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Protein interface prediction

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https://www.readbyqxmd.com/read/28077870/the-role-of-interfacial-lipids-in-stabilizing-membrane-protein-oligomers
#1
Kallol Gupta, Joseph A C Donlan, Jonathan T S Hopper, Povilas Uzdavinys, Michael Landreh, Weston B Struwe, David Drew, Andrew J Baldwin, Phillip J Stansfeld, Carol V Robinson
Oligomerization of membrane proteins in response to lipid binding has a critical role in many cell-signalling pathways but is often difficult to define or predict. Here we report the development of a mass spectrometry platform to determine simultaneously the presence of interfacial lipids and oligomeric stability and to uncover how lipids act as key regulators of membrane-protein association. Evaluation of oligomeric strength for a dataset of 125 α-helical oligomeric membrane proteins reveals an absence of interfacial lipids in the mass spectra of 12 membrane proteins with high oligomeric stability...
January 19, 2017: Nature
https://www.readbyqxmd.com/read/28077569/rain-rna-protein-association-and-interaction-networks
#2
Alexander Junge, Jan C Refsgaard, Christian Garde, Xiaoyong Pan, Alberto Santos, Ferhat Alkan, Christian Anthon, Christian von Mering, Christopher T Workman, Lars Juhl Jensen, Jan Gorodkin
Protein association networks can be inferred from a range of resources including experimental data, literature mining and computational predictions. These types of evidence are emerging for non-coding RNAs (ncRNAs) as well. However, integration of ncRNAs into protein association networks is challenging due to data heterogeneity. Here, we present a database of ncRNA-RNA and ncRNA-protein interactions and its integration with the STRING database of protein-protein interactions. These ncRNA associations cover four organisms and have been established from curated examples, experimental data, interaction predictions and automatic literature mining...
2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28073761/seeing-the-trees-through-the-forest-sequence-based-homo-and-heteromeric-protein-protein-interaction-sites-prediction-using-random-forest
#3
Qingzhen Hou, Paul De Geest, Wim F Vranken, Jaap Heringa, K Anton Feenstra
MOTIVATION: Genome sequencing is producing an ever-increasing amount of associated protein sequences. Few of these sequences have experimentally validated annotations, however, and computational predictions are becoming increasingly successful in producing such annotations. One key challenge remains the prediction of the amino acids in a given protein sequence that are involved in proteinprotein interactions. Such predictions are typically based on machine learning methods that take advantage of the properties and sequence positions of amino acids that are known to be involved in interaction...
January 10, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28067274/computational-and-biochemical-characterization-of-two-partially-overlapping-interfaces-and-multiple-weak-affinity-k-ras-dimers
#4
Priyanka Prakash, Abdallah Sayyed-Ahmad, Kwang-Jin Cho, Drew M Dolino, Wei Chen, Hongyang Li, Barry J Grant, John F Hancock, Alemayehu A Gorfe
Recent studies found that membrane-bound K-Ras dimers are important for biological function. However, the structure and thermodynamic stability of these complexes remained unknown because they are hard to probe by conventional approaches. Combining data from a wide range of computational and experimental approaches, here we describe the structure, dynamics, energetics and mechanism of assembly of multiple K-Ras dimers. Utilizing a range of techniques for the detection of reactive surfaces, protein-protein docking and molecular simulations, we found that two largely polar and partially overlapping surfaces underlie the formation of multiple K-Ras dimers...
January 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28066872/comparative-genomics-and-expression-levels-of-hydrophobins-from-eight-mycorrhizal-genomes
#5
F Rineau, H Lmalem, D Ahren, F Shah, T Johansson, L Coninx, J Ruytinx, H Nguyen, I Grigoriev, A Kuo, A Kohler, E Morin, J Vangronsveld, F Martin, J V Colpaert
Hydrophobins are small secreted proteins that are present as several gene copies in most fungal genomes. Their properties are now well understood: they are amphiphilic and assemble at hydrophilic/hydrophobic interfaces. However, their physiological functions remain largely unexplored, especially within mycorrhizal fungi. In this study, we identified hydrophobin genes and analysed their distribution in eight mycorrhizal genomes. We then measured their expression levels in three different biological conditions (mycorrhizal tissue vs...
