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Protein interface prediction

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https://www.readbyqxmd.com/read/28718782/prediction-of-protein-hotspots-from-whole-protein-sequences-by-a-random-projection-ensemble-system
#1
Jinjian Jiang, Nian Wang, Peng Chen, Chunhou Zheng, Bing Wang
Hotspot residues are important in the determination of protein-protein interactions, and they always perform specific functions in biological processes. The determination of hotspot residues is by the commonly-used method of alanine scanning mutagenesis experiments, which is always costly and time consuming. To address this issue, computational methods have been developed. Most of them are structure based, i.e., using the information of solved protein structures. However, the number of solved protein structures is extremely less than that of sequences...
July 18, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28717196/trib1-is-a-positive-regulator-of-hepatocyte-nuclear-factor-4-alpha
#2
Sébastien Soubeyrand, Amy Martinuk, Ruth McPherson
The TRIB1 locus has been linked to both cardiovascular disease and hepatic steatosis. Recent efforts have revealed TRIB1 to be a major regulator of liver function, largely, but not exclusively, via CEBPA degradation. We recently uncovered a functional interaction between TRIB1 and HNF4A, another key regulator of hepatic function, whose molecular underpinnings remained to be clarified. Here we have extended these findings. In hepatoma models, HNF4A levels were found to depend on TRIB1, independently of its impact on CEBPA...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28716627/membrane-proteins-structures-a-review-on-computational-modeling-tools
#3
REVIEW
Jose G Almeida, Antonio J Preto, Panagiotis I Koukos, Alexandre M J J Bonvin, Irina S Moreira
BACKGROUND: Membrane proteins (MPs) play diverse and important functions in living organisms. They constitute 20% to 30% of the known bacterial, archaean and eukaryotic organisms' genomes. In humans, their importance is emphasized as they represent 50% of all known drug targets. Nevertheless, experimental determination of their three-dimensional (3D) structure has proven to be both time consuming and rather expensive, which has led to the development of computational algorithms to complement the available experimental methods and provide valuable insights...
July 14, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28713396/system-level-and-granger-network-analysis-of-integrated-proteomic-and-metabolomic-dynamics-identifies-key-points-of-grape-berry-development-at-the-interface-of-primary-and-secondary-metabolism
#4
Lei Wang, Xiaoliang Sun, Jakob Weiszmann, Wolfram Weckwerth
Grapevine is a fruit crop with worldwide economic importance. The grape berry undergoes complex biochemical changes from fruit set until ripening. This ripening process and production processes define the wine quality. Thus, a thorough understanding of berry ripening is crucial for the prediction of wine quality. For a systemic analysis of grape berry development we applied mass spectrometry based platforms to analyse the metabolome and proteome of Early Campbell at 12 stages covering major developmental phases...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28710385/electron-transfer-chain-in-respiratory-complex-i
#5
Daniel R Martin, Dmitry V Matyushov
Complex I is a part of the respiration energy chain converting the redox energy into the cross-membrane proton gradient. The electron-transfer chain of iron-sulfur cofactors within the water-soluble peripheral part of the complex is responsible for the delivery of electrons to the proton pumping subunit. The protein is porous to water penetration and the hydration level of the cofactors changes when the electron is transferred along the chain. High reaction barriers and trapping of the electrons at the iron-sulfur cofactors are prevented by the combination of intense electrostatic noise produced by the protein-water interface with the high density of quantum states in the iron-sulfur clusters caused by spin interactions between paramagnetic iron atoms...
July 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28694495/functional-determinants-of-protein-assembly-into-homomeric-complexes
#6
L Therese Bergendahl, Joseph A Marsh
Approximately half of proteins with experimentally determined structures can interact with other copies of themselves and assemble into homomeric complexes, the overwhelming majority of which (>96%) are symmetric. Although homomerisation is often assumed to a functionally beneficial result of evolutionary selection, there has been little systematic analysis of the relationship between homomer structure and function. Here, utilizing the large numbers of structures and functional annotations now available, we have investigated how proteins that assemble into different types of homomers are associated with different biological functions...
