Amino Acid Motifs

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  Subject Areas on Research

  • 2B4 utilizes ITAM-containing receptor complexes to initiate intracellular signaling and cytolysis. 
  • A C-terminal PDZ motif in NHE3 binds NHERF-1 and enhances cAMP inhibition of sodium-hydrogen exchange. 
  • A conserved docking motif for CK1 binding controls the nuclear localization of NFAT1. 
  • A critical role of two positively charged amino acids in the Jas motif of Arabidopsis JAZ proteins in mediating coronatine- and jasmonoyl isoleucine-dependent interactions with the COI1 F-box protein. 
  • A new activity of doublecortin in recognition of the phospho-FIGQY tyrosine in the cytoplasmic domain of neurofascin. 
  • A new kinesin tree. 
  • A novel protein geranylgeranyltransferase-I inhibitor with high potency, selectivity, and cellular activity. 
  • A phosphorylated cytoplasmic autoantigen, GW182, associates with a unique population of human mRNAs within novel cytoplasmic speckles. 
  • A role for secondary V(D)J recombination in oncogenic chromosomal translocations? 
  • A study of the repetitive structure and distribution of short motifs in human genomic sequences. 
  • AHI1 mutations cause both retinal dystrophy and renal cystic disease in Joubert syndrome. 
  • ATM: genome stability, neuronal development, and cancer cross paths. 
  • Absence of the CAAX endoprotease Rce1: effects on cell growth and transformation. 
  • Activation of orphan receptor-mediated transcription by Ca(2+)/calmodulin-dependent protein kinase IV. 
  • Adaptive interactions between HLA and HIV-1: highly divergent selection imposed by HLA class I molecules with common supertype motifs. 
  • Adeno-associated virus type 2 contains an integrin alpha5beta1 binding domain essential for viral cell entry. 
  • An interdomain interaction of the androgen receptor is required for its aggregation and toxicity in spinal and bulbar muscular atrophy. 
  • Analysis of HIV-1 subtype B third variable region peptide motifs for induction of neutralizing antibodies against HIV-1 primary isolates. 
  • Analysis of the linker for activation of T cells and the linker for activation of B cells in natural killer cells reveals a novel signaling cassette, dual usage in ITAM signaling, and influence on development of the Ly49 repertoire. 
  • Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. 
  • Analysis of the substrate specificity of the Staphylococcus aureus sortase transpeptidase SrtA. 
  • Ankyrins. 
  • Apparent loss-of-function mutant GPCRs revealed as constitutively desensitized receptors. 
  • Arabidopsis DDB1-CUL4 ASSOCIATED FACTOR1 forms a nuclear E3 ubiquitin ligase with DDB1 and CUL4 that is involved in multiple plant developmental processes. 
  • Beta-arrestin 2 mediates endocytosis of type III TGF-beta receptor and down-regulation of its signaling. 
  • Biochemical characterization of purified mammalian ARL13B protein indicates that it is an atypical GTPase and ARL3 guanine nucleotide exchange factor (GEF). 
  • Both heptad repeats of human respiratory syncytial virus fusion protein are potent inhibitors of viral fusion. 
  • C-Terminal glycine-gated radical initiation by GTP 3',8-cyclase in the molybdenum cofactor biosynthesis. 
  • C-terminal regions of the human telomerase catalytic subunit essential for in vivo enzyme activity. 
  • C-terminally truncated derivatives of Escherichia coli Hfq are proficient in riboregulation. 
  • Calmodulin mediates Ca2+ sensitivity of sodium channels. 
  • Caspase-3 cleavage links delta-catenin to the novel nuclear protein ZIFCAT. 
  • Characterization and mechanistic study of a radical SAM dehydrogenase in the biosynthesis of butirosin. 
  • Characterization of the Vibrio cholerae VolA surface-exposed lipoprotein lysophospholipase. 
  • Characterization of the trans-activation properties of equine herpesvirus 1 EICP0 protein. 
  • Cloning of the Arabidopsis clock gene TOC1, an autoregulatory response regulator homolog. 
  • Complementary roles of the DRY motif and C-terminus tail of GPCRS for G protein coupling and beta-arrestin interaction. 
