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https://www.readbyqxmd.com/read/28236240/binding-specificity-profiles-from-computational-peptide-screening
#1
Stefan Wallin
The computational peptide screening method is a Monte Carlo-based procedure to systematically characterize the specificity of a peptide-binding site. The method is based on a generalized-ensemble algorithm in which the peptide sequence has become a dynamic variable, i.e., molecular simulations with ordinary conformational moves are enhanced with a type of "mutational" move such that proper statistics are achieved for multiple sequences in a single run. The peptide screening method has two main steps. In the first, reference simulations of the unbound state are performed and used to parametrize a linear model of the unbound state free energy, determined by requiring that the marginal distribution of peptide sequences is approximately flat...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28111449/association-of-a-missense-mutation-in-the-positional-candidate-gene-grip1-with-backfat-thickness-traits-in-pigs
#2
Jae-Bong Lee, Hee-Bok Park, Chae-Kyoung Yoo, Hee-Sung Kim, In-Cheol Cho, Hyun Tae Lim
Objective: Previously, we reported quantitative trait loci (QTLs) affecting backfat thickness (BFT) traits on pig chromosome 5 (SW1482-SW963) in an F2 intercross population between Landrace and Korean native pigs. The aim of this study was to evaluate glutamate receptor-interacting protein 1 (GRIP1) as a positional candidate gene underlying the QTL affecting BFT traits. Methods: Genotype and phenotype analyses were performed using the 1,105 F2 progeny. A mixed-effect linear model was used to access association between these SNP markers and the BFT traits in the F2 intercross population...
December 27, 2016: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/28063882/mice-lacking-grip1-2-show-increased-social-interactions-and-enhanced-phosphorylation-at-glua2-s880
#3
Mei Han, Rebeca Mejias, Shu-Ling Chiu, Rebecca Rose, Abby Adamczyk, Richard Huganir, Tao Wang
Glutamate receptor interacting proteins 1 and 2 (GRIP1/2) play an important role in regulating synaptic trafficking of AMPA receptor 2/3 (GluA2/3) and synaptic strength. Gain-of-function GRIP1 mutations are implicated in social behavioral deficits in autism. To study mechanisms of Grip1/2-mediated AMPA signaling in the regulation of social behaviors, we performed social behavioral testing on neuron-specific Grip1/2-double knockout (DKO) and wild type (WT) mice that are matched for age, sex, and strain background...
March 15, 2017: Behavioural Brain Research
https://www.readbyqxmd.com/read/28029379/characterization-of-nuclear-foci-targeting-of-luman-creb3-recruitment-factor-lrf-crebrf-and-its-potential-role-in-inhibition-of-herpes-simplex-virus-1-replication
#4
Timothy E Audas, Philip W Hardy-Smith, Jenna Penney, Tiegh Taylor, Ray Lu
The recently identified Luman/CREB3-binding partner LRF (Luman/CREB3 recruitment factor) was shown to localize to discrete sub-nuclear foci. Luman is implicated in herpes simplex virus-1 (HSV-1) latency/reactivation and the unfolded protein response (UPR) pathway; therefore, we sought to characterize the formation of the LRF nuclear foci in the context of cellular signaling and HSV-1 replication. Here, we mapped the nuclear foci-targeting sequence to the central region containing the first leucine zipper (a...
October 26, 2016: European Journal of Cell Biology
https://www.readbyqxmd.com/read/27941904/the-role-of-grip1-and-ephrin-b3-in-blood-pressure-control-and-vascular-smooth-muscle-cell-contractility
#5
Yujia Wang, Zenghui Wu, Hongyu Luo, Junzheng Peng, John Raelson, Georg B Ehret, Patricia B Munroe, Ekatherina Stoyanova, Zhao Qin, Guy Cloutier, W Edward Bradley, Tao Wu, Jian-Zhong Shen, Shenjiang Hu, Jiangping Wu
Several erythropoietin-producing hepatocellular receptor B family (EPHB) and their ligands, ephrinBs (EFNBs), are involved in blood pressure regulation in animal models. We selected 528 single nucleotide polymorphisms (SNPs) within the genes of EPHB6, EFNB2, EFNB3 and GRIP1 in the EPH/EFN signalling system to query the International Blood Pressure Consortium dataset. A SNP within the glutamate receptor interacting protein 1 (GRIP1) gene presented a p-value of 0.000389, approaching the critical p-value of 0...