January 9, 2017: Mycorrhiza
https://www.readbyqxmd.com/read/28063348/the-in-silico-identification-of-small-molecules-for-protein-protein-interaction-inhibition-in-akap-lbc-rhoa-signaling-complex
#6
Asifullah Khan, Mehwish Munir, Sara Aiman, Abdul Wadood, Arif-Ullah Khan
The rational design of small molecules that mimic key residues at the interface of interacting proteins can be a successful approach to target certain biological signaling cascades causing pathophysiological outcome. The A-Kinase Anchoring Protein, i.e. AKAP-Lbc, catalyses nucleotide exchange on RhoA and is involved in cardiac repolarization. The oncogenic AKAP-Lbc induces the RhoA GTPase hyperactivity and aberrantly amplifies the signaling pathway leading to hypertrophic cardiomyocytes. We took advantage of the AKAP-Lbc-RhoA complex crystal structure to design in silico small molecules predicted to inhibit the associated pathological signaling cascade...
December 31, 2016: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28053162/postar-a-platform-for-exploring-post-transcriptional-regulation-coordinated-by-rna-binding-proteins
#7
Boqin Hu, Yu-Cheng T Yang, Yiming Huang, Yumin Zhu, Zhi John Lu
We present POSTAR (http://POSTAR.ncrnalab.org), a resource of POST-trAnscriptional Regulation coordinated by RNA-binding proteins (RBPs). Precise characterization of post-transcriptional regulatory maps has accelerated dramatically in the past few years. Based on new studies and resources, POSTAR supplies the largest collection of experimentally probed (∼23 million) and computationally predicted (approximately 117 million) RBP binding sites in the human and mouse transcriptomes. POSTAR annotates every transcript and its RBP binding sites using extensive information regarding various molecular regulatory events (e...
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28045380/structure-and-conformational-plasticity-of-the-u6-small-nuclear-ribonucleoprotein-core
#8
Eric J Montemayor, Allison L Didychuk, Honghong Liao, Panzhou Hu, David A Brow, Samuel E Butcher
U6 small nuclear RNA (snRNA) is a key component of the active site of the spliceosome, a large ribonucleoprotein complex that catalyzes the splicing of precursor messenger RNA. Prior to its incorporation into the spliceosome, U6 is bound by the protein Prp24, which facilitates unwinding of the U6 internal stem-loop (ISL) so that it can pair with U4 snRNA. A previously reported crystal structure of the `core' of the U6 small nuclear ribonucleoprotein (snRNP) contained an ISL-stabilized A62G mutant of U6 bound to all four RNA-recognition motif (RRM) domains of Prp24 [Montemayor et al...
January 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28038968/combined-use-of-serum-mcp-1-il-10-ratio-and-uterine-artery-doppler-index-significantly-improves-the-prediction-of-preeclampsia
#9
Shihong Cui, Yanan Gao, Linlin Zhang, Yuan Wang, Lindong Zhang, Pingping Liu, Ling Liu, Juan Chen
BACKGROUND: Monocyte chemotactic protein-1 (MCP-1, or CCL2) is a member of the chemokine subfamily involved in recruitment of monocytes in inflammatory tissues. IL-10 is a key regulator for maintaining the balance of anti-inflammatory and pro-inflammatory milieu at the feto-maternal interface. Doppler examination has been routinely performed for the monitoring and management of preeclampsia patients. This study evaluates the efficiency of these factors alone, or in combination, for the predication of preeclampsia...
December 27, 2016: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/28031368/the-structural-interface-between-hiv-1-vif-and-human-apobec3h
#10
Marcel Ooms, Michael Letko, Viviana Simon
: Human APOBEC3H (A3H) is a cytidine deaminase that inhibits HIV-1 replication. To evade this restriction, the HIV-1 Vif protein binds A3H and mediates its proteasomal degradation. To date, little information on the Vif-A3H interface is available. To decipher how both proteins interact we first mapped the Vif-binding site on A3H by functionally testing a large set of A3H mutants in single cycle infectivity and replication assays. Our data show that the two A3H α-helixes α3 and α4 represent the Vif-binding site of A3H...
