Genomes and Genes
Experts and Doctors on sequence alignment in Bethesda, Maryland, United States
Locale: Bethesda, Maryland, United States
Topic: sequence alignment
Publications338 found, 100 shown here
- Krajcikova D, Hartley R. A new member of the bacterial ribonuclease inhibitor family from Saccharopolyspora erythraea. FEBS Lett. 2004;557:164-8 pubmed..Soluble protein was isolated and purified to homogeneity. Inhibition constants of complex of Sti and RNase Sa3 or barnase were determined at pH 7 as 5 x 10(-12) or 7 x 10(-7), respectively...
- Sabol S, Brewer H, Santamarina Fojo S. The human ABCG1 gene: identification of LXR response elements that modulate expression in macrophages and liver. J Lipid Res. 2005;46:2151-67 pubmed..These studies clarify the mechanism of transcriptional upregulation of the ABCG1 gene by oxysterols in macrophages and liver, two key tissues where ABCG1 expression may affect cholesterol balance and atherogenesis...
- Jenkins L, Yamaguchi H, Hayashi R, Cherry S, Tropea J, Miller M, et al. Two distinct motifs within the p53 transactivation domain bind to the Taz2 domain of p300 and are differentially affected by phosphorylation. Biochemistry. 2009;48:1244-55 pubmed publisher..However, the more negative value of DeltaC(p) for Taz2 binding to the first (-330 cal/(mol.K)) compared to the second site (-234 cal/(mol.K)) suggests that the importance of nonpolar and polar interactions differs between the two sites. ..
- Zhang D, Hughes R, Ollivierre Wilson H, Ghosh M, Rouault T. A ferroportin transcript that lacks an iron-responsive element enables duodenal and erythroid precursor cells to evade translational repression. Cell Metab. 2009;9:461-73 pubmed publisher..In erythroid precursor cells, we hypothesize that FPN1B expression enhances real-time sensing of systemic iron status and facilitates restriction of erythropoiesis in response to low systemic iron. ..
- Cui F, Sirotin M, Zhurkin V. Impact of Alu repeats on the evolution of human p53 binding sites. Biol Direct. 2011;6:2 pubmed publisher..One of the selective factors responsible for the frequent occurrence of Alu repeats in introns may be related to the p53-mediated regulation of Alu transcription, which, in turn, influences expression of the host genes. ..
- Robles Espinoza C, Harland M, Ramsay A, Aoude L, Quesada V, Ding Z, et al. POT1 loss-of-function variants predispose to familial melanoma. Nat Genet. 2014;46:478-481 pubmed publisher..These findings suggest that POT1 variants predispose to melanoma formation via a direct effect on telomeres. ..
- Choi Y, Ekholm D, Krall J, Ahmad F, Degerman E, Manganiello V, et al. Identification of a novel isoform of the cyclic-nucleotide phosphodiesterase PDE3A expressed in vascular smooth-muscle myocytes. Biochem J. 2001;353:41-50 pubmed
- Hayton K, Gaur D, Liu A, Takahashi J, Henschen B, Singh S, et al. Erythrocyte binding protein PfRH5 polymorphisms determine species-specific pathways of Plasmodium falciparum invasion. Cell Host Microbe. 2008;4:40-51 pubmed publisher..nancymaae erythrocytes. Our results also suggest that PfRH5 is a parasite ligand for human infection, and that amino acid substitutions can cause its binding domain to recognize different human erythrocyte surface receptors...
- Tanoue K, Miller Jenkins L, Durell S, Debnath S, Sakai H, Tagad H, et al. Binding of a third metal ion by the human phosphatases PP2CÎ± and Wip1 is required for phosphatase activity. Biochemistry. 2013;52:5830-43 pubmed publisher..These results suggest that phosphatase activity toward phosphopeptide substrates by PP2CÎ± and Wip1 requires the binding of a MgÂ²âº ion to the low-affinity site. ..
- Shi J, Yang X, Ballew B, Rotunno M, Calista D, Fargnoli M, et al. Rare missense variants in POT1 predispose to familial cutaneous malignant melanoma. Nat Genet. 2014;46:482-6 pubmed publisher..We also identified two rare recurrent POT1 variants in US and French familial melanoma cases. Our findings suggest that POT1 is a major susceptibility gene for familial melanoma in several populations. ..
- Li Q, Herrler M, Landsberger N, Kaludov N, Ogryzko V, Nakatani Y, et al. Xenopus NF-Y pre-sets chromatin to potentiate p300 and acetylation-responsive transcription from the Xenopus hsp70 promoter in vivo. EMBO J. 1998;17:6300-15 pubmed..We suggest two steps in chromatin modification at the Xenopus hsp70 promoter: first the binding of NF-Y to the Y-boxes to pre-set chromatin and second the recruitment of p300 to modulate transcriptional activity. ..
