Experts and Doctors on binding sites in Baltimore, Maryland, United States


Locale: Baltimore, Maryland, United States
Topic: binding sites

Top Publications

  1. Zhu X, Evans J. Analysis of the roles of RGD-binding integrins, alpha(4)/alpha(9) integrins, alpha(6) integrins, and CD9 in the interaction of the fertilin beta (ADAM2) disintegrin domain with the mouse egg membrane. Biol Reprod. 2002;66:1193-202 pubmed
  2. Gnatt A. Elongation by RNA polymerase II: structure-function relationship. Biochim Biophys Acta. 2002;1577:175-90 pubmed
    ..Structural studies of RNA polymerases are described below within the context of the process of transcription elongation, its regulation and function. ..
  3. Chen J, Taipale J, Young K, Maiti T, Beachy P. Small molecule modulation of Smoothened activity. Proc Natl Acad Sci U S A. 2002;99:14071-6 pubmed
    ..The mechanistic differences between the Smo antagonists may be useful in the therapeutic manipulation of Hh signaling. ..
  4. Datta S, Larkin C, Schildbach J. Structural insights into single-stranded DNA binding and cleavage by F factor TraI. Structure. 2003;11:1369-79 pubmed
    ..The full positive charge on the Mg(2+) and the architecture of the active site suggest multiple roles for Mg(2+) in DNA cleavage...
  5. Griffith K, Wolf R. Genetic evidence for pre-recruitment as the mechanism of transcription activation by SoxS of Escherichia coli: the dominance of DNA binding mutations of SoxS. J Mol Biol. 2004;344:1-10 pubmed
    ..Lastly, with the SoxRS system as an example, we discuss the physiological requirement for stringent regulation of transcriptional activators that function by pre-recruitment. ..
  6. Amanchy R, Kalume D, Iwahori A, Zhong J, Pandey A. Phosphoproteome analysis of HeLa cells using stable isotope labeling with amino acids in cell culture (SILAC). J Proteome Res. 2005;4:1661-71 pubmed
    ..Because of its sensitivity and general applicability, our approach will be useful for investigating signaling pathways in a global fashion and for using phosphoproteomics for functional annotation of genomes. ..
  7. Brunelle J, Youngman E, Sharma D, Green R. The interaction between C75 of tRNA and the A loop of the ribosome stimulates peptidyl transferase activity. RNA. 2006;12:33-9 pubmed
  8. Thickman K, Swenson M, Kabogo J, Gryczynski Z, Kielkopf C. Multiple U2AF65 binding sites within SF3b155: thermodynamic and spectroscopic characterization of protein-protein interactions among pre-mRNA splicing factors. J Mol Biol. 2006;356:664-83 pubmed
    ..Comparison of the SF3b155 sites defines an (R/K)nXRW(DE) consensus sequence for predicting U2AF65-UHM ligands from genomic sequences, where parentheses denote residues that contribute to, but are not required for binding. ..
  9. Fan J, Zhan M, Shen J, Martindale J, Yang X, Kawai T, et al. En masse nascent transcription analysis to elucidate regulatory transcription factors. Nucleic Acids Res. 2006;34:1492-500 pubmed
    ..The strategies described here permit the successful identification of the TFs responsible for implementing adaptive gene expression programs in response to cellular stimulation. ..

More Information

Publications235 found, 100 shown here

  1. Priyakumar U, MacKerell A. Role of the adenine ligand on the stabilization of the secondary and tertiary interactions in the adenine riboswitch. J Mol Biol. 2010;396:1422-38 pubmed publisher
    ..The possibility of methodological artifacts and force-field inaccuracies impacting the present observations was checked by additional molecular dynamics simulations in the presence of 2,6-diaminopurine and in the crystal environment. ..
  2. Krout D, Pramod A, Dahal R, Tomlinson M, Sharma B, Foster J, et al. Inhibitor mechanisms in the S1 binding site of the dopamine transporter defined by multi-site molecular tethering of photoactive cocaine analogs. Biochem Pharmacol. 2017;142:204-215 pubmed publisher
    ..These findings set a structure-function baseline for comparison of typical and atypical DAT inhibitors and how their interactions with DAT could lead to the loss of cocaine-like behaviors. ..
  3. Li R, Bianchet M, Talalay P, Amzel L. The three-dimensional structure of NAD(P)H:quinone reductase, a flavoprotein involved in cancer chemoprotection and chemotherapy: mechanism of the two-electron reduction. Proc Natl Acad Sci U S A. 1995;92:8846-50 pubmed
  4. Garvie C, Hagman J, Wolberger C. Structural studies of Ets-1/Pax5 complex formation on DNA. Mol Cell. 2001;8:1267-76 pubmed
    ..The ability of one protein to alter the DNA sequence-specific contacts of another provides a general mechanism for combinatorial regulation of transcription. ..
