Experts and Doctors on sequence alignment in New York, United States


Locale: New York, United States
Topic: sequence alignment

Top Publications

  1. Burne R, Penders J. Characterization of the Streptococcus mutans GS-5 fruA gene encoding exo-beta-D-fructosidase. Infect Immun. 1992;60:4621-32 pubmed
    ..The data begin to define functional domains of the FruA protein and potential regulatory sites for induction, repression, growth rate control, and posttranslational localization of this multifunctional enzyme...
  2. Catz D, Fischer L, Moschella M, Tobias M, Kelley D. Sexually dimorphic expression of a laryngeal-specific, androgen-regulated myosin heavy chain gene during Xenopus laevis development. Dev Biol. 1992;154:366-76 pubmed
    ..Thus, LM appears to be a male-specific, testosterone-regulated MHC isoform in Xenopus laevis. The LM gene will permit analysis of androgen-directed sexual differentiation in this highly sexually dimorphic tissue. ..
  3. Lopez Casillas F, Cheifetz S, Doody J, Andres J, Lane W, Massague J. Structure and expression of the membrane proteoglycan betaglycan, a component of the TGF-beta receptor system. Cell. 1991;67:785-95 pubmed
    ..The unique features of betaglycan suggest important roles in cell interaction with TGF-beta. ..
  4. Simmons G, Kwok W, Matulonis P, Venkatesh T. Polymorphism and divergence at the prune locus in Drosophila melanogaster and D. simulans. Mol Biol Evol. 1994;11:666-71 pubmed
    ..The pattern of silent versus replacement polymorphism and divergence at prune is consistent with either a model of weakly deleterious selection against amino acid substitutions or balancing selection. ..
  5. Mikami B, Hehre E, Sato M, Katsube Y, Hirose M, Morita Y, et al. The 2.0-A resolution structure of soybean beta-amylase complexed with alpha-cyclodextrin. Biochemistry. 1993;32:6836-45 pubmed
    ..We envision a significant role for the methyl groups of Leu 383 at the cleft entrance with respect to the productive binding of the outer chains of starch. ..
  6. Jun S, Desplan C. Cooperative interactions between paired domain and homeodomain. Development. 1996;122:2639-50 pubmed
    ..We propose a model by which Pax proteins recognize different target genes in vivo through various combinations of their DNA binding domains, thus expanding their recognition repertoire. ..
  7. Gosser Y, Nomanbhoy T, Aghazadeh B, Manor D, Combs C, Cerione R, et al. C-terminal binding domain of Rho GDP-dissociation inhibitor directs N-terminal inhibitory peptide to GTPases. Nature. 1997;387:814-9 pubmed
    ..These results lead to a model of rhoGDI function in which the carboxy-terminal binding domain targets the amino-terminal inhibitory region to GTPases, resulting in membrane extraction and inhibition of nucleotide cycling. ..
  8. Chen H, Einbond A, Kwak S, Linn H, Koepf E, Peterson S, et al. Characterization of the WW domain of human yes-associated protein and its polyproline-containing ligands. J Biol Chem. 1997;272:17070-7 pubmed
  9. Itoh K, Meffre E, Albesiano E, Farber A, Dines D, Stein P, et al. Immunoglobulin heavy chain variable region gene replacement As a mechanism for receptor revision in rheumatoid arthritis synovial tissue B lymphocytes. J Exp Med. 2000;192:1151-64 pubmed
    ..A relationship between these secondary V(H) gene rearrangements and the autoimmunity characteristic of RA should be considered. ..

More Information

Publications318 found, 100 shown here

  1. Mahnke K, Guo M, Lee S, Sepulveda H, Swain S, Nussenzweig M, et al. The dendritic cell receptor for endocytosis, DEC-205, can recycle and enhance antigen presentation via major histocompatibility complex class II-positive lysosomal compartments. J Cell Biol. 2000;151:673-84 pubmed
    ..Therefore, the DEC-205 cytosolic domain mediates a new pathway of receptor-mediated endocytosis that entails efficient recycling through late endosomes and a greatly enhanced efficiency of antigen presentation to CD4(+) T cells. ..
  2. Huang C, Liu P. New insights into the Rh superfamily of genes and proteins in erythroid cells and nonerythroid tissues. Blood Cells Mol Dis. 2001;27:90-101 pubmed
    ..Further inquires into the structure, function, biosynthesis, and interaction of Rh proteins will shed new light on ammonia homeostasis in a wide range of human physiological and pathological states. ..
