Experts and Doctors on amino acid motifs in Piscataway, New Jersey, United States


Locale: Piscataway, New Jersey, United States
Topic: amino acid motifs

Top Publications

  1. Lee D, Gershenzon N, Gupta M, Ioshikhes I, Reinberg D, Lewis B. Functional characterization of core promoter elements: the downstream core element is recognized by TAF1. Mol Cell Biol. 2005;25:9674-86 pubmed
    ..Finally, these data argue that TFIID is, in fact, a core promoter recognition complex. ..
  2. Pandey A, Dixit U, Kholodovych V, Comollo T, Pandey V. The ?1'-?2' Motif of the RNase H Domain of Human Immunodeficiency Virus Type 1 Reverse Transcriptase Is Responsible for Conferring Open Conformation to the p66 Subunit by Displacing the Connection Domain from the Polymerase Cleft. Biochemistry. 2017;56:3434-3442 pubmed publisher
    ..The unstable elongated p66 molecule may then readily dimerize with p51 to assume a stable dimeric conformation. ..
  3. Wang L, Rajan H, Pitman J, McKeown M, Tsai C. Histone deacetylase-associating Atrophin proteins are nuclear receptor corepressors. Genes Dev. 2006;20:525-30 pubmed
  4. Okajima T, Xu A, Lei L, Irvine K. Chaperone activity of protein O-fucosyltransferase 1 promotes notch receptor folding. Science. 2005;307:1599-603 pubmed
    ..This ability of OFUT1 to facilitate folding of Notch did not require its fucosyltransferase activity. Thus, a glycosyltransferase can bind its substrate in the endoplasmic reticulum to facilitate normal folding. ..
  5. Ahmed S, Palermo C, Wan S, Walworth N. A novel protein with similarities to Rb binding protein 2 compensates for loss of Chk1 function and affects histone modification in fission yeast. Mol Cell Biol. 2004;24:3660-9 pubmed
    ..We postulate that Msc1 plays an important role in regulating chromatin structure and that this function modulates the cellular response to DNA damage. ..
  6. Singh A, Hitchcock Degregori S. Local destabilization of the tropomyosin coiled coil gives the molecular flexibility required for actin binding. Biochemistry. 2003;42:14114-21 pubmed
    ..Models based on tropomyosin crystal structures give insight into possible effects of the mutations on the structure. We conclude that the significance of the Ala clusters in allowing flexibility of tropomyosin is stability-driven. ..
  7. Kim S, Wadsworth W. Positioning of longitudinal nerves in C. elegans by nidogen. Science. 2000;288:150-4 pubmed
    ..By examining migration of a single axon in vivo, we show that nidogen is required for the axon to switch from circumferential to longitudinal migration. Specialized basement membranes may thus regulate nerve position. ..
  8. Liu H, Rodgers N, Jiao X, Kiledjian M. The scavenger mRNA decapping enzyme DcpS is a member of the HIT family of pyrophosphatases. EMBO J. 2002;21:4699-708 pubmed
  9. Ho D, Coburn G, Kang Y, Cullen B, Georgiadis M. The crystal structure and mutational analysis of a novel RNA-binding domain found in the human Tap nuclear mRNA export factor. Proc Natl Acad Sci U S A. 2002;99:1888-93 pubmed
    ..The second critical CTE-interacting surface on Tap is defined by three previously identified residues on the surface of the ribonucleoprotein domain. The structural and mutational data define a novel RNA-binding site on the Tap protein. ..