  5. Kenedy A, Cohen K, Loveys D, Kato G, Dang C. Identification and characterization of the novel centrosome-associated protein CCCAP. Gene. 2003;303:35-46 pubmed
    ..We further discovered that the C-terminal portion of hCCCAP is identical to the human colon cancer autoantigen NY-CO-8 (Human Gene Nomenclature symbol SDCCAG8). ..
  6. Vazquez F, Matsuoka S, Sellers W, Yanagida T, Ueda M, Devreotes P. Tumor suppressor PTEN acts through dynamic interaction with the plasma membrane. Proc Natl Acad Sci U S A. 2006;103:3633-8 pubmed
    ..The dynamic membrane association could be modulated temporally or spatially to alter PTEN activity in specific physiological situations and could have important implications for tumor suppressor function. ..
  7. Brown D, Collins K. Dihydroorotase from Escherichia coli. Substitution of Co(II) for the active site Zn(II). J Biol Chem. 1991;266:1597-604 pubmed
    ..5 implicates an active site thiol group as a ligand to the metal ion. The spectrum is inconsistent with tetrahedral coordination of the active site metal ion and is most consistent with a pentacoordinate structure. ..
  8. Yellen G, Jurman M, Abramson T, MacKinnon R. Mutations affecting internal TEA blockade identify the probable pore-forming region of a K+ channel. Science. 1991;251:939-42 pubmed
    ..Further, a stretch of only eight amino acid residues must traverse 80 percent of the transmembrane electric potential difference. ..
  9. Wood T, Griffith K, Fawcett W, Jair K, Schneider T, Wolf R. Interdependence of the position and orientation of SoxS binding sites in the transcriptional activation of the class I subset of Escherichia coli superoxide-inducible promoters. Mol Microbiol. 1999;34:414-30 pubmed
    ..Analysis by molecular information theory of DNA sequences known to bind SoxS in vitro is consistent with the opposite orientation of the zwf and fpr soxboxes. ..
  10. Chen J, Opperman K, Greider C. A critical stem-loop structure in the CR4-CR5 domain of mammalian telomerase RNA. Nucleic Acids Res. 2002;30:592-7 pubmed
    ..1 loop, allowed RNA-protein binding but significantly impaired telomerase activity. These data establish the presence of the P6.1 stem-loop and its importance for the assembly and enzymatic activity of the mammalian telomerase complex. ..
  11. Li H, Nicholas J. Identification of amino acid residues of gp130 signal transducer and gp80 alpha receptor subunit that are involved in ligand binding and signaling by human herpesvirus 8-encoded interleukin-6. J Virol. 2002;76:5627-36 pubmed
  12. Cha B, Kim J, Hut H, Hogema B, Nadarja J, Zizak M, et al. cGMP inhibition of Na+/H+ antiporter 3 (NHE3) requires PDZ domain adapter NHERF2, a broad specificity protein kinase G-anchoring protein. J Biol Chem. 2005;280:16642-50 pubmed
  13. Dohm J, Hsu M, Hwu J, Huang R, Moudrianakis E, Lattman E, et al. Influence of ions, hydration, and the transcriptional inhibitor P4N on the conformations of the Sp1 binding site. J Mol Biol. 2005;349:731-44 pubmed
    ..Although P4N was not visualized unambiguously in the electron density maps, the effect of the drug is evident from significant differences in the lattice constants, crystal packing, and overall conformation of the structure. ..
  14. Molina H, Horn D, Tang N, Mathivanan S, Pandey A. Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry. Proc Natl Acad Sci U S A. 2007;104:2199-204 pubmed
    ..Overall, ETD is an excellent method for localization of phosphorylation sites and should be an integral component of any strategy for comprehensive phosphorylation analysis. ..
  15. Ye B, Yu W, Thomas G, Huganir R. GRASP-1 is a neuronal scaffold protein for the JNK signaling pathway. FEBS Lett. 2007;581:4403-10 pubmed
    ..These results suggest that GRASP-1 serves as a scaffold protein to facilitate MEKK-1 activation of JNK signaling in neurons. ..
  16. Soper T, Mandin P, Majdalani N, Gottesman S, Woodson S. Positive regulation by small RNAs and the role of Hfq. Proc Natl Acad Sci U S A. 2010;107:9602-7 pubmed publisher
    ..These studies demonstrate that binding of Hfq to the rpoS mRNA is critical for sRNA regulation under normal conditions, but if the stability of the sRNA*mRNA complex is sufficiently high, the requirement for Hfq can be bypassed. ..
