Experts and Doctors on molecular sequence data in Texas, United States

Summary

Locale: Texas, United States
Topic: molecular sequence data

Top Publications

  1. Ji H, Zhao R, Chen Z, Shetty S, Idell S, Matalon S. ? ENaC: a novel divergent amiloride-inhibitable sodium channel. Am J Physiol Lung Cell Mol Physiol. 2012;303:L1013-26 pubmed publisher
    ..Here, we review the progress of research on ? ENaC in genomics, biophysics, proteomics, physiology, pharmacology, and clinical medicine. ..
  2. Huang Q, Abdulrahman S, Yin J, Zwieb C. Systematic site-directed mutagenesis of human protein SRP54: interactions with signal recognition particle RNA and modes of signal peptide recognition. Biochemistry. 2002;41:11362-71 pubmed
    ..We propose that the SRP RNA and a small region centered at a bulky nonpolar amino acid residue at position 329 of protein SRP54 play a critical role in the SRP-dependent binding and release of signal peptides. ..
  3. Sakakibara Y, Yanagisawa K, Katafuchi J, Ringer D, Takami Y, Nakayama T, et al. Molecular cloning, expression, and characterization of novel human SULT1C sulfotransferases that catalyze the sulfonation of N-hydroxy-2-acetylaminofluorene. J Biol Chem. 1998;273:33929-35 pubmed
    ..The results provide a foundation for the investigation into the functional relevance of these new SULT1C sulfotransferases in different human tissues/organs...
  4. Evans A, Henning T, Gelsleichter J, Nunez B. Molecular classification of an elasmobranch angiotensin receptor: quantification of angiotensin receptor and natriuretic peptide receptor mRNAs in saltwater and freshwater populations of the Atlantic stingray. Comp Biochem Physiol B Biochem Mol Biol. 2010;157:423-31 pubmed publisher
    ..sabina AT. Molecular classification of the elasmobranch angiotensin receptor as an AT(1)-like protein provides fundamental insight into the evolution of the vertebrate RAS. ..
  5. Draper R, Hudson R, Hu T. Use of aminoglycoside antibiotics and related compounds to study ADP-ribosylation factor (ARF)/coatomer function in Golgi traffic. Methods Enzymol. 2001;329:372-9 pubmed
  6. Yang C, Szeliga J, Jordan J, Faske S, Sever Chroneos Z, Dorsett B, et al. Identification of the surfactant protein A receptor 210 as the unconventional myosin 18A. J Biol Chem. 2005;280:34447-57 pubmed
    ..Antibodies raised against the neck domain of MyoXVIIIA blocked the binding of SP-A to macrophages. Together, these findings indicate that MyoXVIIIA constitutes a novel receptor for SP-A. ..
  7. Morrison A, Shen X. Chromatin remodelling beyond transcription: the INO80 and SWR1 complexes. Nat Rev Mol Cell Biol. 2009;10:373-84 pubmed publisher
    ..This research reveals that INO80 and SWR1 ATP-dependent chromatin remodelling is an integral component of pathways that maintain genomic integrity. ..
  8. Miller M, Tanner J, Alpaugh M, Benedik M, Krause K. 2.1 A structure of Serratia endonuclease suggests a mechanism for binding to double-stranded DNA. Nat Struct Biol. 1994;1:461-8 pubmed
    ..Electrostatic calculations reveal a strongly polarized molecular surface and suggest that a cleft between this long helix and loop, near His 89, may contain the active site of the enzyme. ..
  9. Christensen L, Conti C, Fischer S, Vasquez K. Mutation frequencies in murine keratinocytes as a function of carcinogenic status. Mol Carcinog. 2004;40:122-33 pubmed
    ..These data suggested that a strong mutator phenotype was not required for progression to an advanced malignant phenotype in our model system. ..

More Information

Publications84

  1. Tang S, Bhatia B, Maldonado C, Yang P, Newman R, Liu J, et al. Evidence that arachidonate 15-lipoxygenase 2 is a negative cell cycle regulator in normal prostate epithelial cells. J Biol Chem. 2002;277:16189-201 pubmed
    ..Taken together, these results suggest that 15-LOX2 could be a suppressor of prostate cancer development, which functions by restricting cell cycle progression. ..