December 28, 2016: Journal of Virology
https://www.readbyqxmd.com/read/28026921/n-a-and-n-d-oligomer-and-partner-specification-by-asparagine-in-coiled-coil-interfaces
#11
Jordan M Fletcher, Gail J Bartlett, Aimee L Boyle, Jonathan J Danon, Laura E Rush, Andrei N Lupas, Derek N Woolfson
The α-helical coiled coil is one of the best-studied protein-protein interaction motifs. As a result, sequence-to-structure relationships are available for the prediction of natural coiled-coil sequences and the de novo design of new ones. However, coiled coils adopt a wide range of oligomeric states and topologies, and our understanding of the specification of these and the discrimination between them remains incomplete. Gaps in our knowledge assume more importance as coiled coils are used increasingly to construct biomimetic systems of higher complexity; for this, coiled-coil components need to be robust, orthogonal and transferable between contexts...
December 27, 2016: ACS Chemical Biology
https://www.readbyqxmd.com/read/28024445/role-of-structural-water-for-prediction-of-cation-binding-sites-in-apoproteins
#12
L A Uroshlev, I V Kulakovskiy, N G Esipova, V G Tumanyan, S V Rahmanov, V J Makeev
: Structures of many metal-binding proteins are often obtained without structural cations, in their apoprotein forms. Missing cation coordinates are usually updated from structural templates constructed from many holoprotein structures. Such templates usually do not include structural water, the important contributor to the ion binding energy. Structural templates are also inconvenient for taking into account structural modifications around the binding site at apo-/holo- transitions. An approach based upon statistical potentials readily takes into account structural modifications associated with binding as well as contribution of structural water molecules...
December 26, 2016: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28024402/relative-binding-free-energy-calculations-applied-to-protein-homology-models
#13
Daniel Cappel, Michelle Lynn Hall, Eelke B Lenselink, Thijs Beuming, Jun Qi, James Bradner, Woody Sherman
A significant challenge and potential high-value application of computer-aided drug design is the accurate prediction of protein-ligand binding affinities. Free energy perturbation (FEP) using molecular dynamics (MD) sampling is among the most suitable approaches to achieve accurate binding free energy predictions, due to the rigorous statistical framework of the methodology, correct representation of the energetics, and thorough treatment of the important degrees of freedom in the system (including explicit waters)...
December 27, 2016: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28012872/mapping-the-naloxone-binding-sites-on-the-mu-opioid-receptor-using-cell-based-photocrosslinkers
#14
Yi-Yu Ke, Yi-Han Huang, Wei-Chuan Chien, Horace H Loh, Jian-Ying Chuang, Shiu-Hwa Yeh
Naloxone is an alkaloid antagonist that acts as an antidote to opioids through the mu-opioid receptor (MOR), a G protein-coupled receptor. However, its binding site on the MOR remains unknown. To investigate the binding interfaces necessary for naloxone and MOR, available structural information was combined with a cell-based photocrosslinking approach. Computer prediction revealed that four binding sites on MOR were required for naloxone binding. In addition, in the photocrosslinking approach, an amber stop codon was used to replace the sense codon of the MOR at 266 selected individual positions, in order to introduce the photoreactive amino acid p-benzoyl-l-phenylalanine (BzF) into MOR to evaluate the results of the computer analysis...
December 22, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28007020/hb-a2-episkopi-a-novel-%C3%AE-globin-chain-variant-hbd-c-428c-t-in-a-family-of-mixed-cypriot-lebanese-descent
#15
Carsten W Lederer, Eleni Pavlou, George A Tanteles, Paola Evangelidou, Carolina Sismani, Annita Kolnagou, Maria Sitarou, Soteroulla Christou, Michael Hadjigavriel, Marina Kleanthous
OBJECTIVES: Thalassaemia is a potentially lethal inherited anaemia, caused by reduced or absent synthesis of globin chains. Measurement of the minor adult haemoglobin Hb A2, combining α- with δ-globin, is critical for the routine diagnosis of carrier status for α- or β-thalassaemia. Here, we aim to characterize a novel δ-globin variant, Hb A2 Episkopi, in a single family of mixed Lebanese and Cypriot ancestry with mild hypochromic anaemia and otherwise normal globin genotype, which also presents with a coincidental 0...