  17. Mulepati S, Bailey S. Structural and biochemical analysis of nuclease domain of clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein 3 (Cas3). J Biol Chem. 2011;286:31896-903 pubmed publisher
    ..Overall, these results provide a framework for understanding the role of Cas3 in the CRISPR system. ..
  18. Willis C, Oashi T, Busby B, MacKerell A, Bloch R. Hydrophobic residues in small ankyrin 1 participate in binding to obscurin. Mol Membr Biol. 2012;29:36-51 pubmed publisher
    ..Our results suggest that hydrophobic interactions contribute to the higher affinity of Obsc????????? for sAnk1 and to the dominant role exhibited by this sequence in binding. ..
  19. Xu Q, Wang Y, Dabdoub A, Smallwood P, Williams J, Woods C, et al. Vascular development in the retina and inner ear: control by Norrin and Frizzled-4, a high-affinity ligand-receptor pair. Cell. 2004;116:883-95 pubmed
    ..These data define a Norrin-Fz4 signaling system that plays a central role in vascular development in the eye and ear, and they indicate that ligands unrelated to Wnts can act through Fz receptors. ..
  20. Sun B, Hursh D, Jackson D, Beachy P. Ultrabithorax protein is necessary but not sufficient for full activation of decapentaplegic expression in the visceral mesoderm. EMBO J. 1995;14:520-35 pubmed
    ..In addition, a distinct regulatory mode not directly involving Ubx protein also appears to contribute to PS7-specific expression. ..
  21. Carra J, Schleif R. Formation of AraC-DNA sandwiches. Nucleic Acids Res. 1993;21:435-8 pubmed
    ..This behavior is consistent with the protein's ability to form DNA loops by binding to separated half sites in the absence of arabinose and its preference for binding to adjacent half-sites in the presence of arabinose. ..
  22. Hwang C, Mandrup S, MacDougald O, Geiman D, Lane M. Transcriptional activation of the mouse obese (ob) gene by CCAAT/enhancer binding protein alpha. Proc Natl Acad Sci U S A. 1996;93:873-7 pubmed
    ..Mutation of this site blocked transactivation by C/EBP alpha. Taken together, these findings implicate C/EBP alpha as a transcriptional activator of the ob gene promoter and identify the functional C/EBP binding site in the promoter. ..
  23. Matheos D, Kingsbury T, Ahsan U, Cunningham K. Tcn1p/Crz1p, a calcineurin-dependent transcription factor that differentially regulates gene expression in Saccharomyces cerevisiae. Genes Dev. 1997;11:3445-58 pubmed
    ..We propose that different promoters are sensitive to variations in the strength of Ca2+ signals generated by these stimuli and to effects of other signaling pathways. ..
  24. Kim I, Mohammadi E, Huang R. Isolation and characterization of IPP, a novel human gene encoding an actin-binding, kelch-like protein. Gene. 1999;228:73-83 pubmed
    ..Cosedimentation assays performed with these domains expressed as glutathione S-transferase fusion proteins demonstrate an actin-binding activity mediated specifically by the kelch repeat domain of IPP. ..
  25. Zhang J, Clatterbuck R, Rigamonti D, Chang D, Dietz H. Interaction between krit1 and icap1alpha infers perturbation of integrin beta1-mediated angiogenesis in the pathogenesis of cerebral cavernous malformation. Hum Mol Genet. 2001;10:2953-60 pubmed
    ..Loss-of-function KRIT1 mutations, as observed in CCM1, would shift the balance with predicted consequences for endothelial cell performance during integrin beta1-dependent angiogenesis. ..
  26. Kerr C, Hanna W, Shaper J, Wright W. Characterization of zona pellucida glycoprotein 3 (ZP3) and ZP2 binding sites on acrosome-intact mouse sperm. Biol Reprod. 2002;66:1585-95 pubmed
    ..Finally, we demonstrate that extracellular calcium as well as capacitation and maturation of sperm are required for these sites to bind their respective ligands. ..
  27. Cheng W, Von Kobbe C, Opresko P, Fields K, Ren J, Kufe D, et al. Werner syndrome protein phosphorylation by abl tyrosine kinase regulates its activity and distribution. Mol Cell Biol. 2003;23:6385-95 pubmed
    ..These findings suggest a novel signaling pathway by which c-Abl mediates WRN nuclear localization and catalytic activities in response to DNA damage. ..
  28. Prigge S, Eipper B, Mains R, Amzel L. Dioxygen binds end-on to mononuclear copper in a precatalytic enzyme complex. Science. 2004;304:864-7 pubmed
    ..These insights may apply to other copper oxygen-activating enzymes, such as dopamine beta-monooxygenase, and to the design of biomimetic complexes. ..