More Information


  1. Lawson C, Benoff B, Berger T, Berman H, Carey J. E. coli trp repressor forms a domain-swapped array in aqueous alcohol. Structure. 2004;12:1099-108 pubmed
    ..Small angle X-ray scattering measurements show that the self-association properties of trpR in solution are fundamentally altered by isopropanol. ..
  2. Banta S, Anderson S. Verification of a novel NADH-binding motif: combinatorial mutagenesis of three amino acids in the cofactor-binding pocket of Corynebacterium 2,5-diketo-D-gluconic acid reductase. J Mol Evol. 2002;55:623-31 pubmed
    ..This screen is a valuable tool for improving 2,5-DKG reductase, and it could easily be modified for improving other aspects of this protein or similar enzymes. ..
  3. Shafer B, Chu C, Shatkin A. Human mRNA cap methyltransferase: alternative nuclear localization signal motifs ensure nuclear localization required for viability. Mol Cell Biol. 2005;25:2644-9 pubmed
    ..However, an enzymatically active 144-476 truncation mutant missing the three nuclear localization signals was mostly cytoplasmic and ineffective in preventing siRNA-induced loss of viability. ..
  4. Chang H, Rongo C. Cytosolic tail sequences and subunit interactions are critical for synaptic localization of glutamate receptors. J Cell Sci. 2005;118:1945-56 pubmed
  5. Cai S, Hernandez L, Wang Y, Park K, Sesti F. MPS-1 is a K+ channel beta-subunit and a serine/threonine kinase. Nat Neurosci. 2005;8:1503-9 pubmed
    ..These data are consistent with a model that predicts that the MPS-1-dependent phosphorylation of KVS-1 sustains cell excitability by controlling K+ flux. ..
  6. Yan Y, Stein S, Ding J, Shen M, Abate Shen C. A novel PF/PN motif inhibits nuclear localization and DNA binding activity of the ESX1 homeoprotein. Mol Cell Biol. 2000;20:661-71 pubmed
  7. Wang N, Yamanaka K, Inouye M. Acquisition of double-stranded DNA-binding ability in a hybrid protein between Escherichia coli CspA and the cold shock domain of human YB-1. Mol Microbiol. 2000;38:526-34 pubmed
    ..These results indicate that the loop region between the beta3 and beta4 strands of Y-box proteins, which is a little longer and more basic than that of CspA, plays an important role in their binding to dsDNA. ..
  8. Wu Q, Dibona V, Bernard L, Zhang H. The polarity protein partitioning-defective 1 (PAR-1) regulates dendritic spine morphogenesis through phosphorylating postsynaptic density protein 95 (PSD-95). J Biol Chem. 2012;287:30781-8 pubmed publisher
    ..Together, our findings uncover a role of PAR-1 in spine morphogenesis in hippocampal neurons through phosphorylating PSD-95. ..
  9. Li C, Ai N, Dinh G, Welsh W, Chen J. Human ADA3 regulates RARalpha transcriptional activity through direct contact between LxxLL motifs and the receptor coactivator pocket. Nucleic Acids Res. 2010;38:5291-303 pubmed publisher
    ..These results suggest that hADA3 is a bona fide transcriptional coactivator for RAR?, acting through a conserved mechanism involving direct contacts between NR boxes and the receptor's co-activator pocket. ..
  10. Li W, Yu S, Liu T, Kim J, Blank V, Li H, et al. Heterodimerization with small Maf proteins enhances nuclear retention of Nrf2 via masking the NESzip motif. Biochim Biophys Acta. 2008;1783:1847-56 pubmed publisher
    ..For the first time, we show that under the physiological condition, the NESzip motif can be switched-off by heterodimerization. ..
  11. Dul B, Walworth N. The plant homeodomain fingers of fission yeast Msc1 exhibit E3 ubiquitin ligase activity. J Biol Chem. 2007;282:18397-406 pubmed
    ..We speculate that the target of the E3 ubiquitin ligase activity of Msc1 is likely to be a chromatin-associated protein. ..
  12. Li M, Stollar V. Distinct sites on the Sindbis virus RNA-dependent RNA polymerase for binding to the promoters for the synthesis of genomic and subgenomic RNA. J Virol. 2007;81:4371-3 pubmed publisher
    ..Our findings indicate that nsP4 has distinct sites for the recognition of the G and SG promoters...
  13. Perez E, Stock A. Characterization of the Thermotoga maritima chemotaxis methylation system that lacks pentapeptide-dependent methyltransferase CheR:MCP tethering. Mol Microbiol. 2007;63:363-78 pubmed
  14. Cook J, Lee J, Yang Z, Krause C, Herth N, Hoffmann R, et al. FBXO11/PRMT9, a new protein arginine methyltransferase, symmetrically dimethylates arginine residues. Biochem Biophys Res Commun. 2006;342:472-81 pubmed
    ..Structurally, this protein is distinct from all other known PRMTs implying that convergent evolution allowed this protein to develop the ability to methylate arginine residues and evolved elements conserved in PRMTs to accomplish this. ..
  15. Greenfield N, Kostyukova A, Hitchcock Degregori S. Structure and tropomyosin binding properties of the N-terminal capping domain of tropomodulin 1. Biophys J. 2005;88:372-83 pubmed