July 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28692290/top-down-atmospheric-ionization-mass-spectrometry-microscopy-combined-with-proteogenomics
#7
Cheng-Chih Hsu, Michael W Baker, Terry Gaasterland, Michael J Meehan, Eduardo R Macagno, Pieter C Dorrestein
Mass spectrometry-based protein analysis has become an important methodology for proteogenomic mapping by providing evidence for the existence of proteins predicted at the genomic level. However, screening and identification of proteins directly on tissue samples, where histological information is preserved, remain challenging. Here we demonstrate that the ambient ionization source, nanospray desorption electrospray ionization (nanoDESI), interfaced with light microscopy allows for protein profiling directly on animal tissues at the microscopic scale...
July 10, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28679759/mutational-analysis-of-lassa-virus-glycoprotein-highlights-regions-required-for-alpha-dystroglycan-utilization
#8
Marissa Acciani, Jacob T Alston, Guohui Zhao, Hayley Reynolds, Afroze M Ali, Brian Xu, Melinda A Brindley
Lassa virus (LASV) is an enveloped RNA virus endemic to West Africa and responsible for severe cases of hemorrhagic fever. Virus entry is mediated by the glycoprotein complex consisting of a stable signal peptide, a receptor-binding subunit GP1, and a viral-host membrane fusion subunit GP2. Several cellular receptors can interact with the GP1 subunit and mediate viral entry, including alpha-dystroglycan (αDG) and lysosomal associated membrane protein 1 (LAMP1). In order to define the regions within GP1 that interact with the cellular receptors, we implemented insertional mutagenesis, carbohydrate shielding, and alanine scanning mutagenesis...
July 5, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28671670/multimerin-2-is-a-ligand-for-group-14-family-c-type-lectins-clec14a-cd93-and-cd248-spanning-the-endothelial-pericyte-interface
#9
K A Khan, A J Naylor, A Khan, P J Noy, M Mambretti, P Lodhia, J Athwal, A Korzystka, C D Buckley, B E Willcox, F Mohammed, R Bicknell
The C-type lectin domain containing group 14 family members CLEC14A and CD93 are proteins expressed by endothelium and are implicated in tumour angiogenesis. CD248 (alternatively known as endosialin or tumour endothelial marker-1) is also a member of this family and is expressed by tumour-associated fibroblasts and pericytes. Multimerin-2 (MMRN2) is a unique endothelial specific extracellular matrix protein that has been implicated in angiogenesis and tumour progression. We show that the group 14 C-type lectins CLEC14A, CD93 and CD248 directly bind to MMRN2 and only thrombomodulin of the family does not...
July 3, 2017: Oncogene
https://www.readbyqxmd.com/read/28670277/nano-lazar-read-across-predictions-for-nanoparticle-toxicities-with-calculated-and-measured-properties
#10
Christoph Helma, Micha Rautenberg, Denis Gebele
The lazar framework for read across predictions was expanded for the prediction of nanoparticle toxicities, and a new methodology for calculating nanoparticle descriptors from core and coating structures was implemented. Nano-lazar provides a flexible and reproducible framework for downloading data and ontologies from the open eNanoMapper infrastructure, developing and validating nanoparticle read across models, open-source code and a free graphical interface for nanoparticle read-across predictions. In this study we compare different nanoparticle descriptor sets and local regression algorithms...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28655276/modified-random-sequential-adsorption-model-for-understanding-kinetics-of-proteins-adsorption-at-a-liquid-solid-interface
#11
Hwall Min, Eugene Freeman, Weiwei Zhang, Chowdhury Ashraf, David L Allara, Adri C T van Duin, Srinivas Tadigadapa
In this paper we experimentally measure the adsorption kinetics of Human Serum Albumin (HSA) on a hydrophobic hexadecane thiolated gold surface. We use a micromachined quartz crystal resonators with a fundamental frequency of 70 MHz to accomplish these measurements in real time. In this work, we focus on two key results (i) asymptotic behavior of the sensor responses upon HSA adsorption and (ii) the jamming limit of adsorbed layer formed by both single-injection and multi-injection experiments with the same value of final concentration...