  29. Zhang C, Williams E, Guo Y, Lum L, Beachy P. Extensive phosphorylation of Smoothened in Hedgehog pathway activation. Proc Natl Acad Sci U S A. 2004;101:17900-7 pubmed
    ..Our studies confirm and extend previous studies showing a positive effect for cAMP-dependent protein kinase and uncover a positive role for casein kinase 1alpha in Hh pathway activation. ..
  30. Chung J, Webster S. Binding sites of crustacean hyperglycemic hormone and its second messengers on gills and hindgut of the green shore crab, Carcinus maenas: a possible osmoregulatory role. Gen Comp Endocrinol. 2006;147:206-13 pubmed
    ..Thus, it seems likely that CHH is a pertinent neurohormone involved in osmoregulation, thus expanding its many functions as a pleiotropic hormone in crustaceans. ..
  31. Chen C, Saxena A, Simcoke W, Garboczi D, Pedersen P, Ko Y. Mitochondrial ATP synthase. Crystal structure of the catalytic F1 unit in a vanadate-induced transition-like state and implications for mechanism. J Biol Chem. 2006;281:13777-83 pubmed
    ..H., Bianchet, M., Amzel, L. M., and Pedersen, P. L. (1997) J. Biol. Chem. 272, 18875-18881; Ko, Y. H., Hong, S., and Pedersen, P. L. (1999) J. Biol. Chem. 274, 28853-28856). ..
  32. Li S, Wakefield J, Self S. A transdimensional Bayesian model for pattern recognition in DNA sequences. Biostatistics. 2008;9:668-85 pubmed publisher
    ..The performance is also compared to other computational methods, including 2 statistical approaches, AlignACE and multiple expectation maximization for motif elicitation, and 1 word numeration-based approach, yeast motif finder (YMF). ..
  33. Park E, Griffin D. The nsP3 macro domain is important for Sindbis virus replication in neurons and neurovirulence in mice. Virology. 2009;388:305-14 pubmed publisher
    ..The nsP3 macro domain is important for SINV replication and age-dependent susceptibility to encephalomyelitis. ..
  34. Lien C, Fang C, Huso D, Livak F, Lu R, Pitha P. Critical role of IRF-5 in regulation of B-cell differentiation. Proc Natl Acad Sci U S A. 2010;107:4664-8 pubmed publisher
  35. Stine Z, McGaughey D, Bessling S, Li S, McCallion A. Steroid hormone modulation of RET through two estrogen responsive enhancers in breast cancer. Hum Mol Genet. 2011;20:3746-56 pubmed publisher
    ..Taken collectively, these data suggest that RET transcription in breast cancer cells is modulated by E2 via ESR1 acting on multiple elements collectively. ..
  36. Ekker S, von Kessler D, Beachy P. Differential DNA sequence recognition is a determinant of specificity in homeotic gene action. EMBO J. 1992;11:4059-72 pubmed
    ..Such differences in DNA sequence recognition and target activation provide a biochemical basis for at least part of the biological specificity of homeotic gene action. ..
  37. Kofuji P, Wang J, Moss S, Huganir R, Burt D. Generation of two forms of the gamma-aminobutyric acidA receptor gamma 2-subunit in mice by alternative splicing. J Neurochem. 1991;56:713-5 pubmed
    ..The eight-amino-acid insertion encodes a potential consensus serine phosphorylation site for protein kinase C. These results suggest a novel mechanism for the regulation of the GABAA receptor by protein phosphorylation. ..
  38. Qu A, Leahy D. Crystal structure of the I-domain from the CD11a/CD18 (LFA-1, alpha L beta 2) integrin. Proc Natl Acad Sci U S A. 1995;92:10277-81 pubmed
  39. Craparo A, O Neill T, Gustafson T. Non-SH2 domains within insulin receptor substrate-1 and SHC mediate their phosphotyrosine-dependent interaction with the NPEY motif of the insulin-like growth factor I receptor. J Biol Chem. 1995;270:15639-43 pubmed
    ..We conclude that the interactions of SHC and IRS-1 with the IGFIR are similar to those which we have previously defined with the insulin receptor. ..
  40. Hosmane R, Hong M. How important is the N-3 sugar moiety in the tight-binding interaction of coformycin with adenosine deaminase?. Biochem Biophys Res Commun. 1997;236:88-93 pubmed
    ..The first two were both found to be competitive inhibitors of ADA with Ki's in the range of 10(-5) M, while the last one was inactive. ..
  41. Garland C, Tarien E, Nirmala R, Clark P, Rifkind J, Eichhorn G. Curvature of dinucleotide poised for formation of trinucleotide in transcription with Escherichia coli RNA polymerase. Biochemistry. 1999;38:3421-5 pubmed
    ..These studies show curvature to be a significant feature in the interaction between DNA template and RNA elongate even at the very beginning of transcription. ..