December 12, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27885724/identification-of-lactoferrin-and-glutamate-receptor-interacting-protein-1-in-bovine-cervical-mucus-a-putative-marker-for-oestrous-detection
#6
W Y Lee, M H Park, K W Kim, H Song, K B Kim, C S Lee, N K Kim, J K Park, B C Yang, K B Oh, G S Im, H J Chung
Accurate detection of oestrus is important for artificial insemination. The aim of this study was to identify oestrous-specific bovine cervical mucus proteins that could be used to determine the optimal time for artificial insemination. Non-oestrous and controlled internal drug release (CIDR)-induced oestrous-stage mucus proteins were purified and subjected to surface-enhanced laser desorption/ionization time-of-flight mass spectrometry, sodium dodecyl sulphate polyacrylamide gel electrophoresis and MALDI-TOF/TOF...
November 25, 2016: Reproduction in Domestic Animals, Zuchthygiene
https://www.readbyqxmd.com/read/27631377/glutamate-receptor-interacting-protein-1-mediates-platelet-adhesion-and-thrombus-formation
#7
Kristina L Modjeski, Sara K Ture, David J Field, Scott J Cameron, Craig N Morrell
Thrombosis-associated pathologies, such as myocardial infarction and stroke, are major causes of morbidity and mortality worldwide. Because platelets are necessary for hemostasis and thrombosis, platelet directed therapies must balance inhibiting platelet function with bleeding risk. Glutamate receptor interacting protein 1 (GRIP1) is a large scaffolding protein that localizes and organizes interacting proteins in other cells, such as neurons. We have investigated the role of GRIP1 in platelet function to determine its role as a molecular scaffold in thrombus formation...
2016: PloS One
https://www.readbyqxmd.com/read/27568566/upregulation-of-%C3%AE-3a-drives-homeostatic-plasticity-by-rerouting-ampar-into-the-recycling-endosomal-pathway
#8
Celine C Steinmetz, Vedakumar Tatavarty, Ken Sugino, Yasuyuki Shima, Anne Joseph, Heather Lin, Michael Rutlin, Mary Lambo, Chris M Hempel, Benjamin W Okaty, Suzanne Paradis, Sacha B Nelson, Gina G Turrigiano
Synaptic scaling is a form of homeostatic plasticity driven by transcription-dependent changes in AMPA-type glutamate receptor (AMPAR) trafficking. To uncover the pathways involved, we performed a cell-type-specific screen for transcripts persistently altered during scaling, which identified the μ subunit (μ3A) of the adaptor protein complex AP-3A. Synaptic scaling increased μ3A (but not other AP-3 subunits) in pyramidal neurons and redistributed dendritic μ3A and AMPAR to recycling endosomes (REs). Knockdown of μ3A prevented synaptic scaling and this redistribution, while overexpression (OE) of full-length μ3A or a truncated μ3A that cannot interact with the AP-3A complex was sufficient to drive AMPAR to REs...
September 6, 2016: Cell Reports
https://www.readbyqxmd.com/read/27490364/high-resolution-genomic-scans-reveal-genetic-architecture-controlling-alcohol-preference-in-bidirectionally-selected-rat-model
#9
Chiao-Ling Lo, Amy C Lossie, Tiebing Liang, Yunlong Liu, Xiaoling Xuei, Lawrence Lumeng, Feng C Zhou, William M Muir
Investigations on the influence of nature vs. nurture on Alcoholism (Alcohol Use Disorder) in human have yet to provide a clear view on potential genomic etiologies. To address this issue, we sequenced a replicated animal model system bidirectionally-selected for alcohol preference (AP). This model is uniquely suited to map genetic effects with high reproducibility, and resolution. The origin of the rat lines (an 8-way cross) resulted in small haplotype blocks (HB) with a corresponding high level of resolution...
August 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27464507/the-transcriptional-coregulator-grip1-controls-macrophage-polarization-and-metabolic-homeostasis
#10
Maddalena Coppo, Yurii Chinenov, Maria A Sacta, Inez Rogatsky
Diet-induced obesity causes chronic macrophage-driven inflammation in white adipose tissue (WAT) leading to insulin resistance. WAT macrophages, however, differ in their origin, gene expression and activities: unlike infiltrating monocyte-derived inflammatory macrophages, WAT-resident macrophages counteract inflammation and insulin resistance, yet, the mechanisms underlying their transcriptional programming remain poorly understood. We recently reported that a nuclear receptor cofactor-glucocorticoid receptor (GR)-interacting protein (GRIP)1-cooperates with GR to repress inflammatory genes...