  2. Liu J, Zhao L, Xia T. The dynamic structural basis of differential enhancement of conformational stability by 5'- and 3'-dangling ends in RNA. Biochemistry. 2008;47:5962-75 pubmed publisher
    ..By resolving these populations that are dynamically exchanging on fast time scales, we elucidated the correlation between dynamic conformational distributions and thermodynamic stability. ..
  3. Rosas P, Nagaraja G, Kaur P, Panossian A, Wickman G, Garcia L, et al. Hsp72 (HSPA1A) Prevents Human Islet Amyloid Polypeptide Aggregation and Toxicity: A New Approach for Type 2 Diabetes Treatment. PLoS ONE. 2016;11:e0149409 pubmed publisher
  4. Lucey D, Dolan M, Moss C, Garcia M, Hollis D, Wegner S, et al. Relapsing illness due to Rochalimaea henselae in immunocompetent hosts: implication for therapy and new epidemiological associations. Clin Infect Dis. 1992;14:683-8 pubmed
    ..He became permanently asymptomatic after serial 2-week courses of chloramphenicol and erythromycin. The greater efficacy of lysis-centrifugation blood cultures in the recovery of R. henselae was noted...
  5. Lacy W, Washenick K, Cook R, Dunbar B. Molecular cloning and expression of an abundant rabbit ovarian protein with 20 alpha-hydroxysteroid dehydrogenase activity. Mol Endocrinol. 1993;7:58-66 pubmed
    ..This is the first example of an abundant crystallin-related protein with known enzymatic activity in a tissue other than the lens. ..
  6. Wen J, Gray D. Ff gene 5 single-stranded DNA-binding protein assembles on nucleotides constrained by a DNA hairpin. Biochemistry. 2004;43:2622-34 pubmed
    ..Moreover, the finding that hairpins of U-4 can dimerize emphasizes the unexpected nature of sequence-dependent structures that can be recognized by the g5p ssDNA-binding protein. ..
  7. Flores A, Olsen R, Wünsche A, Kumaraswami M, Shelburne S, Carroll R, et al. Natural variation in the promoter of the gene encoding the Mga regulator alters host-pathogen interactions in group a Streptococcus carrier strains. Infect Immun. 2013;81:4128-38 pubmed publisher
    ..Our findings provide new insight into the molecular basis of the carrier state of an important human pathogen. ..
  8. Qi Y, Pei J, Grishin N. C-terminal domain of gyrase A is predicted to have a beta-propeller structure. Proteins. 2002;47:258-64 pubmed
    ..The prediction rationalizes available experimental data and sheds light on the spatial properties of the largest topoisomerase domain that lacks structural information. ..
  9. Forsman Z, Lednicky J, Fox G, Willson R, White Z, Halvorson S, et al. Phylogenetic analysis of polyomavirus simian virus 40 from monkeys and humans reveals genetic variation. J Virol. 2004;78:9306-16 pubmed
  10. Jain N, Zhao L, Liu J, Xia T. Heterogeneity and dynamics of the ligand recognition mode in purine-sensing riboswitches. Biochemistry. 2010;49:3703-14 pubmed publisher
  11. Jia Y, Perez J. Recombinant expression and affinity purification of snake venom gland parvalbumin in Escherichia coli. Comp Biochem Physiol A Mol Integr Physiol. 2009;153:303-8 pubmed publisher
    ..This specific occurrence indicates a specialized function of AplPV in snake venom glands. ..
  12. Lee J, Sayegh J, Daniel J, Clarke S, Bedford M. PRMT8, a new membrane-bound tissue-specific member of the protein arginine methyltransferase family. J Biol Chem. 2005;280:32890-6 pubmed
    ..PRMT8 is thus an active arginine methyltransferase that is membrane-associated and tissue-specific, two firsts for this family of enzymes. ..
  13. Wen J, Gray C, Gray D. SELEX selection of high-affinity oligonucleotides for bacteriophage Ff gene 5 protein. Biochemistry. 2001;40:9300-10 pubmed
    ..Thus, G-rich motifs may form structures favorable for initiation of g5p binding and also provide the actual g5p-binding sites. ..