  42. Wong G, Zhu X, Prater C, Oh E, Evans J. Analysis of fertilin alpha (ADAM1)-mediated sperm-egg cell adhesion during fertilization and identification of an adhesion-mediating sequence in the disintegrin-like domain. J Biol Chem. 2001;276:24937-45 pubmed
    ..8, inhibited the binding of recombinant fertilin alpha to eggs in one type of binding assay, suggesting that, under certain conditions, fertilin alpha may interact with a KMC.8-sensitive binding site on the egg plasma membrane. ..
  43. Dann C, Hsieh J, Rattner A, Sharma D, Nathans J, Leahy D. Insights into Wnt binding and signalling from the structures of two Frizzled cysteine-rich domains. Nature. 2001;412:86-90 pubmed
    ..This work provides a framework for studies of homologous CRDs in proteins including muscle-specific kinase and Smoothened, a component of the Hedgehog signalling pathway. ..
  44. Larkin C, Datta S, Nezami A, Dohm J, Schildbach J. Crystallization and preliminary X-ray characterization of the relaxase domain of F factor TraI. Acta Crystallogr D Biol Crystallogr. 2003;59:1514-6 pubmed
    ..The resulting crystals were trigonal and diffracted to a resolution of 3.1 A or better using synchrotron radiation. ..
  45. Inesi G, Ma H, Lewis D, Xu C. Ca2+ occlusion and gating function of Glu309 in the ADP-fluoroaluminate analog of the Ca2+-ATPase phosphoenzyme intermediate. J Biol Chem. 2004;279:31629-37 pubmed
    ..Experiments on limited proteolysis reveal that a long range conformational change, involving displacement of headpiece domains and transmembrane helices, plays a mechanistic role. ..
  46. Sekine Aizawa Y, Huganir R. Imaging of receptor trafficking by using alpha-bungarotoxin-binding-site-tagged receptors. Proc Natl Acad Sci U S A. 2004;101:17114-9 pubmed
    ..The BBS tag is a flexible approach for labeling membrane proteins and studying their dynamic trafficking. ..
  47. DiVall S, Radovick S, Wolfe A. Egr-1 binds the GnRH promoter to mediate the increase in gene expression by insulin. Mol Cell Endocrinol. 2007;270:64-72 pubmed
    ..Thus, Egr-1 binds the GnRH promoter at a site between -67 and -76bp from the transcriptional start site to mediate the insulin-induced increase in GnRH gene transcription. ..
  48. Bouyain S, Leahy D. Structure-based mutagenesis of the substrate-recognition domain of Nrdp1/FLRF identifies the binding site for the receptor tyrosine kinase ErbB3. Protein Sci. 2007;16:654-61 pubmed
    ..This observation suggests that Nrdp1 uses a common binding site to recognize its targets in different species. ..
  49. Katayama H, Chung J. The specific binding sites of eyestalk- and pericardial organ-crustacean hyperglycaemic hormones (CHHs) in multiple tissues of the blue crab, Callinectes sapidus. J Exp Biol. 2009;212:542-9 pubmed publisher
  50. Gupta A, Cao W, Chellaiah M. Integrin ?v?3 and CD44 pathways in metastatic prostate cancer cells support osteoclastogenesis via a Runx2/Smad 5/receptor activator of NF-?B ligand signaling axis. Mol Cancer. 2012;11:66 pubmed publisher
    ..These observations imply a novel mechanistic insight into the role of these proteins in bone loss associated with bone metastases in patients with prostate cancer. ..
  51. Soisson S, MacDougall Shackleton B, Schleif R, Wolberger C. Structural basis for ligand-regulated oligomerization of AraC. Science. 1997;276:421-5 pubmed
    ..The ligand-gated oligomerization as seen in AraC provides the basis of a plausible mechanism for modulating the protein's DNA-looping properties. ..
  52. Harmer T, Wu M, Schleif R. The role of rigidity in DNA looping-unlooping by AraC. Proc Natl Acad Sci U S A. 2001;98:427-31 pubmed
    ..These results are consistent with the light switch mechanism for the action of AraC, refine the model, and extend the range of experimental tests to which it has been subjected. ..
  53. Bernardin F, Friedman A. AML1 stimulates G1 to S progression via its transactivation domain. Oncogene. 2002;21:3247-52 pubmed
    ..Inactivation of AML in acute leukemia is expected to slow proliferation unless additional genetic alterations co-exist which accelerate G1. ..
  54. Chufan E, De M, Eipper B, Mains R, Amzel L. Amidation of bioactive peptides: the structure of the lyase domain of the amidating enzyme. Structure. 2009;17:965-73 pubmed publisher
    ..A reaction mechanism is proposed based on this structural data and validated by biochemical analysis of site-directed PALcc mutants. ..