July 28, 2016: Nature Communications
https://www.readbyqxmd.com/read/27425598/structural-insight-into-grip1-pdz6-in-alzheimer-s-disease-study-from-protein-expression-data-to-molecular-dynamics-simulations
#11
Paulami Chatterjee, Debjani Roy
Protein-protein interaction domain, PDZ, plays a critical role in efficient synaptic transmission in brain. Dysfunction of synaptic transmission is thought to be the underlying basis of many neuropsychiatric and neurodegenerative disorders including Alzheimer's disease (AD). In this study, Glutamate Receptor Interacting Protein1 (GRIP1) was identified as one of the most important differentially expressed, topologically significant proteins in the protein-protein interaction network. To date, very few studies have analyzed the detailed structural basis of PDZ-mediated protein interaction of GRIP1...
August 1, 2016: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/27342949/urolithin-a-suppresses-the-proliferation-of-endometrial-cancer-cells-by-mediating-estrogen-receptor-%C3%AE-dependent-gene-expression
#12
Wei Zhang, Jo-Hsin Chen, Irene Aguilera-Barrantes, Chung-Wai Shiau, Xiugui Sheng, Li-Shu Wang, Gary D Stoner, Yi-Wen Huang
SCOPE: Obese and overweight women are at high risk of developing endometrial cancer; indeed, many of endometrial cancer patients are obese. The increased number and size of adipocytes due to obesity elevate levels of circulating estrogens that stimulate cell proliferation in the endometrium. However, black raspberries are a promising approach to preventing endometrial cancer. METHODS AND RESULTS: We examined 17 black raspberry constituents and metabolites (10 μM or 10 μg/mL, 48 h) for their ability to prevent endometrial cancer cells from proliferating...
November 2016: Molecular Nutrition & Food Research
https://www.readbyqxmd.com/read/27085678/lxr%C3%AE-represses-lps-induced-inflammatory-responses-by-competing-with-irf3-for-grip1-in-kupffer-cells
#13
Chun-Mu Miao, Kun He, Pei-Zhi Li, Zuo-Jin Liu, Xi-Wen Zhu, Zhi-Bing Ou, Xiong-Zhong Ruan, Jian-Ping Gong, Chang-An Liu
Liver X receptors (LXRs) in the nucleus play important roles in lipid metabolism and inflammation. The mechanism of LXR regulation of the LPS-induced Toll-like receptor 4 (TLR4) inflammatory signaling pathway remains to be elucidated. C57/BL6 mice were randomly divided into four groups: control, T0901317 (a LXRs agonist), LPS and T0901317+LPS. Additionally, Kupffer cells isolated from male C57/BL6 mice were divided into the same four groups. A decreased amount of inflammatory cells infiltrated the portal areas and the hepatic sinusoids in the livers of mice in the T0901317+LPS group than in those of mice in the LPS group...
June 2016: International Immunopharmacology
https://www.readbyqxmd.com/read/26916741/skin-metabolite-farnesyl-pyrophosphate-regulates-epidermal-response-to-inflammation-oxidative-stress-and-migration
#14
Irena Pastar, Olivera Stojadinovic, Andrew P Sawaya, Rivka C Stone, Linsey E Lindley, Nkemcho Ojeh, Sasa Vukelic, Herbert H Samuels, Marjana Tomic-Canic
Skin produces cholesterol and a wide array of sterols and non-sterol mevalonate metabolites, including isoprenoid derivative farnesyl pyrophosphate (FPP). To characterize FPP action in epidermis, we generated transcriptional profiles of primary human keratinocytes treated with zaragozic acid (ZGA), a squalene synthase inhibitor that blocks conversion of FPP to squalene resulting in endogenous accumulation of FPP. The elevated levels of intracellular FPP resulted in regulation of epidermal differentiation and adherens junction signaling, insulin growth factor (IGF) signaling, oxidative stress response and interferon (IFN) signaling...
November 2016: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/26601915/glutamate-receptor-interacting-protein-1-regulates-cd4-ctla-4-expression-and-transplant-rejection
#15
K L Modjeski, S C Levy, S K Ture, D J Field, G Shi, K Ko, Q Zhu, C N Morrell
PDZ domains are common 80- to 90-amino-acid regions named after the first three proteins discovered to share these domains: postsynaptic density 95, discs large, and zonula occludens. PDZ domain-containing proteins typically interact with the C-terminus of membrane receptors. Glutamate receptor interacting protein 1 (GRIP1), a seven-PDZ domain protein scaffold, regulates glutamate receptor surface expression and trafficking in neurons. We have found that human and mouse T cells also express GRIP1. T cell-specific GRIP1(-/-) mice >11 weeks old had prolonged cardiac allograft survival...