  14. Gu J, Wagner M, Haan E, Wells D. Detection of a megabase deletion in a patient with branchio-oto-renal syndrome (BOR) and tricho-rhino-phalangeal syndrome (TRPS): implications for mapping and cloning the BOR gene. Genomics. 1996;31:201-6 pubmed
    ..3. These data narrowed the most likely location of the BOR gene to a region corresponding to the proximal two-thirds of YAC 869E10 between D8S543 and D8S279...
  15. Cremers F, Armstrong S, Seabra M, Brown M, Goldstein J. REP-2, a Rab escort protein encoded by the choroideremia-like gene. J Biol Chem. 1994;269:2111-7 pubmed
    ..In the retina, REP-2 may be only partially effective, leading eventually to retinal degeneration and blindness...
  16. Sugahara T, Liu C, Pai T, Collodi P, Suiko M, Sakakibara Y, et al. Sulfation of hydroxychlorobiphenyls. Molecular cloning, expression, and functional characterization of zebrafish SULT1 sulfotransferases. Eur J Biochem. 2003;270:2404-11 pubmed
    ..Among 10 different divalent metal cations tested, Co2+, Zn2+, Cd2+, and Pb2+ exhibited considerable inhibitory effects, while Hg2+ and Cu2+ rendered both enzymes virtually inactive. ..
  17. Zhang X, Griko N, Corona S, Bulla L. Enhanced exocytosis of the receptor BT-R(1) induced by the Cry1Ab toxin of Bacillus thuringiensis directly correlates to the execution of cell death. Comp Biochem Physiol B Biochem Mol Biol. 2008;149:581-8 pubmed publisher
    ..Obviously, movement of BT-R(1) is mediated by toxin-induced signal transduction and amplification of this signaling apparently is critical to the execution of cell death. ..
  18. Mursinna R, Lincecum T, Martinis S. A conserved threonine within Escherichia coli leucyl-tRNA synthetase prevents hydrolytic editing of leucyl-tRNALeu. Biochemistry. 2001;40:5376-81 pubmed
    ..This provides a molecular example of an amino acid discrimination mechanism in the tRNA synthetase's editing active site. ..
  19. Conde J, Claunch C, Romo H, Benito Martín A, Ballestero R, GONZALEZ GARCIA M. Identification of a motif in BMRP required for interaction with Bcl-2 by site-directed mutagenesis studies. J Cell Biochem. 2012;113:3498-508 pubmed publisher
    ..These results suggest that the apoptosis-inducing ability of wild-type BMRP is blocked by Bcl-2 through several mechanisms. ..
  20. Vincent F, Openshaw M, Trautwein M, Gaskell S, Kohn H, Widger W. Rho transcription factor: symmetry and binding of bicyclomycin. Biochemistry. 2000;39:9077-83 pubmed
    ..The proposed mechanism of RNA translocation coupled with ATP hydrolysis changes the overall symmetry of rho from C6 to C6/C3. ..
  21. Kiupakis A, Reitzer L. ArgR-independent induction and ArgR-dependent superinduction of the astCADBE operon in Escherichia coli. J Bacteriol. 2002;184:2940-50 pubmed
    ..The transcriptional regulation of the ast operon in E. coli differs from that in Salmonella enterica serovar Typhimurium, in which ArgR is required for ast operon expression. ..
  22. Kaneko M, Cahill G. Light-dependent development of circadian gene expression in transgenic zebrafish. PLoS Biol. 2005;3:e34 pubmed
    ..In summary, per3-luc zebrafish has revealed complex interactions among developmental events, light, and temperature in the expression of a clock gene...
  23. Sihn C, Kim H, Woltz R, Yarov Yarovoy V, Yang P, Xu J, et al. Mechanisms of Calmodulin Regulation of Different Isoforms of Kv7.4 K+ Channels. J Biol Chem. 2016;291:2499-509 pubmed publisher
    ..4 channels. This report provides mechanistic insights into the critical roles of Ca(2+)/CaM regulation of the Kv7.4 channel under physiological and pathological conditions. ..