  55. Gao H, Wu X, Fossett N. Upregulation of the Drosophila Friend of GATA gene U-shaped by JAK/STAT signaling maintains lymph gland prohemocyte potency. Mol Cell Biol. 2009;29:6086-96 pubmed publisher
  56. Dixit A, Ray K, Black L. Compression of the DNA substrate by a viral packaging motor is supported by removal of intercalating dye during translocation. Proc Natl Acad Sci U S A. 2012;109:20419-24 pubmed publisher
  57. Egan S, Schleif R. DNA-dependent renaturation of an insoluble DNA binding protein. Identification of the RhaS binding site at rhaBAD. J Mol Biol. 1994;243:821-9 pubmed
  58. Carra J, Schleif R. Variation of half-site organization and DNA looping by AraC protein. EMBO J. 1993;12:35-44 pubmed
  59. He W, Craparo A, Zhu Y, O Neill T, Wang L, Pierce J, et al. Interaction of insulin receptor substrate-2 (IRS-2) with the insulin and insulin-like growth factor I receptors. Evidence for two distinct phosphotyrosine-dependent interaction domains within IRS-2. J Biol Chem. 1996;271:11641-5 pubmed
    ..Our findings suggest the existence of a previously unidentified phosphotyrosine-dependent binding domain within the central region of IRS-2. ..
  60. Mann H, Ladenheim B, Hirata H, Moran T, Cadet J. Differential toxic effects of methamphetamine (METH) and methylenedioxymethamphetamine (MDMA) in multidrug-resistant (mdr1a) knockout mice. Brain Res. 1997;769:340-6 pubmed
  61. Digel J, Abugo O, Kobayashi T, Gryczynski Z, Lakowicz J, Collins J. Calcium- and magnesium-dependent interactions between the C-terminus of troponin I and the N-terminal, regulatory domain of troponin C. Arch Biochem Biophys. 2001;387:243-9 pubmed
    ..Our results provide the first indica- tion that the C-terminus of TnI may play an important role in the regulation of vertebrate striated muscle through Ca2+-dependent interactions with the regula- tory domain of TnC. ..
  62. Wang Q, Friedman A. CCAAT/enhancer-binding proteins are required for granulopoiesis independent of their induction of the granulocyte colony-stimulating factor receptor. Blood. 2002;99:2776-85 pubmed
    ..One requisite activity may be activation of the C/EBPepsilon gene by C/EBPalpha, as either C/EBPalpha-ER or C/EBPbeta-ER rapidly elevated C/EBPepsilon RNA in 32D cl3 cells in the presence of cycloheximide but not actinomycin D. ..
  63. Li L, Lu A. The C-terminal domain of Escherichia coli MutY is involved in DNA binding and glycosylase activities. Nucleic Acids Res. 2003;31:3038-49 pubmed
    ..These results strongly support that the C-terminal domain of MutY is involved not only in 8-oxoG recognition, but also affects the binding and catalytic activities toward A/G mismatches. ..
  64. Southworth D, Green R. Ribosomal translocation: sparsomycin pushes the button. Curr Biol. 2003;13:R652-4 pubmed
  65. Gabelli S, Bianchet M, Azurmendi H, Xia Z, Sarawat V, Mildvan A, et al. Structure and mechanism of GDP-mannose glycosyl hydrolase, a Nudix enzyme that cleaves at carbon instead of phosphorus. Structure. 2004;12:927-35 pubmed
    ..Changes in the Nudix motif result in loss of binding of at least one Mg(2+) ion, and shortening of a loop by 6 residues shifts the catalytic base by approximately 10 A. ..
  66. Lin K, Luu A, Baidoo K, Hashemzadeh Gargari H, Chen M, Brenneman K, et al. A new high affinity technetium-99m-bombesin analogue with low abdominal accumulation. Bioconjug Chem. 2005;16:43-50 pubmed
    ..Scintigraphic images showed specific, high contrast delineation of prostate cancer PC-3 xenografts in SCID mice. Thus, the new peptide has a great potential for imaging BN/GRP receptor-positive cancers located even in the abdomen. ..
  67. Kuwahara I, Lillehoj E, Hisatsune A, Lu W, Isohama Y, Miyata T, et al. Neutrophil elastase stimulates MUC1 gene expression through increased Sp1 binding to the MUC1 promoter. Am J Physiol Lung Cell Mol Physiol. 2005;289:L355-62 pubmed
    ..These results indicate the increase in MUC1 gene transcription by NE is mediated through increase in Sp1 binding to -99/-90 segment of MUC1 promoter. ..