May 2016: American Journal of Transplantation
https://www.readbyqxmd.com/read/26505218/novel-carm1-interacting-protein-dzip3-is-a-transcriptional-coactivator-of-estrogen-receptor-%C3%AE
#16
Daniel J Purcell, Swati Chauhan, Diane Jimenez-Stinson, Kathleen R Elliott, Tenzin D Tsewang, Young-Ho Lee, Brian Marples, David Y Lee
Coactivator-associated arginine methyltransferase 1 (CARM1) is known to promote estrogen receptor (ER)α-mediated transcription in breast cancer cells. To further characterize the regulation of ERα-mediated transcription by CARM1, we screened CARM1-interacting proteins by yeast two-hybrid. Here, we have identified an E3 ubiquitin ligase, DAZ (deleted in azoospermia)-interacting protein 3 (DZIP3), as a novel CARM1-binding protein. DZIP3-dependent ubiquitination of histone H2A has been associated with repression of transcription...
December 2015: Molecular Endocrinology
https://www.readbyqxmd.com/read/26386246/complex-translocation-t-1-12-14-q42-q14-q32-and-hmga2-deletion-in-a-fetus-presenting-growth-delay-and-bilateral-cataracts
#17
Laure Raymond, Bruno Francou, François Petit, Lucie Tosca, Audrey Briand-Suleau, Corinne Metay, Jelena Martinovic, Anne-Gaël Cordier, Alexandra Benachi, Dominique Pineau, Anne Guiochon-Mantel, Michel Goossens, Gérard Tachdjian, Sophie Brisset
We report the prenatal detection of a de novo unbalanced complex chromosomal rearrangement (CCR), in a fetus with growth delay and bilateral cataracts. Standard karyotype and FISH analyses on amniotic fluid revealed a complex de novo translocation, resulting in a 46,XY,t(1;12;14)(q42;q14;q32) karyotype. CGH-array showed a significant deletion of 387  kb at 12q14.3, at a distance of only 200-700 kb from the breakpoint at 12q14, which encompassed the HMGA2 gene and occurred de novo. Although 12q14 microdeletions are associated with growth delay in several reports in the literature, we present here the smallest deletion prenatally detected, and we detail the clinical description of the fetus...
November 2015: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/26216979/grip1-is-required-for-homeostatic-regulation-of-ampar-trafficking
#18
Han L Tan, Bridget N Queenan, Richard L Huganir
Homeostatic plasticity is a negative feedback mechanism that stabilizes neurons during periods of perturbed activity. The best-studied form of homeostatic plasticity in the central nervous system is the scaling of excitatory synapses. Postsynaptic AMPA-type glutamate receptors (AMPARs) can be inserted into synapses to compensate for neuronal inactivity or removed to compensate for hyperactivity. However, the molecular mechanisms underlying the homeostatic regulation of AMPARs remain elusive. Here, we show that the expression of GRIP1, a multi-PDZ (postsynaptic density 95/discs large/zona occludens) domain AMPAR-binding protein, is bidirectionally altered by neuronal activity...
August 11, 2015: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/26202160/the-recurrent-chromosomal-translocation-t-12-18-q14-15-q12-21-causes-the-fusion-gene-hmga2-setbp1-and-hmga2-expression-in-lipoma-and-osteochondrolipoma
#19
Ioannis Panagopoulos, Ludmila Gorunova, Bodil Bjerkehagen, Ingvild Lobmaier, Sverre Heim
Lipomas are the most common soft tissue tumors in adults. They often carry chromosome aberrations involving 12q13~15 leading to rearrangements of the HMGA2 gene in 12q14.3, with breakpoints occurring within or outside of the gene. Here, we present eleven lipomas and one osteochondrolipoma with a novel recurrent chromosome aberration, t(12;18)(q14~15;q12~21). Molecular studies on eight of the tumors showed that full-length HMGA2 transcript was expressed in three and a chimeric HMGA2 transcript in five of them...
September 2015: International Journal of Oncology
https://www.readbyqxmd.com/read/26110643/protein-trap-insertional-mutagenesis-uncovers-new-genes-involved-in-zebrafish-skin-development-including-a-neuregulin-2a-based-erbb-signaling-pathway-required-during-median-fin-fold-morphogenesis
#20
Stephanie E Westcot, Julia Hatzold, Mark D Urban, Stefânia K Richetti, Kimberly J Skuster, Rhianna M Harm, Roberto Lopez Cervera, Noriko Umemoto, Melissa S McNulty, Karl J Clark, Matthias Hammerschmidt, Stephen C Ekker
Skin disorders are widespread, but available treatments are limited. A more comprehensive understanding of skin development mechanisms will drive identification of new treatment targets and modalities. Here we report the Zebrafish Integument Project (ZIP), an expression-driven platform for identifying new skin genes and phenotypes in the vertebrate model Danio rerio (zebrafish). In vivo selection for skin-specific expression of gene-break transposon (GBT) mutant lines identified eleven new, revertible GBT alleles of genes involved in skin development...
2015: PloS One
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