterial, now referred to as the 'biomolecular corona'...
April 18, 2018: ACS Nano
A L Garcia-Garcia, M Alvarez-Vera, L A Montoya-Santiyanes, I Dominguez-Lopez, J L Montes-Seguedo, J C Sosa-Savedra, J D O Barceinas-Sanchez
Friction is the natural response of all tribosystems. In a total knee replacement (TKR) prosthetic device, its measurement is hindered by the complex geometry of its integrating parts and that of the testing simulation rig operating under the ISO 14243-3:2014 standard. To develop prediction models of the coefficient of friction (COF) between AISI 316L steel and ultra-high molecular weight polyethylene (UHMWPE) lubricated with fetal bovine serum dilutions, the arthrokinematics and loading conditions prescribed by the ISO 142433: 2014 standard were translated to a simpler geometrical setup, via Hertz contact theory...
March 27, 2018: Journal of the Mechanical Behavior of Biomedical Materials
Giuseppe Sciortino, Daniele Sanna, Valeria Ugone, Agustí Lledós, Jean-Didier Maréchal, Eugenio Garribba
The interaction of metallodrugs with proteins influences their transport, uptake, and mechanism of action. In this study, we present an integrative approach based on spectroscopic (EPR) and computational (docking) tools to elucidate the noncovalent binding modes of various VIV O compounds with lysozyme, a prototypical model of protein receptor. Five VIV O-flavonoid drug candidates formed by quercetin (que), morin (mor), 7,8-dihydroxyflavone (7,8-dhf), chrysin (chr), and 5-hydroxyflavone (5-hf)-effective against several osteosarcoma cell lines-and two benchmark VIV O species of acetylacetone (acac) and catechol (cat) are evaluated...
April 3, 2018: Inorganic Chemistry
Milu T Cherian, Sergio C Chai, William C Wright, Aman Singh, Morgan Alexandra Casal, Jie Zheng, Jing Wu, Richard E Lee, Patrick R Griffin, Taosheng Chen
The constitutive androstane receptor (CAR) and pregnane X receptor (PXR) are xenobiotic sensors that regulate the expression of drug-metabolizing enzymes and efflux transporters. CAR activation promotes drug elimination, thereby reducing therapeutic effectiveness, or causes adverse drug effects via toxic metabolites. CAR inhibitors could be used to attenuate these adverse drug effects. CAR and PXR share ligands and target genes, confounding the understanding of the regulation of receptor-specific activity. We previously identified a small-molecule inhibitor, CINPA1, that inhibits CAR (without activating PXR at lower concentrations) by altering CAR-coregulator interactions and reducing CAR recruitment to DNA response elements of regulated genes...
March 30, 2018: Biochemical Pharmacology
Adithya Vijaykumar, Pieter Rein Ten Wolde, Peter G Bolhuis
To predict the response of a biochemical system, knowledge of the intrinsic and effective rate constants of proteins is crucial. The experimentally accessible effective rate constant for association can be decomposed in a diffusion-limited rate at which proteins come into contact and an intrinsic association rate at which the proteins in contact truly bind. Reversely, when dissociating, bound proteins first separate into a contact pair with an intrinsic dissociation rate, before moving away by diffusion. While microscopic expressions exist that enable the calculation of the intrinsic and effective rate constants by conducting a single rare event simulation of the protein dissociation reaction, these expressions are only valid when the substrate has just one binding site...
March 28, 2018: Journal of Chemical Physics
Gerard Santiago, Mónica Martínez-Martínez, Sandra Alonso, Rafael Bargiela, Cristina Coscolín, Peter N Golyshin, Víctor Guallar, Manuel Ferrer
Effects of altering the properties of an active site in an enzymatic homogeneous catalyst have been extensively reported. However, the possibility of increasing the number of such sites, as commonly done in heterogeneous catalytic materials, remains unexplored, particularly because those have to accommodate appropriate residues in specific configurations. This possibility was investigated by using a serine ester hydrolase as the target enzyme. By using the Protein Energy Landscape Exploration software, which maps ligand diffusion and binding, we found a potential binding pocket capable of holding an extra catalytic triad and oxyanion hole contacts...
March 30, 2018: Biochemistry
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