  68. Griffith K, Becker S, Wolf R. Characterization of TetD as a transcriptional activator of a subset of genes of the Escherichia coli SoxS/MarA/Rob regulon. Mol Microbiol. 2005;56:1103-17 pubmed
    ..Thus, we conclude that TetD is a bona fide member of the SoxS/MarA/Rob subfamily of positive regulators. ..
  69. Li Z, Hiasa H, DiGate R. Bacillus cereus DNA topoisomerase I and IIIalpha: purification, characterization and complementation of Escherichia coli TopoIII activity. Nucleic Acids Res. 2005;33:5415-25 pubmed
    ..Interestingly, bcTopo I and bcTopo IIIalpha are both able to compensate for the loss of ecTopo III in E.coli cells that lack ecTopo I. In contrast, ecTopo I cannot substitute for ecTopo III under these conditions. ..
  70. Zeller K, Zhao X, Lee C, Chiu K, Yao F, Yustein J, et al. Global mapping of c-Myc binding sites and target gene networks in human B cells. Proc Natl Acad Sci U S A. 2006;103:17834-9 pubmed
  71. Ananyeva N, Makogonenko Y, Sarafanov A, Pechik I, Gorlatova N, Radtke K, et al. Interaction of coagulation factor VIII with members of the low-density lipoprotein receptor family follows common mechanism and involves consensus residues within the A2 binding site 484-509. Blood Coagul Fibrinolysis. 2008;19:543-55 pubmed publisher
    ..We conclude that interaction of factor VIII with the members of the low-density lipoprotein receptor family follows the general mode, requires dissociation of factor VIII from von Willebrand factor, and is activation sensitive. ..
  72. Chiang P, Fortna R, Price D, Li T, Wong P. Specific domains in anterior pharynx-defective 1 determine its intramembrane interactions with nicastrin and presenilin. Neurobiol Aging. 2012;33:277-85 pubmed publisher
    ..We propose a model that identifies critical TMDs of Aph-1 for associations with Nct and PS for the stepwise assembly of ?-secretase components. ..
  73. Araki Y, Lin D, Huganir R. Plasma membrane insertion of the AMPA receptor GluA2 subunit is regulated by NSF binding and Q/R editing of the ion pore. Proc Natl Acad Sci U S A. 2010;107:11080-5 pubmed publisher
    ..These results demonstrate that the plasma membrane delivery of GluA2 containing AMPA receptors is regulated by its unique structural elements. ..
  74. Kallay L, McNickle A, Brennwald P, Hubbard A, Braiterman L. Scribble associates with two polarity proteins, Lgl2 and Vangl2, via distinct molecular domains. J Cell Biochem. 2006;99:647-64 pubmed
    ..J. Cell. Biochem. 99: 647-664, 2006. (c) 2006 Wiley-Liss, Inc. ..
  75. Faig M, Bianchet M, Winski S, Hargreaves R, Moody C, Hudnott A, et al. Structure-based development of anticancer drugs: complexes of NAD(P)H:quinone oxidoreductase 1 with chemotherapeutic quinones. Structure. 2001;9:659-67 pubmed
    ..These structural insights provide important clues for the optimization of chemotherapeutic compounds that utilize this reductive bioactivation pathway. ..
  76. Patel H, Vyas K, Savtchenko R, Roseman S. The monomer/dimer transition of enzyme I of the Escherichia coli phosphotransferase system. J Biol Chem. 2006;281:17570-8 pubmed
    ..C., Kapadia, G., McGuire, M., Carroll, L. J., Noh, S. J., and Dunaway-Mariano, D. (1996) Proc. Natl. Acad. Sci. U. S. A. 93, 2652-2657)), which brings the C-terminal domain with the two bound ligands close to the active site His(189). ..
  77. Boudreau R, Jiang P, Gilmore B, Spengler R, TIRABASSI R, Nelson J, et al. Transcriptome-wide discovery of microRNA binding sites in human brain. Neuron. 2014;81:294-305 pubmed publisher
    ..We demonstrate the utility of this map for exploring clinically relevant miRNA binding sites that may facilitate the translation of genetic studies of complex neuropsychiatric diseases into therapeutics. ..
  78. Deredge D, Li J, Johnson K, Wintrode P. Hydrogen/Deuterium Exchange Kinetics Demonstrate Long Range Allosteric Effects of Thumb Site 2 Inhibitors of Hepatitis C Viral RNA-dependent RNA Polymerase. J Biol Chem. 2016;291:10078-88 pubmed publisher
  79. Kartvelishvili E, Tworowski D, Vernon H, Moor N, Wang J, Wong L, et al. Kinetic and structural changes in HsmtPheRS, induced by pathogenic mutations in human FARS2. Protein Sci. 2017;26:1505-1516 pubmed publisher
    ..Using steady-state kinetic measurements of phenylalanine activation and tRNAPhe aminoacylation, we gained insight into the structural and kinetic effects of mitochondrial disease-related mutations in FARS2 gene. ..