  24. Han S, Xie W, Kim S, Yue L, DeJong J. A short core promoter drives expression of the ALF transcription factor in reproductive tissues of male and female mice. Biol Reprod. 2004;71:933-41 pubmed
    ..Overall, the results define a unique core promoter that is active in both male and female reproductive tissues, and suggest mouse ALF may have a regulatory role in male and female gametogenic gene expression programs. ..
  25. Abramczyk O, Rainey M, Barnes R, Martin L, Dalby K. Expanding the repertoire of an ERK2 recruitment site: cysteine footprinting identifies the D-recruitment site as a mediator of Ets-1 binding. Biochemistry. 2007;46:9174-86 pubmed
    ..Furthermore, cysteine-footprinting is presented as a useful way to interrogate protein-ligand interactions at the resolution of a single amino acid. ..
  26. Park E, Zhu F, Liu B, Xia X, Shen J, Bustos T, et al. Reduction in IkappaB kinase alpha expression promotes the development of skin papillomas and carcinomas. Cancer Res. 2007;67:9158-68 pubmed
    ..Our findings provide evidence that a reduction in IKKalpha expression promotes the development of papillomas and carcinomas and that the integrity of the Ikkalpha gene is required for suppressing skin carcinogenesis. ..
  27. Zhu C, Bogue M, Lim D, Hasty P, Roth D. Ku86-deficient mice exhibit severe combined immunodeficiency and defective processing of V(D)J recombination intermediates. Cell. 1996;86:379-89 pubmed
    ..We suggest that Ku86 may be required to remodel or disassemble DNA-protein complexes containing broken ends, making them available for further processing and joining. ..
  28. Wang A, Johnson D, MacLeod M. Molecular cloning and characterization of a novel mouse epidermal differentiation gene and its promoter. Genomics. 2001;73:284-90 pubmed
    ..Interestingly, Eig3 expression was highly increased in mouse skin papillomas but not in squamous carcinomas. Since there is no E2F consensus binding sequence in the promoter or first intron of Eig3, E2F regulation may be indirect. ..
  29. Sen P, Clark C, Gopalakrishnan R, Hedner U, Esmon C, Pendurthi U, et al. Factor VIIa binding to endothelial cell protein C receptor: differences between mouse and human systems. Thromb Haemost. 2012;107:951-61 pubmed publisher
    ..Our data suggest that one should consider the use of human FVIIa in mouse models to investigate the significance of FVIIa and EPCR interaction. ..
  30. Yanagisawa H, Davis E, Starcher B, Ouchi T, Yanagisawa M, Richardson J, et al. Fibulin-5 is an elastin-binding protein essential for elastic fibre development in vivo. Nature. 2002;415:168-71 pubmed
    ..This function may be mediated by the RGD motif in fibulin-5, which binds to cell surface integrins, and the Ca2+-binding epidermal growth factor (EGF) repeats, which bind elastin...
  31. Lee J, Cox B, Daly C, Lee C, Nuckels R, Tittle R, et al. An ENU mutagenesis screen in zebrafish for visual system mutants identifies a novel splice-acceptor site mutation in patched2 that results in Colobomas. Invest Ophthalmol Vis Sci. 2012;53:8214-21 pubmed publisher
    ..We have identified 18 recessive mutations affecting development of the zebrafish visual system and we have characterized a novel splice-acceptor site mutation in patched2 that results in enhanced Hh pathway activity and colobomas. ..
  32. Liu Q, Hattar S, Endo S, MacPhee K, Zhang H, Cleary L, et al. A developmental gene (Tolloid/BMP-1) is regulated in Aplysia neurons by treatments that induce long-term sensitization. J Neurosci. 1997;17:755-64 pubmed
    ..Aplysia tolloid/BMP-1-like protein (apTBL-1) might regulate the morphology and efficacy of synaptic connections between sensory and motor neurons, which are associated with long-term sensitization...