  • Computation-guided backbone grafting of a discontinuous motif onto a protein scaffold. 
  • Computational design of high-affinity epitope scaffolds by backbone grafting of a linear epitope. 
  • Conserved Residues Control Activation of Mammalian G Protein-Coupled Odorant Receptors. 
  • Control of RhoA methylation by carboxylesterase I. 
  • Control of hepatic gluconeogenesis through the transcriptional coactivator PGC-1. 
  • Coordination chemistry of copper proteins: how nature handles a toxic cargo for essential function. 
  • Coordination of platinum therapeutic agents to met-rich motifs of human copper transport protein1. 
  • Coregulators in nuclear estrogen receptor action: from concept to therapeutic targeting. 
  • Cotranscriptional association of mRNA export factor Yra1 with C-terminal domain of RNA polymerase II. 
  • Cryo-EM structure of a mitochondrial calcium uniporter. 
  • Crystal structure of a PP2A B56-BubR1 complex and its implications for PP2A substrate recruitment and localization. 
  • Crystal structure of a pol alpha family DNA polymerase from the hyperthermophilic archaeon Thermococcus sp. 9 degrees N-7. 
  • Crystal structure of the human LRH-1 DBD-DNA complex reveals Ftz-F1 domain positioning is required for receptor activity. 
  • DDB1 functions as a linker to recruit receptor WD40 proteins to CUL4-ROC1 ubiquitin ligases. 
  • Definition of the molecular basis for estrogen receptor-related receptor-alpha-cofactor interactions. 
  • Degradation of the tumor suppressor PML by Pin1 contributes to the cancer phenotype of breast cancer MDA-MB-231 cells. 
  • Detection of Cytosolic Shigella flexneri via a C-Terminal Triple-Arginine Motif of GBP1 Inhibits Actin-Based Motility. 
  • Development of peptide antagonists that target estrogen receptor beta-coactivator interactions. 
  • Development of peptide antagonists that target estrogen receptor-cofactor interactions. 
  • Difficult-to-neutralize global HIV-1 isolates are neutralized by antibodies targeting open envelope conformations. 
  • Discovery of high-affinity peptide binders to BLyS by phage display. 
  • Distant conserved sequences flanking endothelial-specific promoters contain tissue-specific DNase-hypersensitive sites and over-represented motifs. 
  • Distinct Kinase-Independent Role of RIPK3 in CD11c+ Mononuclear Phagocytes in Cytokine-Induced Tissue Repair. 
  • Distinct mechanisms control the stability of the related S-phase cyclins Clb5 and Clb6. 
  • Drosophila PIWI associates with chromatin and interacts directly with HP1a. 
  • Drosophila stretchin-MLCK is a novel member of the Titin/Myosin light chain kinase family. 
  • E-cadherin polarity is determined by a multifunction motif mediating lateral membrane retention through ankyrin-G and apical-lateral transcytosis through clathrin. 
  • EGFR and EGFRvIII undergo stress- and EGFR kinase inhibitor-induced mitochondrial translocalization: a potential mechanism of EGFR-driven antagonism of apoptosis. 
  • ERAP75 functions as a coactivator to enhance estrogen receptor alpha transactivation in prostate stromal cells. 
  • Effect of torsinA on membrane proteins reveals a loss of function and a dominant-negative phenotype of the dystonia-associated DeltaE-torsinA mutant. 
  • Efficiency, selectivity, and robustness of nucleocytoplasmic transport. 
  • Elite Control, Gut CD4 T Cell Sparing, and Enhanced Mucosal T Cell Responses in Macaca nemestrina Infected by a Simian Immunodeficiency Virus Lacking a gp41 Trafficking Motif. 
  • Emi2-mediated inhibition of E2-substrate ubiquitin transfer by the anaphase-promoting complex/cyclosome through a D-box-independent mechanism. 
  • Evaluation of ligand-dependent changes in AR structure using peptide probes. 
  • Evolutionarily conserved role of calcineurin in phosphodegron-dependent degradation of phosphodiesterase 4D. 
  • Exploring motif composition of eukaryotic promoter regions. 