  80. Lemas M, Fambrough D. Sequence analysis of DNA encoding an avian Na+,K(+)-ATPase beta 2-subunit. Biochim Biophys Acta. 1993;1149:339-42 pubmed
    ..Similar to other Na+,K(+)-ATPase beta 2-isoforms, the chicken beta 2-isoform mRNA is predominantly expressed in brain tissue. ..
  81. Shields J, Yang V. Identification of the DNA sequence that interacts with the gut-enriched Kr├╝ppel-like factor. Nucleic Acids Res. 1998;26:796-802 pubmed
    ..Our results establish GKLF as a sequence-specific transcription factor likely involved in regulation of expression of endogenous genes. ..
  82. Rangan P, Masquida B, Westhof E, Woodson S. Architecture and folding mechanism of the Azoarcus Group I Pre-tRNA. J Mol Biol. 2004;339:41-51 pubmed
    ..This could help prevent premature processing of the 5' and 3' ends of unspliced pre-tRNA...
  83. Woolf T, Tychko M. Simulations of fatty acid-binding proteins. II. Sites for discrimination of monounsaturated ligands. Biophys J. 1998;74:694-707 pubmed
    ..An importance scale, based on motional correlation and interaction energy between protein and ligand, is proposed, to help identify amino acids involved with the discrimination of ligand saturation state or geometric isomerization. ..
  84. Koculi E, Hyeon C, Thirumalai D, Woodson S. Charge density of divalent metal cations determines RNA stability. J Am Chem Soc. 2007;129:2676-82 pubmed
    ..The experimental and simulation results establish that RNA stability is largely determined by a combination of counterion charge and the packing efficiency of condensed cations that depends on the excluded volume of the cations. ..
  85. Mullen G, Serpersu E, Ferrin L, Loeb L, Mildvan A. Metal binding to DNA polymerase I, its large fragment, and two 3',5'-exonuclease mutants of the large fragment. J Biol Chem. 1990;265:14327-34 pubmed
    ..The essential divalent metal activator of the polymerase reaction requires the presence of the dNTP substrate for tight metal binding indicating that the bound substrate coordinates the metal.(ABSTRACT TRUNCATED AT 400 WORDS) ..
  86. Vartikar J, Draper D. S4-16 S ribosomal RNA complex. Binding constant measurements and specific recognition of a 460-nucleotide region. J Mol Biol. 1989;209:221-34 pubmed
    ..Mg2+ is not required to form the specific rRNA complex, at least under conditions which stabilize RNA structure (0.35 M-KCl, 5 degrees C). ..
  87. Qu A, Leahy D. The role of the divalent cation in the structure of the I domain from the CD11a/CD18 integrin. Structure. 1996;4:931-42 pubmed
    ..The cation-dependence of ligand binding thus indicates that the metal ion is either involved in direct interaction with ligand or required to promote a favorable quaternary arrangement of the integrin. ..
  88. Sesaki H, Jensen R. Ugo1p links the Fzo1p and Mgm1p GTPases for mitochondrial fusion. J Biol Chem. 2004;279:28298-303 pubmed
    ..Our data indicate that distinct regions of Ugo1p bind directly to Fzo1p and Mgm1p and thereby link these two GTPases during mitochondrial fusion. ..
  89. Qiu C, Lienhard S, Hynes N, Badache A, Leahy D. Memo is homologous to nonheme iron dioxygenases and binds an ErbB2-derived phosphopeptide in its vestigial active site. J Biol Chem. 2008;283:2734-40 pubmed
    ..Memo thus represents a new class of phosphotyrosine-binding protein. ..
  90. Crawford J, Vagstad A, Ehrlich K, Townsend C. Starter unit specificity directs genome mining of polyketide synthase pathways in fungi. Bioorg Chem. 2008;36:16-22 pubmed publisher
  91. Erill I, O Neill M. A reexamination of information theory-based methods for DNA-binding site identification. BMC Bioinformatics. 2009;10:57 pubmed publisher
  92. Wang J, Xu G, Gonzales V, Coonfield M, Fromholt D, Copeland N, et al. Fibrillar inclusions and motor neuron degeneration in transgenic mice expressing superoxide dismutase 1 with a disrupted copper-binding site. Neurobiol Dis. 2002;10:128-38 pubmed
    ..Overall, our data are consistent with the hypothesis that the aberrant folding/aggregation of mutant SOD1 is a prominent feature in the pathogenesis of motor neuron disease. ..