  3. Pieper U, Eswar N, Stuart A, Ilyin V, Sali A. MODBASE, a database of annotated comparative protein structure models. Nucleic Acids Res. 2002;30:255-9 pubmed
  4. Sterne Marr R, Tesmer J, Day P, Stracquatanio R, Cilente J, O Connor K, et al. G protein-coupled receptor Kinase 2/G alpha q/11 interaction. A novel surface on a regulator of G protein signaling homology domain for binding G alpha subunits. J Biol Chem. 2003;278:6050-8 pubmed
    ..We suggest that this novel protein interaction site on an RH domain be designated the "C" site. ..
  5. Benach J, Lee I, Edstrom W, Kuzin A, Chiang Y, Acton T, et al. The 2.3-A crystal structure of the shikimate 5-dehydrogenase orthologue YdiB from Escherichia coli suggests a novel catalytic environment for an NAD-dependent dehydrogenase. J Biol Chem. 2003;278:19176-82 pubmed
    ..The nature and disposition of the active site residues suggest a novel reaction mechanism in which an aspartate acts as the general acid/base catalyst during the hydride transfer reaction. ..
  6. Musunuru K, Darnell R. Determination and augmentation of RNA sequence specificity of the Nova K-homology domains. Nucleic Acids Res. 2004;32:4852-61 pubmed
    ..These data yield important insights into KH domain function and suggest a strategy by which to engineer KH domains with novel sequence preferences. ..
  7. Wohlbold L, Larochelle S, Liao J, Livshits G, Singer J, Shokat K, et al. The cyclin-dependent kinase (CDK) family member PNQALRE/CCRK supports cell proliferation but has no intrinsic CDK-activating kinase (CAK) activity. Cell Cycle. 2006;5:546-54 pubmed
    ..Our data do not support the proposed function of PNQALRE/CCRK in activating CDKs, but instead reinforce the notion of Cdk7 as the major, and to date the only, CAK in mammalian cells. ..
  8. Klein T, Jenny A, Djiane A, Mlodzik M. CKIepsilon/discs overgrown promotes both Wnt-Fz/beta-catenin and Fz/PCP signaling in Drosophila. Curr Biol. 2006;16:1337-43 pubmed
    ..Furthermore, we have identified the primary kinase target residue of CKIepsilon on Dsh. Thus, our data suggest that CKIepsilon modulates Wnt/beta-catenin and Fz/PCP signaling pathways via kinase-dependent and -independent mechanisms. ..
  9. Naro Maciel E, Le M, Fitzsimmons N, Amato G. Evolutionary relationships of marine turtles: A molecular phylogeny based on nuclear and mitochondrial genes. Mol Phylogenet Evol. 2008;49:659-62 pubmed publisher
  10. Raabe T, Manley J. A human homologue of the Escherichia coli DnaJ heat-shock protein. Nucleic Acids Res. 1991;19:6645 pubmed
  11. Treisman J. Drosophila homologues of the transcriptional coactivation complex subunits TRAP240 and TRAP230 are required for identical processes in eye-antennal disc development. Development. 2001;128:603-15 pubmed
    ..These novel and specific phenotypes suggest that TRAP240 and TRAP230 act in concert to mediate an unknown developmental signal or a combination of signals. ..
  12. Chen B, Zhang D, Pollard J. Progesterone regulation of the mammalian ortholog of methylcitrate dehydratase (immune response gene 1) in the uterine epithelium during implantation through the protein kinase C pathway. Mol Endocrinol. 2003;17:2340-54 pubmed
  13. Liu C, Mao X, Lustig A. Mutational analysis defines a C-terminal tail domain of RAP1 essential for Telomeric silencing in Saccharomyces cerevisiae. Genetics. 1994;138:1025-40 pubmed
    ..These data also suggest a distinct set of C-terminal requirements for telomere size control and telomeric silencing. ..
  14. Blobel F, Erdmann R. Identification of a yeast peroxisomal member of the family of AMP-binding proteins. Eur J Biochem. 1996;240:468-76 pubmed
    ..Pcs60p belongs to the family of proteins which act via an ATP-dependent covalent binding of AMP to their substrates and shows the highest degree of similarity to the Escherichia coli long chain acyl-CoA synthetase...
  15. Glerum D, Muroff I, Jin C, Tzagoloff A. COX15 codes for a mitochondrial protein essential for the assembly of yeast cytochrome oxidase. J Biol Chem. 1997;272:19088-94 pubmed
    ..The existence of COX15 homologs in Schizosaccharomyces pombe and Caenorhabditis elegans suggests that it may be widely distributed in eucaryotic organisms. ..
  16. Hadjigeorgiou G, Kawashima N, Bruno C, Andreu A, Sue C, Rigden D, et al. Manifesting heterozygotes in a Japanese family with a novel mutation in the muscle-specific phosphoglycerate mutase (PGAM-M) gene. Neuromuscul Disord. 1999;9:399-402 pubmed
    ..Two heterozygous family members for the G97D mutation presented with exercise intolerance and muscle cramps. We describe the first PGAM-M mutation in the Japanese population and confirm that heterozygous individuals can be symptomatic. ..