  33. Donoviel D, Freed D, Vogel H, Potter D, Hawkins E, Barrish J, et al. Proteinuria and perinatal lethality in mice lacking NEPH1, a novel protein with homology to NEPHRIN. Mol Cell Biol. 2001;21:4829-36 pubmed
    ..These findings suggest that NEPH1, like NEPHRIN, may play an important role in maintaining the structure of the filtration barrier that prevents proteins from freely entering the glomerular urinary space. ..
  34. Xi L, Cho K, Tu S. Cloning and nucleotide sequences of lux genes and characterization of luciferase of Xenorhabdus luminescens from a human wound. J Bacteriol. 1991;173:1399-405 pubmed
    ..However, the X. luminescens HW luciferase was unusual in the high stability of the 4a-hydroperoxyflavin intermediate and its sensitivity to aldehyde substrate inhibition. ..
  35. Krzywinska E, Krzywinski J. Analysis of expression in the Anopheles gambiae developing testes reveals rapidly evolving lineage-specific genes in mosquitoes. BMC Genomics. 2009;10:300 pubmed publisher
    ..The orphan encoded proteins may represent unique targets of selective anti-mosquito sterilizing agents that will not affect non-target organisms...
  36. Sirajuddin M, Rice L, Vale R. Regulation of microtubule motors by tubulin isotypes and post-translational modifications. Nat Cell Biol. 2014;16:335-44 pubmed publisher
    ..Our results also show that different molecular motors recognize distinctive tubulin 'signatures', which supports the premise of the tubulin-code hypothesis. ..
  37. Schein C, Bowen D, Lewis J, Choi K, Paul A, van der Heden van Noort G, et al. Physicochemical property consensus sequences for functional analysis, design of multivalent antigens and targeted antivirals. BMC Bioinformatics. 2012;13 Suppl 13:S9 pubmed publisher
    ..Other potential applications include deriving target proteins for drug design and diagnostic kits. ..
  38. Aronstein K, Murray K, De Leon J, Qin X, Weinstock G. High mobility group (HMG-box) genes in the honeybee fungal pathogen Ascosphaera apis. Mycologia. 2007;99:553-61 pubmed
    ..This new method allows for identification of a single mating type idiomorph and might become an essential tool for applied and basic research of chalkbrood disease in honeybees...
  39. Schneider B, Kiupakis A, Reitzer L. Arginine catabolism and the arginine succinyltransferase pathway in Escherichia coli. J Bacteriol. 1998;180:4278-86 pubmed
    ..We conclude that the AST pathway is necessary for aerobic arginine catabolism in E. coli and that at least one enzyme of this pathway contributes to ornithine catabolism. ..
  40. Antes T, Costandy H, Mahendran R, Spottswood M, Miller D. Insertional editing of mitochondrial tRNAs of Physarum polycephalum and Didymium nigripes. Mol Cell Biol. 1998;18:7521-7 pubmed
    ..This enrichment of partially edited sequences in unprocessed tRNAs may indicate that editing is required for tRNA processing or at least that RNA editing occurs as an early event in tRNA synthesis...
  41. Che S, El Hodiri H, Wu C, Nelman Gonzalez M, Weil M, Etkin L, et al. Identification and cloning of xp95, a putative signal transduction protein in Xenopus oocytes. J Biol Chem. 1999;274:5522-31 pubmed
    ..These results suggest that Xp95 is an element in a tyrosine kinase signaling pathway that may be involved in progesterone-induced Xenopus oocyte maturation. ..
  42. Han S, Xie W, Hammes S, DeJong J. Expression of the germ cell-specific transcription factor ALF in Xenopus oocytes compensates for translational inactivation of the somatic factor TFIIA. J Biol Chem. 2003;278:45586-93 pubmed
    ..Overall, the results show that the translationally regulated reciprocal expression of ALF and TFIIA allows for the production of an active TFIIA-like general transcription factor throughout oogenesis. ..
  43. Revai K, Patel J, Grady J, Nair S, Matalon R, Chonmaitree T. Association between cytokine gene polymorphisms and risk for upper respiratory tract infection and acute otitis media. Clin Infect Dis. 2009;49:257-61 pubmed publisher
    ..Future studies may be designed to carefully look at the interaction of these genetic polymorphisms with modifiable environmental risk factors. ..
