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Protein interface prediction

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https://www.readbyqxmd.com/read/28453653/the-bologna-annotation-resource-bar-3-0-improving-protein-functional-annotation
#1
Giuseppe Profiti, Pier Luigi Martelli, Rita Casadio
BAR 3.0 updates our server BAR (Bologna Annotation Resource) for predicting protein structural and functional features from sequence. We increase data volume, query capabilities and information conveyed to the user. The core of BAR 3.0 is a graph-based clustering procedure of UniProtKB sequences, following strict pairwise similarity criteria (sequence identity ≥40% with alignment coverage ≥90%). Each cluster contains the available annotation downloaded from UniProtKB, GO, PFAM and PDB. After statistical validation, GO terms and PFAM domains are cluster-specific and annotate new sequences entering the cluster after satisfying similarity constraints...
April 27, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28449074/fireprot-web-server-for-automated-design-of-thermostable-proteins
#2
Milos Musil, Jan Stourac, Jaroslav Bendl, Jan Brezovsky, Zbynek Prokop, Jaroslav Zendulka, Tomas Martinek, David Bednar, Jiri Damborsky
There is a continuous interest in increasing proteins stability to enhance their usability in numerous biomedical and biotechnological applications. A number of in silico tools for the prediction of the effect of mutations on protein stability have been developed recently. However, only single-point mutations with a small effect on protein stability are typically predicted with the existing tools and have to be followed by laborious protein expression, purification, and characterization. Here, we present FireProt, a web server for the automated design of multiple-point thermostable mutant proteins that combines structural and evolutionary information in its calculation core...
April 26, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28427457/integrative-modelling-of-tir-domain-containing-adaptor-molecule-inducing-interferon-%C3%AE-trif-provides-insights-into-its-autoinhibited-state
#3
Jarjapu Mahita, Ramanathan Sowdhamini
BACKGROUND: TRIF is a key protein in antiviral innate immunity, operating downstream of TLRs. TRIF activation leads to the production of interferon-β and pro-inflammatory cytokines. There is evidence from experiments to suggest that the N-terminal domain of TRIF binds to its TIR domain to avoid constitutive activation. However, no structure of a complex between the N-terminal domain and the TIR domain exists till date. The disordered nature of the region connecting the N-terminal domain and the TIR domain compounds the issue of elucidating the mechanism of autoinhibition of TRIF...
April 20, 2017: Biology Direct
https://www.readbyqxmd.com/read/28426652/cheminformatics-aided-discovery-of-small-molecule-protein-protein-interaction-ppi-dual-inhibitors-of-tumor-necrosis-factor-tnf-and-receptor-activator-of-nf-%C3%AE%C2%BAb-ligand-rankl
#4
Georgia Melagraki, Evangelos Ntougkos, Vagelis Rinotas, Christos Papaneophytou, Georgios Leonis, Thomas Mavromoustakos, George Kontopidis, Eleni Douni, Antreas Afantitis, George Kollias
We present an in silico drug discovery pipeline developed and applied for the identification and virtual screening of small-molecule Protein-Protein Interaction (PPI) compounds that act as dual inhibitors of TNF and RANKL through the trimerization interface. The cheminformatics part of the pipeline was developed by combining structure-based with ligand-based modeling using the largest available set of known TNF inhibitors in the literature (2481 small molecules). To facilitate virtual screening, the consensus predictive model was made freely available at: http://enalos...
April 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28426204/parameter-optimization-for-interaction-between-c-terminal-domains-of-hiv-1-capsid-protein
#5
Hao Sha, Fangqiang Zhu
HIV-1 capsid proteins (CAs) assemble into a capsid that encloses the viral RNA. The binding between a pair of C-terminal domains (CTDs) constitutes a major interface in both the CA dimers and the large CA assemblies. Here we attempt to use a general residue-level coarse-grained model to describe the interaction between two isolated CTDs in Monte Carlo simulations. With the standard parameters that depend only on the residue types, the model predicts a much weaker binding in comparison to the experiments. Detailed analysis reveals that some Lennard-Jones parameters are not compatible with the experimental CTD dimer structure, thus resulting in an unfavorable interaction energy...