  17. Onoprishvili I, Andria M, Vilim F, Hiller J, Simon E. The bovine mu-opioid receptor: cloning of cDNA and pharmacological characterization of the receptor expressed in mammalian cells. Brain Res Mol Brain Res. 1999;73:129-37 pubmed
    ..Evidence is presented indicating that the cloned receptor is the same as the bovine mu receptor previously purified to homogeneity in our laboratory. No evidence was found for genes for multiple mu-type opioid receptors. ..
  18. Bao J, Talmage D, Role L, Gautier J. Regulation of neurogenesis by interactions between HEN1 and neuronal LMO proteins. Development. 2000;127:425-35 pubmed
    ..We propose that XHEN1, in concert with XLMO-3, is a critical regulator of neurogenesis. ..
  19. Deng Z, Morse J, Slager S, Cuervo N, Moore K, Venetos G, et al. Familial primary pulmonary hypertension (gene PPH1) is caused by mutations in the bone morphogenetic protein receptor-II gene. Am J Hum Genet. 2000;67:737-44 pubmed
    ..These findings indicate that the bone morphogenetic protein-signaling pathway is defective in patients with primary pulmonary hypertension and may implicate the pathway in the nonfamilial forms of the disease. ..
  20. Jager D, Stockert E, Jager E, Gure A, Scanlan M, Knuth A, et al. Serological cloning of a melanocyte rab guanosine 5'-triphosphate-binding protein and a chromosome condensation protein from a melanoma complementary DNA library. Cancer Res. 2000;60:3584-91 pubmed
    ..These findings provide further support that SEREX can define biologically significant molecules in cancer. ..
  21. Edelmann L, Spiteri E, Koren K, Pulijaal V, Bialer M, Shanske A, et al. AT-rich palindromes mediate the constitutional t(11;22) translocation. Am J Hum Genet. 2001;68:1-13 pubmed
  22. Edelmann L, Stankiewicz P, Spiteri E, Pandita R, Shaffer L, Lupski J, et al. Two functional copies of the DGCR6 gene are present on human chromosome 22q11 due to a duplication of an ancestral locus. Genome Res. 2001;11:208-17 pubmed
    ..Interestingly, a full-length HERV-K provirus integrated into the sc11.1a locus after the divergence of chimpanzees and humans...
  23. Sant Angelo D, Robinson E, Janeway C, Denzin L. Recognition of core and flanking amino acids of MHC class II-bound peptides by the T cell receptor. Eur J Immunol. 2002;32:2510-20 pubmed
    ..However, using an HLA-DM-mediated technique to measure peptide binding to MHC class II molecules, we found that the peptide flanking residues contribute substantially to MHC binding. ..
  24. Wehrens X, Lehnart S, Reiken S, Marks A. Ca2+/calmodulin-dependent protein kinase II phosphorylation regulates the cardiac ryanodine receptor. Circ Res. 2004;94:e61-70 pubmed
    ..CaMKII-mediated phosphorylation of RyR2 may contribute to the enhanced contractility observed at higher heart rates. The full text of this article is available online at ..
  25. Lele K, Wolgemuth D. Distinct regions of the mouse cyclin A1 gene, Ccna1, confer male germ-cell specific expression and enhancer function. Biol Reprod. 2004;71:1340-7 pubmed
    ..3 kb upstream of the putative Ccna1 transcriptional start can direct expression of lacZ to spermatocytes, while sequences located between -4.8 kb and -1.3 kb of the putative transcriptional start site may enhance expression of lacZ. ..
  26. Dodatko T, Fedorov A, Grynberg M, Patskovsky Y, Rozwarski D, Jaroszewski L, et al. Crystal structure of the actin binding domain of the cyclase-associated protein. Biochemistry. 2004;43:10628-41 pubmed
    ..Thus, the unusual right-handed beta-helical fold present in C-CAP appears to support a wide range of biological functions. ..
  27. Zhan C, Yan Q, Patskovsky Y, Li Z, Toro R, Meyer A, et al. Biochemical and structural characterization of the human TL1A ectodomain. Biochemistry. 2009;48:7636-45 pubmed publisher
    ..In summary, these studies provide insights into the structure and function of TL1A and provide the basis for the rational manipulation of its interactions with cognate receptors. ..
  28. Zhang H, Fraser S, Papazoglu C, Hoatlin M, Baron M. Transcriptional activation by the Mixl1 homeodomain protein in differentiating mouse embryonic stem cells. Stem Cells. 2009;27:2884-95 pubmed publisher
    ..These results strongly suggest that Gsc is a direct target gene of Mixl1 during embryogenesis. STEM CELLS 2009;27:2884-2895. ..