June 27, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28654729/signor-a-database-of-causal-relationships-between-biological-entities-a-short-guide-to-searching-and-browsing
#12
Prisca Lo Surdo, Alberto Calderone, Gianni Cesareni, Livia Perfetto
SIGNOR (http://signor.uniroma2.it), the SIGnaling Network Open Resource, is a database designed to store experimentally validated causal interactions, i.e., interactions where a source entity has a regulatory effect (up-regulation, down-regulation, etc.) on a second target entity. SIGNOR acts both as a source of signaling information and a support for data analysis, modeling, and prediction. A user-friendly interface features the ability to search entries for any given protein or group of proteins and to display their interactions graphically in a network view...
June 27, 2017: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/28654001/profiling-the-extended-cleavage-specificity-of-the-house-dust-mite-protease-allergens-der-p-1-der-p-3-and-der-p-6-for-the-prediction-of-new-cell-surface-protein-substrates
#13
Alain Jacquet, Vincenzo Campisi, Martyna Szpakowska, Marie-Eve Dumez, Moreno Galleni, Andy Chevigné
House dust mite (HDM) protease allergens, through cleavages of critical surface proteins, drastically influence the initiation of the Th2 type immune responses. However, few human protein substrates for HDM proteases have been identified so far, mainly by applying time-consuming target-specific individual studies. Therefore, the identification of substrate repertoires for HDM proteases would represent an unprecedented key step toward a better understanding of the mechanism of HDM allergic response. In this study, phage display screenings using totally or partially randomized nonameric peptide substrate libraries were performed to characterize the extended substrate specificities (P₅-P₄') of the HDM proteases Der p 1, Der p 3 and Der p 6...
June 27, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28650961/mfpred-rapid-and-accurate-prediction-of-protein-peptide-recognition-multispecificity-using-self-consistent-mean-field-theory
#14
Aliza B Rubenstein, Manasi A Pethe, Sagar D Khare
Multispecificity-the ability of a single receptor protein molecule to interact with multiple substrates-is a hallmark of molecular recognition at protein-protein and protein-peptide interfaces, including enzyme-substrate complexes. The ability to perform structure-based prediction of multispecificity would aid in the identification of novel enzyme substrates, protein interaction partners, and enable design of novel enzymes targeted towards alternative substrates. The relatively slow speed of current biophysical, structure-based methods limits their use for prediction and, especially, design of multispecificity...
June 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28650154/interrogating-detergent-desolvation-of-nanopore-forming-proteins-by-fluorescence-polarization-spectroscopy
#15
Aaron J Wolfe, Yi-Ching Hsueh, Adam R Blanden, Mohammad M Mohammad, Bach Pham, Avinash K Thakur, Stewart N Loh, Min Chen, Liviu Movileanu
Understanding how membrane proteins interact with detergents is of fundamental and practical significance in structural and chemical biology as well as in nanobiotechnology. Current methods for inspecting protein-detergent complex (PDC) interfaces require high concentrations of protein and are of low throughput. Here, we describe a scalable, spectroscopic approach that uses nanomolar protein concentrations in native solutions. This approach, which is based on steady-state fluorescence polarization (FP) spectroscopy, kinetically resolves the dissociation of detergents from membrane proteins and protein unfolding...
July 10, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28641111/structural-insights-into-modulation-of-neurexin-neuroligin-trans-synaptic-adhesion-by-mdga1-neuroligin-2-complex
#16
Jung A Kim, Doyoun Kim, Seoung Youn Won, Kyung Ah Han, Dongseok Park, Eunju Cho, Nayoung Yun, Hyun Joo An, Ji Won Um, Eunjoon Kim, Jie-Oh Lee, Jaewon Ko, Ho Min Kim
Membrane-associated mucin domain-containing glycosylphosphatidylinositol anchor proteins (MDGAs) bind directly to neuroligin-1 (NL1) and neuroligin-2 (NL2), thereby respectively regulating excitatory and inhibitory synapse development. However, the mechanisms by which MDGAs modulate NL activity to specify development of the two synapse types remain unclear. Here, we determined the crystal structures of human NL2/MDGA1 Ig1-3 complex, revealing their stable 2:2 arrangement with three interaction interfaces. Cell-based assays using structure-guided, site-directed MDGA1 mutants showed that all three contact patches were required for the MDGA's negative regulation of NL2-mediated synaptogenic activity...