April 20, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28418043/predicting-protein-protein-association-rates-using-coarse-grained-simulation-and-machine-learning
#6
Zhong-Ru Xie, Jiawen Chen, Yinghao Wu
Protein-protein interactions dominate all major biological processes in living cells. We have developed a new Monte Carlo-based simulation algorithm to study the kinetic process of protein association. We tested our method on a previously used large benchmark set of 49 protein complexes. The predicted rate was overestimated in the benchmark test compared to the experimental results for a group of protein complexes. We hypothesized that this resulted from molecular flexibility at the interface regions of the interacting proteins...
April 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28414156/modeling-of-interactions-between-functional-domains-of-aldh1l1
#7
David A Horita, Sergey A Krupenko
ALDH1L1, a member of the aldehyde dehydrogenase superfamily of enzymes, catalyzes the conversion of 10-formyltetrahydrofolate to tetrahydrofolate and CO2. The enzyme is a tetramer of identical subunits, with each subunit consisting of three functional domains that originated from unrelated genes. The N- and C-terminal domains are catalytic, while the intermediate domain transfers the reaction intermediate from the N- to the C-terminal domain. The intermediate domain is an acyl carrier protein, possessing the covalently attached 4'-phosphopantetheine (4-PP) prosthetic group...
April 14, 2017: Chemico-biological Interactions
https://www.readbyqxmd.com/read/28407448/draft-genomes-of-the-corallimorpharians-amplexidiscus-fenestrafer-and-discosoma-sp
#8
Xin Wang, Yi Jin Liew, Yong Li, Didier Zoccola, Sylvie Tambutte, Manuel Aranda
Corallimorpharia are the closest non-calcifying relatives of reef-building corals. Aside from their popularity among aquarium hobbyists, their evolutionary position between the Actiniaria (sea anemones) and the Scleractinia (hard corals) makes them ideal candidates for comparative studies aiming at understanding the evolution of hexacorallian orders in general and reef-building corals in particular. Here we have sequenced and assembled two draft genomes for the Corallimorpharia species Amplexidiscus fenestrafer and Discosoma sp...
April 13, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28393921/characterization-of-a-basidiomycota-hydrophobin-reveals-the-structural-basis-for-a-high-similarity-class-i-subdivision
#9
Julie-Anne Gandier, David N Langelaan, Amy Won, Kylie O'Donnell, Julie L Grondin, Holly L Spencer, Philip Wong, Elisabeth Tillier, Christopher Yip, Steven P Smith, Emma R Master
Class I hydrophobins are functional amyloids secreted by fungi. They self-assemble into organized films at interfaces producing structures that include cellular adhesion points and hydrophobic coatings. Here, we present the first structure and solution properties of a unique Class I protein sequence of Basidiomycota origin: the Schizophyllum commune hydrophobin SC16 (hyd1). While the core β-barrel structure and disulphide bridging characteristic of the hydrophobin family are conserved, its surface properties and secondary structure elements are reminiscent of both Class I and II hydrophobins...
April 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28392110/a-transcriptional-program-for-arbuscule-degeneration-during-am-symbiosis-is-regulated-by-myb1
#10
Daniela S Floss, S Karen Gomez, Hee-Jin Park, Allyson M MacLean, Lena M Müller, Kishor K Bhattarai, Veronique Lévesque-Tremblay, Ignacio E Maldonado-Mendoza, Maria J Harrison
During the endosymbiosis formed between plants and arbuscular mycorrhizal (AM) fungi, the root cortical cells are colonized by branched hyphae called arbuscules, which function in nutrient exchange with the plant [1]. Despite their positive function, arbuscules are ephemeral structures, and their development is followed by a degeneration phase, in which the arbuscule and surrounding periarbuscular membrane and matrix gradually disappear from the root cell [2, 3]. Currently, the root cell's role in this process and the underlying regulatory mechanisms are unknown...
