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. 
  • A role for Mediator complex subunit MED13L in Rb/E2F-induced growth arrest. 
  • ARHGDIA mutations cause nephrotic syndrome via defective RHO GTPase signaling. 
  • Alpha-internexin is structurally and functionally associated with the neurofilament triplet proteins in the mature CNS. 
  • An extracellular biochemical screen reveals that FLRTs and Unc5s mediate neuronal subtype recognition in the retina. 
  • An organelle-specific protein landscape identifies novel diseases and molecular mechanisms. 
  • 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. 
  • Co-evolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating protein-protein interactions. 
  • Complementary roles of the DRY motif and C-terminus tail of GPCRS for G protein coupling and beta-arrestin interaction. 
  • Construction and analysis of protein-protein interaction networks based on proteomics data of prostate cancer. 
  • Crystal structure of the phage T4 recombinase UvsX and its functional interaction with the T4 SF2 helicase UvsW. 
  • Crystal structure of the serine protease domain of Sesbania mosaic virus polyprotein and mutational analysis of residues forming the S1-binding pocket. 
  • DIG--a system for gene annotation and functional discovery. 
  • DOMINE: a comprehensive collection of known and predicted domain-domain interactions. 
  • DOMINE: a database of protein domain interactions. 
  • 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 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. 
  • Functional domain organization of human APOBEC3G. 
  • Global Mapping of the Inc-Human Interactome Reveals that Retromer Restricts Chlamydia Infection. 
  • High-throughput inference of protein-protein interfaces from unassigned NMR data 
  • Hsp90, an unlikely ally in the war on cancer. 
  • Human immunodeficiency virus type 1 Tat protein inhibits the SIRT1 deacetylase and induces T cell hyperactivation. 
  • Human inter-α-inhibitor is a substrate for factor XIIIa and tissue transglutaminase. 
  • Human transcription elongation factor CA150 localizes to splicing factor-rich nuclear speckles and assembles transcription and splicing components into complexes through its amino and carboxyl regions. 
  • 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. 
  • Interaction between the T4 helicase-loading protein (gp59) and the DNA polymerase (gp43): a locking mechanism to delay replication during replisome assembly. 
  • 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 phenotypic landscapes using DNA micro-arrays. 
  • 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. 
  • 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. 
  • Primary cilium-dependent and -independent Hedgehog signaling inhibits p16(INK4A). 
  • Protease-activated quantum dot probes. 
  • Protein-Protein Docking Benchmark 2.0: an update. 
  • Protein-protein docking: overview and performance analysis. 
  • Protein-protein interfaces: properties, preferences, and projections. 
  • 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. 
  • RNA-binding protein HuR enhances p53 translation in response to ultraviolet light irradiation. 
  • 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. 
  • Small near-infrared photochromic protein for photoacoustic multi-contrast imaging and detection of protein interactions in vivo. 
  • Stacking interactions of W271 and H275 of SeMV serine protease with W43 of natively unfolded VPg confer catalytic activity to protease. 
  • 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 Chlamydia type III secretion system C-ring engages a chaperone-effector protein complex. 
  • 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. 
  • ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5. 
  • 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, James B. Duke Distinguished Professor 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, Pharmacology & Cancer Biology
  • Milano, Carmelo Alessio, Professor of Surgery, Surgery, Cardiovascular and Thoracic Surgery