  • Expression of the vaccinia virus A2.5L redox protein is required for virion morphogenesis. 
  • Extensive phosphorylation with overlapping specificity by Mycobacterium tuberculosis serine/threonine protein kinases. 
  • Functional analysis of the putative integrin recognition motif on adeno-associated virus 9. 
  • GIPC interacts with the beta1-adrenergic receptor and regulates beta1-adrenergic receptor-mediated ERK activation. 
  • GYGD pore motifs in neighbouring potassium channel subunits interact to determine ion selectivity. 
  • Genome-wide identification of calcium-response factor (CaRF) binding sites predicts a role in regulation of neuronal signaling pathways. 
  • Gibberellin-induced DELLA recognition by the gibberellin receptor GID1. 
  • Good fungi gone bad: the corruption of calcineurin. 
  • HIV envelope V3 region mimic embodies key features of a broadly neutralizing antibody lineage epitope. 
  • HIV-1 gp140 epitope recognition is influenced by immunoglobulin DH gene segment sequence. 
  • High affinity for farnesyltransferase and alternative prenylation contribute individually to K-Ras4B resistance to farnesyltransferase inhibitors. 
  • Human retroviral gag- and gag-pol-like proteins interact with the transforming growth factor-beta receptor activin receptor-like kinase 1. 
  • Identification and characterization of a highly conserved calcineurin binding protein, CBP1/calcipressin, in Cryptococcus neoformans. 
  • Identification and functional characterization of the human glutathione S-transferase P1 gene as a novel transcriptional target of the p53 tumor suppressor gene. 
  • Identification of ENV determinants in V3 that influence the molecular anatomy of CCR5 utilization. 
  • Identification of a binding motif in the S5 helix that confers cholesterol sensitivity to the TRPV1 ion channel. 
  • Identification of a motif in the carboxyl terminus of beta -arrestin2 responsible for activation of JNK3. 
  • Identification of a negative regulatory surface within estrogen receptor alpha provides evidence in support of a role for corepressors in regulating cellular responses to agonists and antagonists. 
  • Identification of an ADAMTS-4 cleavage motif using phage display leads to the development of fluorogenic peptide substrates and reveals matrilin-3 as a novel substrate. 
  • Identification of ligand-selective peptide antagonists of the mineralocorticoid receptor using phage display. 
  • Immunodominance of Antibody Recognition of the HIV Envelope V2 Region in Ig-Humanized Mice. 
  • Immunotoxin FN18-CRM9 induces stronger T cell signaling than unconjugated monoclonal antibody FN18. 
  • Importance of a surface hydrophobic pocket on protein phosphatase-1 catalytic subunit in recognizing cellular regulators. 
  • In vivo attenuation of simian immunodeficiency virus by disruption of a tyrosine-dependent sorting signal in the envelope glycoprotein cytoplasmic tail. 
  • Inflammatory stimuli induce inhibitory S-nitrosylation of the deacetylase SIRT1 to increase acetylation and activation of p53 and p65. 
  • Influence of the Envelope gp120 Phe 43 Cavity on HIV-1 Sensitivity to Antibody-Dependent Cell-Mediated Cytotoxicity Responses. 
  • Informative priors based on transcription factor structural class improve de novo motif discovery. 
  • Inhibition of translation and induction of apoptosis by Bunyaviral nonstructural proteins bearing sequence similarity to reaper. 
  • Integrative regulatory mapping indicates that the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability. 
  • Interaction of proliferating cell nuclear antigen with PMS2 is required for MutLα activation and function in mismatch repair. 
  • Keeping G proteins at bay: a complex between G protein-coupled receptor kinase 2 and Gbetagamma. 
  • Kinetic role of helix caps in protein folding is context-dependent. 
  • LAD-1, the Caenorhabditis elegans L1CAM homologue, participates in embryonic and gonadal morphogenesis and is a substrate for fibroblast growth factor receptor pathway-dependent phosphotyrosine-based signaling. 
  • Mammalian class I odorant receptors exhibit a conserved vestibular-binding pocket. 
  • Mapping Hfq-RNA interaction surfaces using tryptophan fluorescence quenching. 