  29. Piatkevich K, Malashkevich V, Almo S, Verkhusha V. Engineering ESPT pathways based on structural analysis of LSSmKate red fluorescent proteins with large Stokes shift. J Am Chem Soc. 2010;132:10762-70 pubmed publisher
    ..These data suggest that different chromophores formed by distinct tripeptides in different environments can be rationally modified to yield RFPs with novel photochemical properties. ..
  30. Lyons P, Ma L, Baker R, Fricker L. Carboxypeptidase A6 in zebrafish development and implications for VIth cranial nerve pathfinding. PLoS ONE. 2010;5:e12967 pubmed publisher
    ..If mutations in CPA6 contribute to Duane syndrome, our results also suggest that Duane syndrome can be a chondrogenic rather than a myogenic or neurogenic developmental disorder. ..
  31. Kim J, Almo S. Structural basis for hypermodification of the wobble uridine in tRNA by bifunctional enzyme MnmC. BMC Struct Biol. 2013;13:5 pubmed publisher
    ..The structures of MnmC also reveal the detailed atomic interactions at the interdomain interface and provide spatial restraints relevant to the overall catalytic mechanism. ..
  32. Mirels L, Ball W. Neonatal rat submandibular gland protein SMG-A and parotid secretory protein are alternatively regulated members of a salivary protein multigene family. J Biol Chem. 1992;267:2679-87 pubmed
    ..These findings indicate that rat SMG-A and PSP arise from alternatively regulated members of a multigene family. ..
  33. Yu Y, Hirsch J. An essential gene pair in Saccharomyces cerevisiae with a potential role in mating. DNA Cell Biol. 1995;14:411-8 pubmed
    ..Because mating efficiency was increased by extra copies of the SSF genes and decreased by elimination of the gene products, it is likely that these genes play a role in mating as well as in an essential function. ..
  34. Scanlan M, Raj B, Calvo B, Garin Chesa P, Sanz Moncasi M, Healey J, et al. Molecular cloning of fibroblast activation protein alpha, a member of the serine protease family selectively expressed in stromal fibroblasts of epithelial cancers. Proc Natl Acad Sci U S A. 1994;91:5657-61 pubmed
  35. Bai C, Li Z, Tolias P. Developmental characterization of a Drosophila RNA-binding protein homologous to the human systemic lupus erythematosus-associated La/SS-B autoantigen. Mol Cell Biol. 1994;14:5123-9 pubmed
    ..These results suggest that D-La may play a more specialized role during fly development as opposed to a rather general role inferred by its homology to La proteins from other organisms. ..
  36. Rosenfeld M, Wong E, Dalmau J, Manley G, Egan D, Posner J, et al. Sera from patients with Lambert-Eaton myasthenic syndrome recognize the beta-subunit of Ca2+ channel complexes. Ann N Y Acad Sci. 1993;681:408-11 pubmed
  37. Sherwood P, Tsang S, Osley M. Characterization of HIR1 and HIR2, two genes required for regulation of histone gene transcription in Saccharomyces cerevisiae. Mol Cell Biol. 1993;13:28-38 pubmed
    ..The sequence of the HIR2 gene predicts a protein of 98 kDa. Both gene products contain nuclear targeting signals, and the Hir2 protein is localized in the nucleus. ..
  38. Ogata I, Auster A, Matsui A, Greenwel P, Geerts A, D Amico T, et al. Up-regulation of type I procollagen C-proteinase enhancer protein messenger RNA in rats with CCl4-induced liver fibrosis. Hepatology. 1997;26:611-7 pubmed
    ..These data suggest that PCPE may play an important role in the processing of type I collagen during liver fibrogenesis, and that TGF-beta1 and TNF-alpha regulate its expression. ..
  39. Srivastava S, Osten P, Vilim F, Khatri L, Inman G, States B, et al. Novel anchorage of GluR2/3 to the postsynaptic density by the AMPA receptor-binding protein ABP. Neuron. 1998;21:581-91 pubmed
    ..ABP and GRIP also form homo- and heteromultimers through PDZ-PDZ interactions but do not bind PSD-95. We suggest that the ABP/GRIP and PSD-95 families form distinct scaffolds that anchor, respectively, AMPA and NMDA receptors. ..
  40. Martin Serrano J, Li K, Bieniasz P. Cyclin T1 expression is mediated by a complex and constitutively active promoter and does not limit human immunodeficiency virus type 1 Tat function in unstimulated primary lymphocytes. J Virol. 2002;76:208-19 pubmed
    ..These results strongly suggest that CycT1 expression levels in unstimulated primary lymphocytes do not profoundly limit HIV-1 gene expression or provide an adequate mechanistic explanation for proviral latency in vivo. ..