April 24, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28383913/an-ensemble-based-protocol-for-the-computational-prediction-of-helix-helix-interactions-in-g-protein-coupled-receptors-using-coarse-grained-molecular-dynamics
#11
Nojood A Altwaijry, Michael Baron, David W Wright, Peter Vivian Coveney, Andrea Townsend-Nicholson
The accurate identification of the specific points of interaction between G protein-coupled receptor (GPCR) oligomers is essential for the design of receptor ligands targeting oligomeric receptor targets. A coarse-grained molecular dynamics computer simulation approach would provide a compelling means of identifying these specific protein-protein interactions and could be applied both for known oligomers of interest and as a high-throughput screen to identify novel oligomeric targets. However, to be effective, this in silico modeling must provide accurate, precise, and reproducible information...
April 6, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28383703/mcsm-na-predicting-the-effects-of-mutations-on-protein-nucleic-acids-interactions
#12
Douglas E V Pires, David B Ascher
Over the past two decades, several computational methods have been proposed to predict how missense mutations can affect protein structure and function, either by altering protein stability or interactions with its partners, shedding light into potential molecular mechanisms giving rise to different phenotypes. Effectively and efficiently predicting consequences of mutations on protein-nucleic acid interactions, however, remained until recently a great and unmet challenge. Here we report an updated webserver for mCSM-NA, the only scalable method we are aware of capable of quantitatively predicting the effects of mutations in protein coding regions on nucleic acid binding affinities...
April 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28383276/predicting-the-initial-steps-of-salt-stable-cowpea-chlorotic-mottle-virus-capsid-assembly-with-atomistic-force-fields
#13
Zoltan Antal, Janos Szoverfi, Szilard N Fejer
Computational prediction of native protein-protein interfaces still remains a challenging task. In virus capsids, each protein unit is in contact with copies of itself through several interfaces. The relative strengths of the different contacts affect the dynamics of the assembly, especially if the process is hierarchical. We investigate the dimerization of the salt-stable cowpea chlorotic mottle virus (CCMV) capsid protein using a combination of different computational tools. The best predictions of dimer configurations provided by blind docking with ZDOCK are rescored using geometry optimization with the Amber and Rosetta force fields...
April 24, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28383034/pulmonary-microrna-profiles-identify-involvement-of-creb1-and-sec14l3-in-bronchial-epithelial-changes-in-allergic-asthma
#14
Sabine Bartel, Nikola Schulz, Francesca Alessandrini, Andrea C Schamberger, Philipp Pagel, Fabian J Theis, Katrin Milger, Elfriede Noessner, Stephen M Stick, Anthony Kicic, Oliver Eickelberg, Robert J Freishtat, Susanne Krauss-Etschmann
Asthma is highly prevalent, but current therapies cannot influence the chronic course of the disease. It is thus important to understand underlying early molecular events. In this study, we aimed to use microRNAs (miRNAs) - which are critical regulators of signaling cascades - to identify so far uncharacterized asthma pathogenesis pathways. Therefore, deregulation of miRNAs was assessed in whole lungs from mice with ovalbumin (OVA)-induced allergic airway inflammation (AAI). In silico predicted target genes were confirmed in reporter assays and in house-dust-mite (HDM) induced AAI and primary human bronchial epithelial cells (NHBE) cultured at the air-liquid interface...
April 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28379697/extending-the-solvation-layer-interface-condition-slic-continum-electrostatic-model-to-linearized-poisson-boltzmann-solvent
#15
Amirhossein Molavi Tabrizi, Spencer Goossens, Ali Mehdizadeh Rahimi, Christopher D Cooper, Matthew G Knepley, Jaydeep P Bardhan
We extend the linearized Poisson-Boltzmann (LPB) continuum electrostatic model for molecular solvation to address charge-hydration asymmetry. Our new solvation-layer interface condition (SLIC)/LPB corrects for first-shell response by perturbing the traditional continuum-theory interface conditions at the protein-solvent and the Stern-layer interfaces. We also present a GPU-accelerated treecode implementation capable of simulating large proteins, and our results demonstrate that the new model exhibits significant accuracy improvements over traditional LPB models, while reducing the number of fitting parameters from dozens (atomic radii) to just five parameters, which have physical meanings related to first-shell water behavior at an uncharged interface...