  • Molecular basis of calmodulin tethering and Ca2+-dependent inactivation of L-type Ca2+ channels. 
  • Motif module map reveals enforcement of aging by continual NF-kappaB activity. 
  • Motifs within the CLN3 protein: modulation of cell growth rates and apoptosis. 
  • MutLalpha and proliferating cell nuclear antigen share binding sites on MutSbeta. 
  • Mutation of SIMPLE in Charcot-Marie-Tooth 1C alters production of exosomes. 
  • Mutational analysis of active site residues in the Staphylococcus aureus transpeptidase SrtA. 
  • Mutational analysis of the Drosophila DNA repair and recombination gene mei-9. 
  • Mutations of the serine phosphorylated in the protein phosphatase-1-binding motif in the skeletal muscle glycogen-targeting subunit. 
  • Mutations that Separate the Functions of the Proofreading Subunit of the Escherichia coli Replicase. 
  • NKG2D-DAP10 triggers human NK cell-mediated killing via a Syk-independent regulatory pathway. 
  • Nanospring behaviour of ankyrin repeats. 
  • Nature of Amorphous Hydrophilic Block Affects Self-Assembly of an Artificial Viral Coat Polypeptide. 
  • Ncd motor binding and transport in the spindle. 
  • Negative-stain electron microscopy of inside-out FtsZ rings reconstituted on artificial membrane tubules show ribbons of protofilaments. 
  • Network motifs are enriched with transcription factors whose transcripts have short half-lives. 
  • Noncanonical agonist PPARγ ligands modulate the response to DNA damage and sensitize cancer cells to cytotoxic chemotherapy. 
  • Novel PMS1 alleles preferentially affect the repair of primer strand loops during DNA replication. 
  • Novel imprinted DLK1/GTL2 domain on human chromosome 14 contains motifs that mimic those implicated in IGF2/H19 regulation. 
  • Novel motif in calcineurin catalytic subunit is required for septal localization of calcineurin in Aspergillus fumigatus. 
  • O-glycosylation as a sorting determinant for cell surface delivery in yeast. 
  • On the physiological importance of endoproteolysis of CAAX proteins: heart-specific RCE1 knockout mice develop a lethal cardiomyopathy. 
  • Open chromatin mapping identifies transcriptional networks regulating human epididymis epithelial function. 
  • PLP1 alternative splicing in differentiating oligodendrocytes: characterization of an exonic splicing enhancer. 
  • Parc-ing p53 in the cytoplasm. 
  • Peptide affinity reagents for AAV capsid recognition and purification. 
  • Peptidoglycan-Sensing Receptors Trigger the Formation of Functional Amyloids of the Adaptor Protein Imd to Initiate Drosophila NF-κB Signaling. 
  • Phosphorylation of Calcineurin at a novel serine-proline rich region orchestrates hyphal growth and virulence in Aspergillus fumigatus. 
  • Phosphorylation of Glutathione S-Transferase P1 (GSTP1) by Epidermal Growth Factor Receptor (EGFR) Promotes Formation of the GSTP1-c-Jun N-terminal kinase (JNK) Complex and Suppresses JNK Downstream Signaling and Apoptosis in Brain Tumor Cells. 
  • Phosphorylation-dependent control of ZIPK nuclear import is species specific. 
  • Plasma membrane localization is required for RasA-mediated polarized morphogenesis and virulence of Aspergillus fumigatus. 
  • Plasminogen structural domains exhibit different functions when associated with cell surface GRP78 or the voltage-dependent anion channel. 
  • Platelet-derived growth factor receptor association with Na(+)/H(+) exchanger regulatory factor potentiates receptor activity. 
  • Primary infection by a human immunodeficiency virus with atypical coreceptor tropism. 
  • Programmable mutually exclusive alternative splicing for generating RNA and protein diversity. 
  • Proteome-wide analysis reveals widespread lysine acetylation of major protein complexes in the malaria parasite. 
  • Putative calmodulin-binding domains in aflatoxin biosynthesis-regulatory proteins. 
  • R9AP targeting to rod outer segments is independent of rhodopsin and is guided by the SNARE homology domain. 
  • RECQ5 helicase associates with the C-terminal repeat domain of RNA polymerase II during productive elongation phase of transcription. 