    ..Residues 55-62 and 76-92 display negative 1H-15N heteronuclear Overhauser enhancements showing they are flexible. The conformational dynamics of these residues may be important for actin capping activity. ..
  16. Yan Y, Liu J, Luo Y, E C, Haltiwanger R, Abate Shen C, et al. Dual roles of Cripto as a ligand and coreceptor in the nodal signaling pathway. Mol Cell Biol. 2002;22:4439-49 pubmed
    ..Our findings highlight the significance of extracellular modulation of ligand activity as an important means of regulating TGF beta signaling pathways during vertebrate development. ..
  17. Zhu Y, Inouye M. The role of the G2 box, a conserved motif in the histidine kinase superfamily, in modulating the function of EnvZ. Mol Microbiol. 2002;45:653-63 pubmed
    ..The G2 box may modulate the interaction between these two domains in response to extracellular osmolarity. ..
  18. Minakhin L, Severinov K. On the role of the Escherichia coli RNA polymerase sigma 70 region 4.2 and alpha-subunit C-terminal domains in promoter complex formation on the extended -10 galP1 promoter. J Biol Chem. 2003;278:29710-8 pubmed
    ..2 but not alpha CTD was required for open promoter complex formation on galP1 derivatives with extended -10 motif. We propose a model involving sigma 70 region 4.2 interaction with the beta flap domain that explains these observations. ..
  19. Wang Z, Jiao X, Carr Schmid A, Kiledjian M. The hDcp2 protein is a mammalian mRNA decapping enzyme. Proc Natl Acad Sci U S A. 2002;99:12663-8 pubmed
    ..Therefore the mammalian homologue of the yeast Dcp2 protein is an mRNA decapping enzyme demonstrated to contain intrinsic decapping activity. ..
  20. Su L, Agapito M, Li M, Simonson W, Huttenlocher A, Habas R, et al. TRPM7 regulates cell adhesion by controlling the calcium-dependent protease calpain. J Biol Chem. 2006;281:11260-70 pubmed
    ..Together, our results suggest that the ion channel TRPM7 regulates cell adhesion through m-calpain by mediating the local influx of calcium into peripheral adhesion complexes. ..
  21. Caban K, Kinzy S, Copeland P. The L7Ae RNA binding motif is a multifunctional domain required for the ribosome-dependent Sec incorporation activity of Sec insertion sequence binding protein 2. Mol Cell Biol. 2007;27:6350-60 pubmed
    ..5-kDa protein-U4 snRNA complex strongly supports a two-site model for L7Ae domain function within SBP2. These results provide evidence that the SBP2-ribosome interaction is essential for Sec incorporation. ..
  22. Maruyama R, Velarde N, Klancer R, Gordon S, Kadandale P, Parry J, et al. EGG-3 regulates cell-surface and cortex rearrangements during egg activation in Caenorhabditis elegans. Curr Biol. 2007;17:1555-60 pubmed
    ..Therefore, EGG-3 plays a central role in egg activation by influencing polarized F-actin dynamics and the localization or activity of molecules that are directly involved in executing the egg-to-embryo transition. ..
  23. Ozturk S, Kinzy T. Guanine nucleotide exchange factor independence of the G-protein eEF1A through novel mutant forms and biochemical properties. J Biol Chem. 2008;283:23244-53 pubmed publisher
    ..The biochemical properties of these eEF1A mutants provide insight into the mechanism behind GEF-independent G-protein function. ..
  24. Ishikawa H, Takeuchi H, Haltiwanger R, Irvine K. Four-jointed is a Golgi kinase that phosphorylates a subset of cadherin domains. Science. 2008;321:401-4 pubmed publisher
    ..Our results indicate that Four-jointed regulates Fat signaling by phosphorylating cadherin domains of Fat and Dachsous as they transit through the Golgi. ..
  25. Jan Y, Heck D, Gray J, Zheng H, Casillas R, Laskin D, et al. Selective targeting of selenocysteine in thioredoxin reductase by the half mustard 2-chloroethyl ethyl sulfide in lung epithelial cells. Chem Res Toxicol. 2010;23:1045-53 pubmed publisher
    ..Taken together, these data suggest that sulfur mustard vesicants target TrxR and that this may be an important mechanism mediating oxidative stress and tissue injury. ..
  26. Piccirillo C, Khanna R, Kiledjian M. Functional characterization of the mammalian mRNA decapping enzyme hDcp2. RNA. 2003;9:1138-47 pubmed
  27. Kuksa P, Pavlovic V. Efficient motif finding algorithms for large-alphabet inputs. BMC Bioinformatics. 2010;11 Suppl 8:S1 pubmed publisher
  28. Pan G, Feng Y, Ambegaonkar A, Sun G, Huff M, Rauskolb C, et al. Signal transduction by the Fat cytoplasmic domain. Development. 2013;140:831-42 pubmed publisher
  29. Cruz J, Rothenbacher F, Maehigashi T, Lane W, Dunham C, Woychik N. Doc toxin is a kinase that inactivates elongation factor Tu. J Biol Chem. 2014;289:7788-98 pubmed publisher
    ..Moreover, we have established that all characterized Fic domain proteins, even those that phosphorylate, target pivotal GTPases for inactivation through a post-translational modification at a single functionally critical acceptor site. ..