  41. Romanowski M, Bonanno J, Burley S. Crystal structure of the Streptococcus pneumoniae phosphomevalonate kinase, a member of the GHMP kinase superfamily. Proteins. 2002;47:568-71 pubmed publisher
  42. Davey M, Fang L, McInerney P, Georgescu R, O Donnell M. The DnaC helicase loader is a dual ATP/ADP switch protein. EMBO J. 2002;21:3148-59 pubmed
    ..This dual switching process may underlie the sensitivity of DnaB to even small fluctuations in DnaC levels. ..
  43. Hu J, Liu J, Ghirlando R, Saltiel A, Hubbard S. Structural basis for recruitment of the adaptor protein APS to the activated insulin receptor. Mol Cell. 2003;12:1379-89 pubmed
    ..This structure provides a molecular visualization of one of the initial downstream recruitment events following insulin activation of its dimeric receptor. ..
  44. Lambert L, Wei Y, Schirf V, Demeler B, Werner M. T4 AsiA blocks DNA recognition by remodeling sigma70 region 4. EMBO J. 2004;23:2952-62 pubmed publisher
    ..AsiA simultaneously occupies the surface of region 4 that ordinarily contacts core RNA polymerase (RNAP), suggesting that an AsiA-bound sigma70 may also undergo conformational changes in the context of the RNAP holoenzyme...
  45. Mhatre A, Li Y, Feng L, Gasperin A, Lalwani A. SDHB, SDHC, and SDHD mutation screen in sporadic and familial head and neck paragangliomas. Clin Genet. 2004;66:461-6 pubmed
    ..The etiology of sporadic PGL remains to be elucidated. ..
  46. Reverter D, Wu K, Erdene T, Pan Z, Wilkinson K, Lima C. Structure of a complex between Nedd8 and the Ulp/Senp protease family member Den1. J Mol Biol. 2005;345:141-51 pubmed
  47. Rao K, Bonanno J, Burley S, Swaminathan S. Crystal structure of glycerophosphodiester phosphodiesterase from Agrobacterium tumefaciens by SAD with a large asymmetric unit. Proteins. 2006;65:514-8 pubmed
  48. Xiang S, Usunow G, Lange G, Busch M, Tong L. Crystal structure of 1-deoxy-D-xylulose 5-phosphate synthase, a crucial enzyme for isoprenoids biosynthesis. J Biol Chem. 2007;282:2676-82 pubmed publisher
    ..The structures identify residues that may have important roles in catalysis, which have been confirmed by our mutagenesis studies...
  49. Wang L, Nandakumar J, Schwer B, Shuman S. The C-terminal domain of T4 RNA ligase 1 confers specificity for tRNA repair. RNA. 2007;13:1235-44 pubmed
    ..Alanine scanning of the N domain identified Ser103, Leu104, Lys117, and Ser118 as important for pRNA ligation in vitro and tRNA repair in vivo. ..
  50. Mofunanya A, Li F, Hsieh J, Takemaru K. Chibby forms a homodimer through a heptad repeat of leucine residues in its C-terminal coiled-coil motif. BMC Mol Biol. 2009;10:41 pubmed publisher
    ..Although monomeric Cby is sufficient to bind to beta-catenin and block beta-catenin-mediated transcriptional activation, homodimer formation of Cby is indispensable for its efficient nuclear import. ..
  51. Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, et al. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell. 2010;141:129-41 pubmed publisher
    ..The precise mapping of binding sites across the transcriptome will be critical to the interpretation of the rapidly emerging data on genetic variation between individuals and how these variations contribute to complex genetic diseases. ..
  52. Little D. DNA barcode sequence identification incorporating taxonomic hierarchy and within taxon variability. PLoS ONE. 2011;6:e20552 pubmed publisher
    ..g. mini-barcode queries against a full-length barcode database). BRONX consistently produced better identifications at the genus-level for all query types. ..
  53. Bass A, Lawrence M, Brace L, Ramos A, Drier Y, Cibulskis K, et al. Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion. Nat Genet. 2011;43:964-968 pubmed publisher
    ..This study shows previously unidentified levels of genomic rearrangements in colorectal carcinoma that can lead to essential gene fusions and other oncogenic events. ..
  54. Lelli K, Noro B, Mann R. Variable motif utilization in homeotic selector (Hox)-cofactor complex formation controls specificity. Proc Natl Acad Sci U S A. 2011;108:21122-7 pubmed publisher
    ..We propose that using different binding mechanisms with the same cofactor may be one strategy to achieve functional specificity in vivo. ..