  • Recognition of U-rich RNA by Hfq from the Gram-positive pathogen Listeria monocytogenes. 
  • Recurrent signature patterns in HIV-1 B clade envelope glycoproteins associated with either early or chronic infections. 
  • Regulation of macrophage motility by Irgm1. 
  • Regulatory network motifs and hotspots of cancer genes in a mammalian cellular signalling network. 
  • Role of unusual P loop ejection and autophosphorylation in HipA-mediated persistence and multidrug tolerance. 
  • S-nitrosylation: spectrum and specificity. 
  • SIRT5 regulates the mitochondrial lysine succinylome and metabolic networks. 
  • Selective LXXLL peptides antagonize transcriptional activation by the retinoid-related orphan receptor RORgamma. 
  • Self and non-self discrimination of intracellular membranes by the innate immune system. 
  • Sequence Directionality Dramatically Affects LCST Behavior of Elastin-Like Polypeptides. 
  • Sequence- or position-specific mutations in the carboxyl-terminal FL motif of the kidney sodium bicarbonate cotransporter (NBC1) disrupt its basolateral targeting and alpha-helical structure. 
  • Small ubiquitin-related modifier-1 modification mediates resolution of CREB-dependent responses to hypoxia. 
  • Statistical characterization of protein ensembles. 
  • Stress and death: breaking up the c-Abl/14-3-3 complex in apoptosis. 
  • Structural analysis of the unmutated ancestor of the HIV-1 envelope V2 region antibody CH58 isolated from an RV144 vaccine efficacy trial vaccinee. 
  • Structural basis for allosteric control of the transcription regulator CcpA by the phosphoprotein HPr-Ser46-P. 
  • Structural basis for diverse N-glycan recognition by HIV-1-neutralizing V1-V2-directed antibody PG16. 
  • Structural basis of JAZ repression of MYC transcription factors in jasmonate signalling. 
  • Structural basis of core promoter recognition in a primitive eukaryote. 
  • Structural insights into corepressor recognition by antagonist-bound estrogen receptors. 
  • Structural mechanism of Staphylococcus aureus Hfq binding to an RNA A-tract. 
  • Structure of FitAB from Neisseria gonorrhoeae bound to DNA reveals a tetramer of toxin-antitoxin heterodimers containing pin domains and ribbon-helix-helix motifs. 
  • Structure of HIV-1 gp120 V1/V2 domain with broadly neutralizing antibody PG9. 
  • Structure of an OhrR-ohrA operator complex reveals the DNA binding mechanism of the MarR family. 
  • Structure of the endonuclease domain of MutL: unlicensed to cut. 
  • Structures of archaeal DNA segregation machinery reveal bacterial and eukaryotic linkages. 
  • Structures of maintenance of carboxysome distribution Walker-box McdA and McdB adaptor homologs. 
  • Structures of the T. brucei kRNA editing factor MRB1590 reveal unique RNA-binding pore motif contained within an ABC-ATPase fold. 
  • Structures of the activator of K. pneumonia biofilm formation, MrkH, indicates PilZ domains involved in c-di-GMP and DNA binding. 
  • Structures of the pleiotropic translational regulator Hfq and an Hfq-RNA complex: a bacterial Sm-like protein. 
  • Subcellular localization directs signaling specificity of the Cryptococcus neoformans Ras1 protein. 
  • TCR repertoire and CDR3 motif analyses depict the role of αβ T cells in Ankylosing spondylitis. 
  • The CapZ interacting protein Rcsd1 is required for cardiogenesis downstream of Wnt11a in Xenopus laevis. 
  • The DELLA motif is essential for gibberellin-induced degradation of RGA. 
  • The Drosophila protein palmitoylome: characterizing palmitoyl-thioesterases and DHHC palmitoyl-transferases. 
  • The Haemophilus influenzae hFbpABC Fe3+ transporter: analysis of the membrane permease and development of a gallium-based screen for mutants. 
  • The NMDA receptor M3 segment is a conserved transduction element coupling ligand binding to channel opening. 
  • The PDZ motif of the α1C subunit is not required for surface trafficking and adrenergic modulation of CaV1.2 channel in the heart. 