  44. Ahn J, Ludecke H, Lindow S, Horton W, Lee B, Wagner M, et al. Cloning of the putative tumour suppressor gene for hereditary multiple exostoses (EXT1). Nat Genet. 1995;11:137-43 pubmed
    ..However, recent studies in sporadic and exostosis-derived chondrosarcomas suggest that the 8q24.1-encoded EXT1 gene may have tumour suppressor function...
  45. Hou J, Parrish J, Ludecke H, Sapru M, Wang Y, Chen W, et al. A 4-megabase YAC contig that spans the Langer-Giedion syndrome region on human chromosome 8q24.1: use in refining the location of the trichorhinophalangeal syndrome and multiple exostoses genes (TRPS1 and EXT1). Genomics. 1995;29:87-97 pubmed
  46. Beale J, Foster J. Carbohydrate fluxes into alginate biosynthesis in Azotobacter vinelandii NCIB 8789: NMR investigations of the triose pools. Biochemistry. 1996;35:4492-501 pubmed
    ..The obligatory intermediacy of triose intermediates in alginate biosynthesis was proved. The experiments and results presented in this paper constitute a new method for distinguishing the E-D pathway from glycolysis in bacteria...
  47. Gomelsky M, Kaplan S. The Rhodobacter sphaeroides 2.4.1 rho gene: expression and genetic analysis of structure and function. J Bacteriol. 1996;178:1946-54 pubmed
    ..The gene downstream of rho is homologous to thdF, whose product is involved in thiophene and furan oxidation...
  48. Murakami T, Reiter L, Lupski J. Genomic structure and expression of the human heme A:farnesyltransferase (COX10) gene. Genomics. 1997;42:161-4 pubmed
    ..This gene is expressed in multiple tissues with highest expression observed in the heart, skeletal muscle, and testis. ..
  49. Yuen P, Kwak Y. R7, a spontaneous mutant of Moloney murine sarcoma virus 124 with three direct repeats and an in-frame truncated gag-mos gene, induces brain lesions. Virology. 1997;236:213-8 pubmed
    ..We have also confirmed that molecularly cloned R7 induces the same disease phenotype as that induced by the nonmolecularly cloned R7. ..
  50. Iakhiaeva E, Iakhiaev A, Zwieb C. Identification of amino acid residues in protein SRP72 required for binding to a kinked 5e motif of the human signal recognition particle RNA. BMC Mol Biol. 2010;11:83 pubmed publisher
    ..A model for how a ligand binding pocket of SRP72 can accommodate a new RNA K-turn in the 5e region of the eukaryotic SRP RNA is proposed. ..
  51. Venugopal R, Jaiswal A. Nrf2 and Nrf1 in association with Jun proteins regulate antioxidant response element-mediated expression and coordinated induction of genes encoding detoxifying enzymes. Oncogene. 1998;17:3145-56 pubmed
    ..Nrf2 containing one mutated leucine in its leucine zipper region was more efficient in upregulation of ARE-mediated gene expression, as compared to Nrf1 with two mutated leucines. ..
  52. Upadhyaya A, Lee S, DeJong J. Identification of a general transcription factor TFIIAalpha/beta homolog selectively expressed in testis. J Biol Chem. 1999;274:18040-8 pubmed
    ..Overall, the data show that ALF is a functional homolog of human general transcription factor TFIIAalpha/beta that may be uniquely important to testis biology. ..
  53. Kim J, Lee J, Yadav N, Wu Q, Carter C, Richard S, et al. Loss of CARM1 results in hypomethylation of thymocyte cyclic AMP-regulated phosphoprotein and deregulated early T cell development. J Biol Chem. 2004;279:25339-44 pubmed
    ..These results demonstrate that CARM1 plays a significant role in promoting the differentiation of early thymocyte progenitors, possibly through its direct action on TARPP. ..
  54. Krishnan U, Barsamian A, Miller D. Evolution of RNA editing sites in the mitochondrial small subunit rRNA of the Myxomycota. Methods Enzymol. 2007;424:197-220 pubmed
    ..These trees indicate that editing sites change rapidly relative to mtDNA sequence divergence and suggest that some editing sites have been created more than once during the evolution of the Myxomycota...