  55. Evering T, Mehandru S, Racz P, Tenner Racz K, Poles M, Figueroa A, et al. Absence of HIV-1 evolution in the gut-associated lymphoid tissue from patients on combination antiviral therapy initiated during primary infection. PLoS Pathog. 2012;8:e1002506 pubmed publisher
  56. Doitsidou M, Flames N, Topalidou I, Abe N, Felton T, Remesal L, et al. A combinatorial regulatory signature controls terminal differentiation of the dopaminergic nervous system in C. elegans. Genes Dev. 2013;27:1391-405 pubmed publisher
    ..Dopaminergic neurons in the mouse olfactory bulb express a similar combinatorial transcription factor collective of Ets/Dlx/Pbx factors, suggesting deep phylogenetic conservation of dopaminergic regulatory programs. ..
  57. Romere C, Duerrschmid C, Bournat J, Constable P, Jain M, Xia F, et al. Asprosin, a Fasting-Induced Glucogenic Protein Hormone. Cell. 2016;165:566-79 pubmed publisher
    ..Asprosin represents a glucogenic protein hormone, and therapeutically targeting it may be beneficial in type II diabetes and metabolic syndrome. ..
  58. Cotter P, Baumann M, Bishop D. Enzymatic defect in "X-linked" sideroblastic anemia: molecular evidence for erythroid delta-aminolevulinate synthase deficiency. Proc Natl Acad Sci U S A. 1992;89:4028-32 pubmed
    ..The amino acid substitution occurred in the exon containing the putative pyridoxal 5'-phosphate binding site and may account for the reduced ability of the cofactor to catalyze the formation of delta-aminolevulinic acid. ..
  59. Wu X, Knudsen B, Feller S, Zheng J, Sali A, Cowburn D, et al. Structural basis for the specific interaction of lysine-containing proline-rich peptides with the N-terminal SH3 domain of c-Crk. Structure. 1995;3:215-26 pubmed
    ..The c-Crk SH3 domain engages in an unusual lysine-specific interaction that is rarely seen in protein structures, and which appears to be a key determinant of its unique ability to bind the C3G peptides with high affinity. ..
  60. Cirillo J, Weisbrod T, Pascopella L, Bloom B, Jacobs W. Isolation and characterization of the aspartokinase and aspartate semialdehyde dehydrogenase operon from mycobacteria. Mol Microbiol. 1994;11:629-39 pubmed
    ..Primer extension analysis revealed that the only transcriptional start in this region is found 5' of the ask gene. This observation indicates that the mycobacterial ask and asd genes are in an operon...
  61. Wu C, Xu W, Kozak C, Desnick R. Mouse uroporphyrinogen decarboxylase: cDNA cloning, expression, and mapping. Mamm Genome. 1996;7:349-52 pubmed
    ..The availability of the mouse URO-decarboxylase should facilitate studies of the structure and organization of the mouse genomic sequence and the development of a mouse model of this inherited porphyria. ..
  62. Yoder J, Yen R, Vertino P, Bestor T, Baylin S. New 5' regions of the murine and human genes for DNA (cytosine-5)-methyltransferase. J Biol Chem. 1996;271:31092-7 pubmed
    ..Tanigawa, G., and Szyf, M. (1992) J. Biol. Chem. 267, 7368-7377) actually lies in an intron that is more than 5 kilobases downstream of the transcription start sites. ..
  63. Vega Saenz de Miera E, Rudy B, Sugimori M, Llin s R. Molecular characterization of the sodium channel subunits expressed in mammalian cerebellar Purkinje cells. Proc Natl Acad Sci U S A. 1997;94:7059-64 pubmed
    ..Conversely, jolting mice with a mutated Scn8a message demonstrates PC abnormalities in rapid, simple spike generation, linking CerIII to the persistent sodium current...
  64. Allen P, Ouimet C, Greengard P. Spinophilin, a novel protein phosphatase 1 binding protein localized to dendritic spines. Proc Natl Acad Sci U S A. 1997;94:9956-61 pubmed
    ..g., neurotransmitter receptors, which mediate the regulation of synaptic function by PP1. ..
  65. Wong B, Rho J, Arron J, Robinson E, Orlinick J, Chao M, et al. TRANCE is a novel ligand of the tumor necrosis factor receptor family that activates c-Jun N-terminal kinase in T cells. J Biol Chem. 1997;272:25190-4 pubmed
    ..These results suggest a role for this TNF-related ligand in the regulation of the T cell-dependent immune response. ..
  66. Kollmar R, Montgomery L, Fak J, Henry L, Hudspeth A. Predominance of the alpha1D subunit in L-type voltage-gated Ca2+ channels of hair cells in the chicken's cochlea. Proc Natl Acad Sci U S A. 1997;94:14883-8 pubmed
    ..We conclude that most, if not all, voltage-gated Ca2+ channels in hair cells contain an alpha1D subunit. Furthermore, we propose that the alpha1D subunit plays a hitherto undocumented role at tonic synapses. ..