December 22, 2016: Hematology (Amsterdam, Netherlands)
https://www.readbyqxmd.com/read/28005336/mapping-of-molecular-structure-of-the-nanoscale-surface-in-bionanoparticles
#16
Luciana M Herda, Delyan R Hristov, Maria Cristina Lo Giudice, Ester Polo, Kenneth A Dawson
Characterizing the orientation of covalently conjugated proteins on nanoparticles, produced for in vitro and in vivo targeting, though an important feature of such a system, has proved challenging. Although extensive physicochemical characterization of targeting nanoparticles can be addressed in detail, relevant biological characterization of the nanointerface is crucial in order to select suitable nanomaterials for further in vitro or in vivo experiments. In this work, we adopt a methodology using antibody fragments (Fab) conjugated to gold nanoparticles (immunogold) to map the available epitopes on a transferrin grafted silica particle (SiO2-PEG8-Tf) as a proxy methodology to predict nanoparticle biological function, and therefore cellular receptor engagement...
December 29, 2016: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28003367/attenuation-of-phosphorylation-dependent-activation-of-cystic-fibrosis-transmembrane-conductance-regulator-cftr-by-disease-causing-mutations-at-the-transmission-interface
#17
Stephanie Chin, Donghe Yang, Andrew J Miles, Paul D W Eckford, Steven V Molinski, B A Wallace, Christine E Bear
Cystic fibrosis transmembrane conductance regulator (CFTR) is a multi-domain membrane protein that functions as a phosphorylation regulated anion channel. The interface between its two cytosolic nucleotide binding domains (NBDs) and coupling helices (CHs) conferred by intracellular loops (ICLs) extending from the channel pore domains has been referred to as a transmission interface and is thought to be critical for the regulated channel activity of CFTR. Phosphorylation of the regulatory (R) domain of CFTR by PKA is required for its channel activity...
December 21, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28002737/heterotypic-coiled-coil-formation-is-essential-for-the-correct-assembly-of-the-septin-heterofilament
#18
Fernanda A Sala, Napoleão F Valadares, Joci N A Macedo, Julio C Borges, Richard C Garratt
Protein-protein interactions play a critical role in promoting the stability of protein quaternary structure and in the assembly of large macromolecular complexes. What drives the stabilization of such assemblies is a central question in biology. A limiting factor in fully understanding such systems is the transient nature of many complexes, making structural studies difficult. Septins comprise a conserved family of guanine nucleotide binding proteins that polymerize in the form of heterofilaments. In structural terms, they have a common organization: a central GTPase domain, an N-terminal domain, and a C-terminal domain; the latter is predicted to form a coiled coil...
December 20, 2016: Biophysical Journal
https://www.readbyqxmd.com/read/28000554/a-homodimer-model-can-resolve-the-conundrum-as-to-how-cytochrome-p450-oxidoreductase-and-cytochrome-b5-compete-for-the-same-binding-site-on-cytochrome-p450c17
#19
Jessica K Holien, Michael W Parker, Alan J Conley, C Jo Corbin, Raymond J Rodgers, Lisandra L Martin
Cytochrome P450 17α-hydroxylase, 17,20-lyase (P450c17) is a key enzyme in the synthesis of cortisol in the zona fascicula of the adrenal cortex, and the synthesis of androgen precursors in the adrenal zona reticularis and the gonads. Each of these reactions require electrons transferred by the electron donor cytochrome P450 oxidoreductase. The 17-hydroxylation of its substrate occurs in all cells where P450c17 is expressed. Remarkably, a second, subsequent reaction, namely the 17,20-lyase activity, only occurs in the zona reticularis and gonads...
December 20, 2016: Current Protein & Peptide Science
https://www.readbyqxmd.com/read/27989231/an-unexpected-way-forward-towards-a-more-accurate-and-rigorous-protein-protein-binding-affinity-scoring-function-by-eliminating-terms-from-an-already-simple-scoring-function
#20
Jon Swanson, Joseph Audie
A fundamental and unsolved problem in biophysical chemistry is the development of a computationally simple, physically intuitive and generally applicable method for accurately predicting and physically explaining protein-protein binding affinities from protein-protein interaction (PPI) complex coordinates. Here we propose that the simplification of a previously described six-term PPI scoring function to a four term function results in a simple expression of all physically and statistically meaningful terms that can be used to accurately predict and explain binding affinities for a well-defined subset of PPIs that are characterized by (1) crystallographic coordinates, (2) rigid-body association, (3) normal interface size and hydrophobicity and hydrophilicity, and (4) high quality experimental binding affinity measurements...
December 17, 2016: Journal of Biomolecular Structure & Dynamics
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