  55. Kim E, Muga S, Fischer S. Identification and characterization of a phorbol ester-responsive element in the murine 8S-lipoxygenase gene. J Biol Chem. 2004;279:11188-97 pubmed
    ..These data suggest that increased binding of Sp1, Sp2, and Sp3 to the TRE of the 8S-LOX promoter is a mechanism by which TPA induces 8S-LOX expression in keratinocytes. ..
  56. Frankel A, Yadav N, Lee J, Branscombe T, Clarke S, Bedford M. The novel human protein arginine N-methyltransferase PRMT6 is a nuclear enzyme displaying unique substrate specificity. J Biol Chem. 2002;277:3537-43 pubmed
    ..This novel human PRMT, which resides solely in the nucleus when fused to the green fluorescent protein, joins a family of enzymes with diverse functions within cells. ..
  57. Lu J, Kadakkuzha B, Zhao L, Fan M, Qi X, Xia T. Dynamic ensemble view of the conformational landscape of HIV-1 TAR RNA and allosteric recognition. Biochemistry. 2011;50:5042-57 pubmed publisher
    ..A dynamic model of the ensemble view of the conformational landscape for HIV-1 TAR RNA is proposed, and the implication of the general mechanism of RNA recognition and its impact on RNA-based therapeutics are discussed. ..
  58. Chintharlapalli S, Jasti M, Malladi S, Parsa K, Ballestero R, GONZALEZ GARCIA M. BMRP is a Bcl-2 binding protein that induces apoptosis. J Cell Biochem. 2005;94:611-26 pubmed
    ..These findings suggest that BMRP is a mitochondrial ribosomal protein involved in the regulation of cell death by apoptosis, probably affecting pathways mediated by Bcl-2 and caspases. ..
  59. Zwiefka A, Kohn H, Widger W. Transcription termination factor rho: the site of bicyclomycin inhibition in Escherichia coli. Biochemistry. 1993;32:3564-70 pubmed
    ..These cumulative findings are consistent with the notion that bicyclomycin expresses its activity by interfering with the polyC-dependent ATPase activity of rho. ..
  60. Chen S, Inozentseva Clayton N, Dong J, Gu T, Macdougall M. Binding of two nuclear factors to a novel silencer element in human dentin matrix protein 1 (DMP1) promoter regulates the cell type-specific DMP1 gene expression. J Cell Biochem. 2004;92:332-49 pubmed
    ..We speculate that this silencing cis-element may play a critical role in the regulation of DMP1 cell-specific expression. ..
  61. Shen X. Preparation and analysis of the INO80 complex. Methods Enzymol. 2004;377:401-12 pubmed
  62. Rahman M, Thomas P. Effects of hypoxia exposure on hepatic cytochrome P450 1A (CYP1A) expression in Atlantic croaker: molecular mechanisms of CYP1A down-regulation. PLoS ONE. 2012;7:e40825 pubmed publisher
    ..Moreover, the present study provides the first evidence of a role for antioxidants in hepatic eNOS and IL-1? regulation in aquatic vertebrates during hypoxic stress. ..
  63. Wilson P, de Bouteiller O, Liu Y, Potter K, Banchereau J, Capra J, et al. Somatic hypermutation introduces insertions and deletions into immunoglobulin V genes. J Exp Med. 1998;187:59-70 pubmed
  64. Meng F, Henson R, Wehbe Janek H, Smith H, Ueno Y, Patel T. The MicroRNA let-7a modulates interleukin-6-dependent STAT-3 survival signaling in malignant human cholangiocytes. J Biol Chem. 2007;282:8256-64 pubmed
  65. Xu X, Ahn J, Tam P, Yu E, Batra S, Cram E, et al. Analysis of conserved residues in the betapat-3 cytoplasmic tail reveals important functions of integrin in multiple tissues. Dev Dyn. 2010;239:763-72 pubmed publisher
    ..Our study suggests that the conserved NPXY and TT motifs play important roles in the tissue-specific function of integrin. ..