  67. Bai C, Tolias P. Drosophila clipper/CPSF 30K is a post-transcriptionally regulated nuclear protein that binds RNA containing GC clusters. Nucleic Acids Res. 1998;26:1597-604 pubmed
    ..These results support the existence of a distinct mechanism controlling eukaryotic gene expression through the regulated processing of pre-mRNAs in the nucleus. ..
  68. Santagata S, Bhattacharyya D, Wang F, Singha N, Hodtsev A, Spanopoulou E. Molecular cloning and characterization of a mouse homolog of bacterial ClpX, a novel mammalian class II member of the Hsp100/Clp chaperone family. J Biol Chem. 1999;274:16311-9 pubmed
    ..Our results thus suggest that murine ClpX acts as a tissue-specific mammalian mitochondrial chaperone that may play a role in mitochondrial protein homeostasis. ..
  69. Wex T, Levy B, Wex H, Bromme D. Human cathepsins W and F form a new subgroup of cathepsins that is evolutionary separated from the cathepsin B- and L-like cysteine proteases. Adv Exp Med Biol. 2000;477:271-80 pubmed
  70. Fortin G, Symington L. Mutations in yeast Rad51 that partially bypass the requirement for Rad55 and Rad57 in DNA repair by increasing the stability of Rad51-DNA complexes. EMBO J. 2002;21:3160-70 pubmed
  71. Alexov E. Numerical calculations of the pH of maximal protein stability. The effect of the sequence composition and three-dimensional structure. Eur J Biochem. 2004;271:173-85 pubmed
    ..It was shown that a protein that provides a favorable electrostatic environment for acids and disfavors the bases tends to have high optimum pH and vice versa. ..
  72. Kobayashi M, Buck J, Levin L. Conservation of functional domain structure in bicarbonate-regulated "soluble" adenylyl cyclases in bacteria and eukaryotes. Dev Genes Evol. 2004;214:503-9 pubmed publisher
    ..These data extend the family of organisms possessing bicarbonate-responsive ACs to numerous phyla within the bacterial and eukaryotic kingdoms...
  73. Lee M, She Y, Soskis M, Borella C, Gardner J, Hayes P, et al. Human mitochondrial peptide deformylase, a new anticancer target of actinonin-based antibiotics. J Clin Invest. 2004;114:1107-16 pubmed
    ..We conclude that HsPDF is a new human mitochondrial enzyme that may provide a novel selective target for anticancer therapy by use of actinonin-based antibiotics. ..
  74. Heilmann I, Mekhedov S, King B, Browse J, Shanklin J. Identification of the Arabidopsis palmitoyl-monogalactosyldiacylglycerol delta7-desaturase gene FAD5, and effects of plastidial retargeting of Arabidopsis desaturases on the fad5 mutant phenotype. Plant Physiol. 2004;136:4237-45 pubmed
    ..Tight correlation between leaf 16:3Delta(7,10,13) levels and chlorophyll content suggests a role for plastidial fatty acid desaturases in thylakoid formation. ..
  75. Seiffert E. A new estimate of afrotherian phylogeny based on simultaneous analysis of genomic, morphological, and fossil evidence. BMC Evol Biol. 2007;7:224 pubmed
  76. Benarroch D, Smith P, Shuman S. Characterization of a trifunctional mimivirus mRNA capping enzyme and crystal structure of the RNA triphosphatase domain. Structure. 2008;16:501-12 pubmed publisher
    ..The mimivirus TTM-type RTPase-GTase fusion resembles the capping enzymes of amoebae, providing evidence that the ancestral large DNA virus acquired its capping enzyme from a unicellular host. ..
  77. Desnick J, Kim J, He X, Wasserstein M, Simonaro C, Schuchman E. Identification and characterization of eight novel SMPD1 mutations causing types A and B Niemann-Pick disease. Mol Med. 2010;16:316-21 pubmed publisher
    ..1564A>G (p.N522S) and c.1575G>C (p.Q525H)] that expressed >5% residual ASM activity. Thus, these new mutations provide novel genotype/phenotype correlations and further document the genetic heterogeneity in types A and B NPD. ..
  78. Michta M, Hopcraft S, Narbus C, Kratovac Z, Israelow B, Sourisseau M, et al. Species-specific regions of occludin required by hepatitis C virus for cell entry. J Virol. 2010;84:11696-708 pubmed publisher
    ..Furthermore, this critical region of EC2 is flanked by two conserved cysteine residues that are essential for HCV cell entry, suggesting that a subdomain of EC2 may be defined by a disulfide bond. ..
  79. Bai Y, Srivastava S, Chang J, Manley J, Tong L. Structural basis for dimerization and activity of human PAPD1, a noncanonical poly(A) polymerase. Mol Cell. 2011;41:311-20 pubmed publisher
    ..Surprisingly, our mutagenesis and biochemical studies show that dimerization is required for the catalytic activity of PAPD1. ..