April 5, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28379490/dambe6-new-tools-for-microbial-genomics-phylogenetics-and-molecular-evolution
#16
Xuhua Xia
DAMBE is a comprehensive software workbench for data analysis in molecular biology, phylogenetics and evolution. Several important new functions have been added since version 5 of DAMBE: 1) comprehensive genomic profiling of translation initiation efficiency of different genes in different prokaryotic species, 2) a new index of translation elongation (ITE) that takes into account both tRNA-mediated selection and background mutation on codon-anticodon adaptation, 3) a new and accurate phylogenetic approach based on pairwise alignment only, which is useful for highly divergent sequences from which a reliable multiple sequence alignment is difficult to obtain...
April 4, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/28377624/rpi-bind-a-structure-based-method-for-accurate-identification-of-rna-protein-binding-sites
#17
Jiesi Luo, Liang Liu, Suresh Venkateswaran, Qianqian Song, Xiaobo Zhou
RNA and protein interactions play crucial roles in multiple biological processes, while these interactions are significantly influenced by the structures and sequences of protein and RNA molecules. In this study, we first performed an analysis of RNA-protein interacting complexes, and identified interface properties of sequences and structures, which reveal the diverse nature of the binding sites. With the observations, we built a three-step prediction model, namely RPI-Bind, for the identification of RNA-protein binding regions using the sequences and structures of both proteins and RNAs...
April 4, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28376709/using-structural-knowledge-in-the-protein-data-bank-to-inform-the-search-for-potential-host-microbe-protein-interactions-in-sequence-space-application-to-mycobacterium-tuberculosis
#18
Gaurang Mahajan, Shekhar C Mande
BACKGROUND: A comprehensive map of the human-M. tuberculosis (MTB) protein interactome would help fill the gaps in our understanding of the disease, and computational prediction can aid and complement experimental studies towards this end. Several sequence-based in silico approaches tap the existing data on experimentally validated protein-protein interactions (PPIs); these PPIs serve as templates from which novel interactions between pathogen and host are inferred. Such comparative approaches typically make use of local sequence alignment, which, in the absence of structural details about the interfaces mediating the template interactions, could lead to incorrect inferences, particularly when multi-domain proteins are involved...
April 4, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28376304/origins-of-pdz-binding-specificity-a-computational-and-experimental-study-using-nherf1-and-the-parathyroid-hormone-receptor
#19
Tatyana Mamonova, Qiangmin Zhang, Mintu Chandra, Brett Collins, Edward K Sarfo, Zimei Bu, Kunhong Xiao, Alessandro Bisello, Peter A Friedman
Na+/H+ Exchanger Regulatory Factor-1 (NHERF1) is a scaffolding protein containing two PSD95/discs large/ZO1 (PDZ) domains that modifies signaling, trafficking, and function of the parathyroid hormone receptor (PTHR), a Family B G-protein coupled receptor. PTHR and NHERF1 bind through a PDZ-ligand recognition mechanism. We show that PTH elicits phosphorylation of Thr591 in the canonical -ETVM binding motif of PTHR. Conservative substitution of Thr591 with Cys does not affect PTH(1-34)-induced cAMP production or PTHR binding to NHERF1...
April 4, 2017: Biochemistry
https://www.readbyqxmd.com/read/28374912/a-computational-approach-to-identify-a-potential-alternative-drug-with-its-positive-impact-towards-pmp22
#20
Ashish Kumar Agrahari, George Priya Doss C
Mutations in the peripheral myelin protein 22 (PMP22) leads to Charcot Marie Tooth type 1A (CMT1A, a subtype of CMT1) disease which is the most common inherited neuropathy of peripheral nervous system. In the present study, we used series of in silico prediction methods to screen and identify the most deleterious non-synonymous SNPs (nsSNPs) in PMP22 gene. Out of 48 nsSNPs, five nsSNPs (L16P, L19P, T23R, W28R & L147R) associated with PMP22 were predicted to be highly deleterious and destabilizing the protein...
April 4, 2017: Journal of Cellular Biochemistry
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