  66. Agarwal S, Gourh P, Shete S, Paz G, Divecha D, Reveille J, et al. Association of interleukin 23 receptor polymorphisms with anti-topoisomerase-I positivity and pulmonary hypertension in systemic sclerosis. J Rheumatol. 2009;36:2715-23 pubmed publisher
    ..p = 3x10(-5), p = 1x10(-5), respectively). Polymorphisms in IL23R are associated with susceptibility to ATA-positive SSc and protective against development of PHT in patients with SSc. ..
  67. Yang C, Pflugrath J, Camper D, Foster M, Pernich D, Walsh T. Structural basis for herbicidal inhibitor selectivity revealed by comparison of crystal structures of plant and mammalian 4-hydroxyphenylpyruvate dioxygenases. Biochemistry. 2004;43:10414-23 pubmed
  68. Wattler F, Wattler S, Kelly M, Skinner H, Nehls M. Cloning, chromosomal location, and expression analysis of murine Smarce1-related, a new member of the high-mobility 365 group gene family. Genomics. 1999;60:172-8 pubmed
    ..The linkage of a single nonspecific DNA-binding HMG domain with a KLCC domain makes both proteins the founding members of a third group of HMG proteins. ..
  69. Nazimiec M, Lee C, Tang Y, Ye X, Case R, Tang M. Sequence-dependent interactions of two forms of UvrC with DNA helix-stabilizing CC-1065-N3-adenine adducts. Biochemistry. 2001;40:11073-81 pubmed
    ..These results show that two different forms of UvrC differ in DNA binding properties as well as incision modes at some kinds of DNA damage. ..
  70. Kim M, Li D, Cui Y, Mueller K, Chears W, DeJong J. Regulatory factor interactions and somatic silencing of the germ cell-specific ALF gene. J Biol Chem. 2006;281:34288-98 pubmed
    ..Release of such repression, perhaps in conjunction with other members of the CTCF, RFX, and Sp1 families of transcription factors, could be an important aspect of germ cell gene activation. ..
  71. Callaway K, Abramczyk O, Martin L, Dalby K. The anti-apoptotic protein PEA-15 is a tight binding inhibitor of ERK1 and ERK2, which blocks docking interactions at the D-recruitment site. Biochemistry. 2007;46:9187-98 pubmed
    ..Therefore, in addition to sequestering ERK1/2 in the cytoplasm, PEA-15 has the potential to modulate the activity of ERK2 in cells by competing directly with proteins that contain D-sites. ..
  72. Kihira S, Yu E, Cunningham J, Cram E, Lee M. A novel mutation in β integrin reveals an integrin-mediated interaction between the extracellular matrix and cki-1/p27KIP1. PLoS ONE. 2012;7:e42425 pubmed publisher
    ..Perturbed integrin signaling may lead to the inhibition of SCF ligase activity, mislocalization and elevation of CKI-1/p27(KIP1). These results suggest that adhesion signaling is crucial for cell cycle regulation in vivo. ..
  73. Iakhiaeva E, Bhuiyan S, Yin J, Zwieb C. Protein SRP68 of human signal recognition particle: identification of the RNA and SRP72 binding domains. Protein Sci. 2006;15:1290-302 pubmed
    ..This portion of SRP72 was located within a predicted tandem array of four tetratricopeptide (TPR)-like motifs suggested to form a superhelical structure with a groove to accommodate the C-terminal region of SRP68. ..
  74. Reddy M, Christensen J, Vasquez K. Interplay between human high mobility group protein 1 and replication protein A on psoralen-cross-linked DNA. Biochemistry. 2005;44:4188-95 pubmed
    ..The abundance of HMGB1 suggests that it may play an important role in determining the sensitivity of cells to DNA damage under physiological, experimental, and therapeutic conditions. ..
  75. Xie W, Han S, Khan M, DeJong J. Regulation of ALF gene expression in somatic and male germ line tissues involves partial and site-specific patterns of methylation. J Biol Chem. 2002;277:17765-74 pubmed
    ..This pattern is transient as remethylation of the ALF promoter in haploid germ cell DNA has occurred by the time spermatozoa are present in the epididymis. ..