  • The RGD motif in fibronectin is essential for development but dispensable for fibril assembly. 
  • The SQSTM1-NUP214 fusion protein interacts with Crm1, activates Hoxa and Meis1 genes, and drives leukemogenesis in mice. 
  • The Staphylococcus aureus pSK41 plasmid-encoded ArtA protein is a master regulator of plasmid transmission genes and contains a RHH motif used in alternate DNA-binding modes. 
  • The active conformation of beta-arrestin1: direct evidence for the phosphate sensor in the N-domain and conformational differences in the active states of beta-arrestins1 and -2. 
  • The ammonium transporter RhBG: requirement of a tyrosine-based signal and ankyrin-G for basolateral targeting and membrane anchorage in polarized kidney epithelial cells. 
  • The betagamma subunit of heterotrimeric G proteins interacts with RACK1 and two other WD repeat proteins. 
  • The canine MHC class Ia allele DLA-88*508:01 presents diverse self- and canine distemper virus-origin peptides of varying length that have a conserved binding motif. 
  • The catalytic region and PEST domain of PTPN18 distinctly regulate the HER2 phosphorylation and ubiquitination barcodes. 
  • The cis-Pro touch-turn: a rare motif preferred at functional sites. 
  • The crystal structure and mutational analysis of a novel RNA-binding domain found in the human Tap nuclear mRNA export factor. 
  • The crystal structure of the TetR family transcriptional repressor SimR bound to DNA and the role of a flexible N-terminal extension in minor groove binding. 
  • The cyclophilin-like domain of Ran-binding protein-2 modulates selectively the activity of the ubiquitin-proteasome system and protein biogenesis. 
  • The deubiquitinating enzyme ataxin-3, a polyglutamine disease protein, edits Lys63 linkages in mixed linkage ubiquitin chains. 
  • The essential sequence elements required for RNAP II carboxyl-terminal domain function in yeast and their evolutionary conservation. 
  • The nuclear receptor REV-ERBα modulates Th17 cell-mediated autoimmune disease. 
  • The nuclear receptor-coactivator interaction surface as a target for peptide antagonists of the peroxisome proliferator-activated receptors. 
  • The stem cell-expressed receptor Lgr5 possesses canonical and functionally active molecular determinants critical to β-arrestin-2 recruitment. 
  • The vitamin D receptor interacts preferentially with DRIP205-like LxxLL motifs. 
  • Trafficking of the vesicular acetylcholine transporter in SN56 cells: a dynamin-sensitive step and interaction with the AP-2 adaptor complex. 
  • Ubiquitylation of p53 by the APC/C inhibitor Trim39. 
  • Uncommon structural motifs dominate the antigen binding site in human autoantibodies reactive with basement membrane collagen. 
  • Uncoupling of nucleotide hydrolysis and polymerization in the ParA protein superfamily disrupts DNA segregation dynamics. 
  • Vascular morphogenesis: tales of two syndromes. 
  • WT1 and DAX-1 regulate SF-1-mediated human P450arom gene expression in gonadal cells. 
  • Zinc finger protein binding to DNA: an energy perspective using molecular dynamics simulation and free energy calculations on mutants of both zinc finger domains and their specific DNA bases. 
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  Keywords of People

  • Bennett, Vann, George Barth Geller Distinguished Professor of Molecular Biology, Duke Cancer Institute
  • Erickson, Harold Paul, James B. Duke Distinguished Professor of Cell Biology, Cell Biology
  • Guan, Ziqiang, Research Professor in Biochemistry, Biochemistry
  • Hartemink, Alexander J., Professor in the Department of Computer Science, Biology
  • Juvvadi, Praveen Rao, Associate Professor in Pediatrics, Pediatrics, Infectious Diseases
  • McDonnell, Donald Patrick, Glaxo-Wellcome Distinguished Professor of Molecular Cancer Biology, in the School of Medicine, Duke Innovation & Entrepreneurship
  • Pitt, Geoffrey Stuart, Adjunct Professor in the Department of Medicine, Medicine, Cardiology
  • Taylor, Gregory Alan, Professor in Medicine, Immunology