Protein Interaction Mapping

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  Subject Areas on Research

  • A computational framework for the analysis of peptide microarray antibody binding data with application to HIV vaccine profiling. 
  • A novel domain in Set2 mediates RNA polymerase II interaction and couples histone H3 K36 methylation with transcript elongation. 
  • A nucleosome-guided map of transcription factor binding sites in yeast. 
  • An extracellular biochemical screen reveals that FLRTs and Unc5s mediate neuronal subtype recognition in the retina. 
  • Bayesian inference for genomic data integration reduces misclassification rate in predicting protein-protein interactions. 
  • Bioactive hydrogel substrates: probing leukocyte receptor-ligand interactions in parallel plate flow chamber studies. 
  • Cell division requires a direct link between microtubule-bound RacGAP and Anillin in the contractile ring. 
  • Chikungunya virus nsP3 & nsP4 interacts with HSP-90 to promote virus replication: HSP-90 inhibitors reduce CHIKV infection and inflammation in vivo. 
  • Crystal structure of the phage T4 recombinase UvsX and its functional interaction with the T4 SF2 helicase UvsW. 
  • DIG--a system for gene annotation and functional discovery. 
  • Detecting Cardiovascular Protein-Protein Interactions by Proximity Proteomics. 
  • Deubiquitinases and their emerging roles in β-arrestin-mediated signaling. 
  • Development of human protein reference database as an initial platform for approaching systems biology in humans. 
  • Differential presentation of protein interaction surfaces on the androgen receptor defines the pharmacological actions of bound ligands. 
  • Dimer-specific immunoprecipitation of active caspase-2 identifies TRAF proteins as novel activators. 
  • Discovery of MLL1 binding units, their localization to CpG Islands, and their potential function in mitotic chromatin. 
  • Discovery of high-affinity peptide binders to BLyS by phage display. 
  • Dissociation kinetics of the GroEL-gp31 chaperonin complex studied with Förster resonance energy transfer. 
  • Distinct roles of Rho1, Cdc42, and Cyk3 in septum formation and abscission during yeast cytokinesis. 
  • Distinguishing direct versus indirect transcription factor-DNA interactions. 
  • Domain-oriented edge-based alignment of protein interaction networks. 
  • Dynamic regulation of the translation initiation helicase complex by mitogenic signal transduction to eukaryotic translation initiation factor 4G. 
  • Focal adhesion kinase is a component of antiviral RIG-I-like receptor signaling. 
  • Functional domain organization of human APOBEC3G. 
  • Hsp90, an unlikely ally in the war on cancer. 
  • Inhibition of WNT signaling by G protein-coupled receptor (GPCR) kinase 2 (GRK2). 
  • Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana. 
  • Integrated proteomic and transcriptomic profiling of mouse lung development and Nmyc target genes. 
  • Integrating energy calculations with functional assays to decipher the specificity of G protein-RGS protein interactions. 
  • Interfacial hydration, dynamics and electron transfer: multi-scale ET modeling of the transient [myoglobin, cytochrome b5] complex. 
  • Kinetic mechanism of RGS9-1 potentiation by R9AP. 
  • Loss of tumor suppressor IGFBP4 drives epigenetic reprogramming in hepatic carcinogenesis. 
  • Mapping the interaction surface of scorpion β-toxins with an insect sodium channel. 
  • Mechanism and function of synaptotagmin-mediated membrane apposition. 
  • MicroRNA target site identification by integrating sequence and binding information. 
  • Molecular analyses of the Arabidopsis TUBBY-like protein gene family. 
  • Molecular-Scale Tools for Studying Mechanotransduction. 
  • Monitoring molecular interactions in living cells using flow cytometric analysis of fluorescence resonance energy transfer. 
  • Painting proteins with covalent labels: what's in the picture? 
  • Phosphoproteomic profiling of human myocardial tissues distinguishes ischemic from non-ischemic end stage heart failure. 