June 21, 2017: Neuron
https://www.readbyqxmd.com/read/28637867/full-length-cellular-beta-secretase-has-a-trimeric-subunit-stoichiometry-and-its-sulfur-rich-transmembrane-interaction-site-modulates-cytosolic-copper-compartmentalization
#17
Filip Liebsch, Mark R P Aurousseau, Tobias Bethge, Hugo McGuire, Silvia Scolari, Andreas Herrmann, Rikard Blunck, Derek Bowie, Gerd Multhaup
The beta-secretase (BACE1) initiates processing of the amyloid precursor protein (APP) into Aβ peptides, which have been implicated as central players in the pathology of Alzheimer disease. BACE1 has been described as a copper-binding protein and its oligomeric state as being monomeric, dimeric, and/or multimeric, but the native cellular stoichiometry has remained elusive. Here, by using single-molecule fluorescence and in vitro cross-linking experiments with photo-activatable unnatural amino acids, we show that full-length BACE1, independently of its subcellular localization, exists as trimers in human cells...
June 21, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28636918/actin-filament-strain-promotes-severing-and-cofilin-dissociation
#18
Anthony C Schramm, Glen M Hocky, Gregory A Voth, Laurent Blanchoin, Jean-Louis Martiel, Enrique M De La Cruz
Computational and structural studies have been indispensable in investigating the molecular origins of actin filament mechanical properties and modulation by the regulatory severing protein cofilin. All-atom molecular dynamics simulations of cofilactin filament structures determined by electron cryomicroscopy reveal how cofilin enhances the bending and twisting compliance of actin filaments. Continuum mechanics models suggest that buckled cofilactin filaments localize elastic energy at boundaries between bare and cofilin-decorated segments because of their nonuniform elasticity, thereby accelerating filament severing...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28602916/structural-investigation-of-a-c-terminal-epha2-receptor-mutant-does-mutation-affect-the-structure-and-interaction-properties-of-the-sam-domain
#19
Flavia A Mercurio, Susan Costantini, Concetta Di Natale, Luciano Pirone, Stefano Guariniello, Pasqualina L Scognamiglio, Daniela Marasco, Emilia M Pedone, Marilisa Leone
Ephrin A2 receptor (EphA2) plays a key role in cancer, it is up-regulated in several types of tumors and the process of ligand-induced receptor endocytosis, followed by degradation, is considered as a potential path to diminish tumor malignancy. Protein modulators of this mechanism are recruited at the cytosolic Sterile alpha motif (Sam) domain of EphA2 (EphA2-Sam) through heterotypic Sam-Sam associations. These interactions engage the C-terminal helix of EphA2 and close loop regions (the so called End Helix side)...
June 6, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28587924/prmt7-interacts-with-ass1-and-citrullinemia-mutations-disrupt-the-interaction
#20
Mamta Verma, Ramya Chandar M Charles, Baskar Chakrapani, Mohane Selvaraj Coumar, Gayathri Govindaraju, Arumugam Rajavelu, Sreenivas Chavali, Arunkumar Dhayalan
Protein arginine methyltransferase 7 (PRMT7) catalyzes the introduction of monomethylation marks at the arginine residues of substrate proteins. PRMT7 plays important roles in the regulation of gene expression, splicing, DNA damage, paternal imprinting, cancer and metastasis. However, little is known about the interaction partners of PRMT7. To address this, we performed yeast two-hybrid screening of PRMT7 and identified argininosuccinate synthetase (ASS1) as a potential interaction partner of PRMT7. We confirmed that PRMT7 directly interacts with ASS1 using pull-down studies...
July 21, 2017: Journal of Molecular Biology
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