  80. Ma W, Rai V, Hudson B, Song F, Schmidt A, Barile G. RAGE binds C1q and enhances C1q-mediated phagocytosis. Cell Immunol. 2012;274:72-82 pubmed publisher
    ..C1q induced U937 cell adhesion and phagocytosis was inhibited by antibodies to RAGE or Mac-1. These data link C1q and RAGE to the recruitment of leukocytes and phagocytosis of C1q-coated material. ..
  81. Du J, Zhong X, Bernatavichute Y, Stroud H, Feng S, Caro E, et al. Dual binding of chromomethylase domains to H3K9me2-containing nucleosomes directs DNA methylation in plants. Cell. 2012;151:167-80 pubmed publisher
    ..Our study establishes dual recognition of H3K9me2 marks by BAH and chromo domains and reveals a distinct mechanism of interplay between DNA methylation and histone modification. ..
  82. Cho Park P, Steller H. Proteasome regulation by ADP-ribosylation. Cell. 2013;153:614-27 pubmed publisher
    ..These results unravel a mechanism of proteasome regulation that can be targeted with existing small-molecule inhibitors. ..
  83. Li J, Aderem A. MacMARCKS, a novel member of the MARCKS family of protein kinase C substrates. Cell. 1992;70:791-801 pubmed
  84. Mohammadi M, Schlessinger J, Hubbard S. Structure of the FGF receptor tyrosine kinase domain reveals a novel autoinhibitory mechanism. Cell. 1996;86:577-87 pubmed
    ..Finally, the structure provides a basis for rationalizing the effects of kinase mutations in FGF receptors that lead to developmental disorders in nematodes and humans. ..
  85. Takagaki Y, Manley J. Complex protein interactions within the human polyadenylation machinery identify a novel component. Mol Cell Biol. 2000;20:1515-25 pubmed
    ..These and other data suggest that symplekin may function in assembly of the polyadenylation machinery. ..
  86. Liu Z, Peng J, Mo R, Hui C, Huang C. Rh type B glycoprotein is a new member of the Rh superfamily and a putative ammonia transporter in mammals. J Biol Chem. 2001;276:1424-33 pubmed
    ..Phylogenetic clustering, tissue-specific expression, and plasma membrane location suggest that RhBG homologous proteins are the long sought major ammonium transporters in mammalians. ..
  87. Ghose R, Shekhtman A, Goger M, Ji H, Cowburn D. A novel, specific interaction involving the Csk SH3 domain and its natural ligand. Nat Struct Biol. 2001;8:998-1004 pubmed
    ..NMR relaxation analysis suggests that Csk-SH3 has different dynamic properties in the various subsites important for peptide recognition. ..
  88. Miller I, Hatzivassiliou G, Cattoretti G, Mendelsohn C, Dalla Favera R. IRTAs: a new family of immunoglobulinlike receptors differentially expressed in B cells. Blood. 2002;99:2662-9 pubmed
    ..These structural features suggest that the IRTA receptors may play a role in regulating activation of normal B cells and possibly in the development of neoplasia. ..
  89. Iwahori A, Fraidenraich D, Basilico C. A conserved enhancer element that drives FGF4 gene expression in the embryonic myotomes is synergistically activated by GATA and bHLH proteins. Dev Biol. 2004;270:525-37 pubmed
    ..However, expression of Fgf4 in the myotomes or AER of murine embryos does not appear to be essential for muscle or limb development. ..
  90. Lee J, Yi L, Li J, Schweitzer K, Borgmann M, Naumann M, et al. Crystal structure and versatile functional roles of the COP9 signalosome subunit 1. Proc Natl Acad Sci U S A. 2013;110:11845-50 pubmed publisher
    ..Therefore, the CSN complex uses multiple mechanisms to hinder NF-?B activation, a principle likely to hold true for its regulation of many other targets and pathways...
  91. Grumet M, Mauro V, Burgoon M, Edelman G, Cunningham B. Structure of a new nervous system glycoprotein, Nr-CAM, and its relationship to subgroups of neural cell adhesion molecules. J Cell Biol. 1991;113:1399-412 pubmed
    ..abstract truncated at 400 words) ..
  92. Doukhan L, Predich M, Nair G, Dussurget O, Mandic Mulec I, Cole S, et al. Genomic organization of the mycobacterial sigma gene cluster. Gene. 1995;165:67-70 pubmed
    ..orfX, which has an unknown function, is located between mysA and mysB. The other ORF, located downstream from mysB, encodes a homolog of DtxR, the iron regulatory protein from Corynebacterium diphtheriae (Cd)...