  • Phosphorylation of Threonine 794 on Tie1 by Rac1/PAK1 Reveals a Novel Angiogenesis Regulatory Pathway. 
  • Predicting PY motif-mediated protein-protein interactions in the Nedd4 family of ubiquitin ligases. 
  • Predominantly buried residues in the response regulator Spo0F influence specific sensor kinase recognition. 
  • Protease-activated quantum dot probes. 
  • Protein-Protein Docking Benchmark 2.0: an update. 
  • Protein-protein docking: overview and performance analysis. 
  • Proteomic analysis of mitotic RNA polymerase II reveals novel interactors and association with proteins dysfunctional in disease. 
  • Proteomic analysis of the NOS2 interactome in human airway epithelial cells. 
  • Pseudomonas syringae pv. tomato DC3000 HopPtoM (CEL ORF3) is important for lesion formation but not growth in tomato and is secreted and translocated by the Hrp type III secretion system in a chaperone-dependent manner. 
  • RNA-binding protein HuR enhances p53 translation in response to ultraviolet light irradiation. 
  • Regulation of early adipose commitment by Zfp521. 
  • Resonating to the music of ubiquitination. 
  • Reverse engineering gene regulatory networks. 
  • SUN1/2 and Syne/Nesprin-1/2 complexes connect centrosome to the nucleus during neurogenesis and neuronal migration in mice. 
  • Scanning Quadrupole Data-Independent Acquisition, Part B: Application to the Analysis of the Calcineurin-Interacting Proteins during Treatment of Aspergillus fumigatus with Azole and Echinocandin Antifungal Drugs. 
  • Selective autophagy of the adaptor protein Bcl10 modulates T cell receptor activation of NF-κB. 
  • Selective inhibition of protein secretion by abrogating receptor-coat interactions during ER export. 
  • Small near-infrared photochromic protein for photoacoustic multi-contrast imaging and detection of protein interactions in vivo. 
  • Structural basis for cooperative DNA binding by two dimers of the multidrug-binding protein QacR. 
  • Structural determinants of the interaction between the Haemophilus influenzae Hap autotransporter and fibronectin. 
  • Structure and filament dynamics of the pSK41 actin-like ParM protein: implications for plasmid DNA segregation. 
  • Systematic protein-protein interaction and pathway analyses in the idiopathic inflammatory myopathies. 
  • The Abl family kinases: mechanisms of regulation and signaling. 
  • The mitochondrial targeting chaperone 14-3-3ε regulates a RIG-I translocon that mediates membrane association and innate antiviral immunity. 
  • The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI. 
  • The protein expression landscape of the Arabidopsis root. 
  • The transforming growth factor-beta type III receptor mediates distinct subcellular trafficking and downstream signaling of activin-like kinase (ALK)3 and ALK6 receptors. 
  • Thermodynamic characterization of the binding interaction between the histone demethylase LSD1/KDM1 and CoREST. 
  • Tracking transcription factor mobility and interaction in Arabidopsis roots with fluorescence correlation spectroscopy. 
  • Using BioID to Characterize the RAS Interactome. 
  • ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5. 
  • p38-MAPK induced dephosphorylation of alpha-tropomyosin is associated with depression of myocardial sarcomeric tension and ATPase activity. 
  • β-Arrestin regulation of myosin light chain phosphorylation promotes AT1aR-mediated cell contraction and migration. 
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  Keywords of People

  • Erickson, Harold Paul, Professor Emeritus of Cell Biology, Cell Biology
  • Gordan, Raluca Mihaela, Associate Professor in Biostatistics & Bioinformatics, Computer Science
  • Hartemink, Alexander J., Professor in the Department of Computer Science, Biology
  • Hirschey, Matthew, Associate Professor of Medicine, Cell Biology
  • Milano, Carmelo Alessio, Joseph W. and Dorothy W. Beard Distinguished Professor of Experimental Surgery, Surgery, Cardiovascular and Thoracic Surgery