- Namboodiri M, Corigliano Murphy A, Jiang G, Rollag M, Provencio I. Murine aspartoacylase: cloning, expression and comparison with the human enzyme. Brain Res Mol Brain Res. 2000;77:285-9 pubmed..Our success in preparing the recombinant ASPA in high purity should permit multiple lines of investigations to understand the pathogenic mechanisms of Canavan disease and the functional roles of NAA. ..
- Kostelansky M, Sun J, Lee S, Kim J, Ghirlando R, Hierro A, et al. Structural and functional organization of the ESCRT-I trafficking complex. Cell. 2006;125:113-26 pubmed..The C-terminal domain of Vps28 binds the ESCRT-II complex. The structure shows how ESCRT-I is assembled by a compact core from which the Vps23 UEV domain, the Vps28 C domain, and other domains project to bind their partners. ..
- Gallazzini M, Yu M, Gunaratne R, Burg M, Ferraris J. c-Abl mediates high NaCl-induced phosphorylation and activation of the transcription factor TonEBP/OREBP. FASEB J. 2010;24:4325-35 pubmed publisher..Thus, c-Abl is the kinase responsible for high NaCl-induced phosphorylation of TonEBP/OREBP-Y143, which contributes to its increased activity...
- Kutty G, Ma L, Kovacs J. Characterization of the expression site of the major surface glycoprotein of human-derived Pneumocystis carinii. Mol Microbiol. 2001;42:183-93 pubmed..carinii f. sp. carinii and, in immunosuppressed patients, in whom immune pressures that probably drive antigenic variation are functioning inadequately, P. carinii can express a broad repertoire of MSG variants. ..
- Sam V, Tai C, Garnier J, Gibrat J, Lee B, Munson P. ROC and confusion analysis of structure comparison methods identify the main causes of divergence from manual protein classification. BMC Bioinformatics. 2006;7:206 pubmed..Others may be intrinsic to the problem, suggesting a continuous rather than discrete protein fold space. ..
- Bosmans F, Tytgat J. Sea anemone venom as a source of insecticidal peptides acting on voltage-gated Na+ channels. Toxicon. 2007;49:550-60 pubmed..For this reason, these peptides can be considered as insecticidal lead compounds in the development of insecticides. ..
- Parker H, Kukekova A, Akey D, Goldstein O, Kirkness E, Baysac K, et al. Breed relationships facilitate fine-mapping studies: a 7.8-kb deletion cosegregates with Collie eye anomaly across multiple dog breeds. Genome Res. 2007;17:1562-71 pubmed..This work both establishes that the primary cea mutation arose as a single disease allele in a common ancestor of herding breeds as well as highlights the value of comparative population analysis for refining regions of linkage. ..
- Abhiman S, Iyer L, Aravind L. BEN: a novel domain in chromatin factors and DNA viral proteins. Bioinformatics. 2008;24:458-61 pubmed publisher..The presence of BEN domains in a poxviral early virosomal protein and in polydnaviral proteins also suggests a possible role for them in organization of viral DNA during replication or transcription. ..
- Sastalla I, Chim K, Cheung G, Pomerantsev A, Leppla S. Codon-optimized fluorescent proteins designed for expression in low-GC gram-positive bacteria. Appl Environ Microbiol. 2009;75:2099-110 pubmed publisher..Using optimized GFP as a reporter, we were able to monitor the activity of the protective antigen promoter of B. anthracis and confirm its dependence on bicarbonate and regulators present on virulence plasmid pXO1. ..
- Zhao X, Wu H. Nucleotide sequence of the Staphylococcus aureus signal peptidase II (lsp) gene. FEBS Lett. 1992;299:80-4 pubmed..Unlike the lsp genes from the Gram-negative bacteria, the lsp gene in S. aureus is not flanked by x-ileS and orf149-orf316 as found in E. coli, Ent. aerogenes, and P. fluorescens...
- Koonin E, Tatusov R, Rudd K. Sequence similarity analysis of Escherichia coli proteins: functional and evolutionary implications. Proc Natl Acad Sci U S A. 1995;92:11921-5 pubmed..Sequence similarity with E. coli proteins allows the prediction of functions for a number of important eukaryotic genes, including several whose products are implicated in human diseases. ..
- Phelps D, Dressler G. Identification of novel Pax-2 binding sites by chromatin precipitation. J Biol Chem. 1996;271:7978-85 pubmed..The genomic clones can now be used as sequence tags to identify potential target loci. ..
- Lu J, Li Q, Xie H, Chen Z, Borovitskaya A, Maclaren N, et al. Identification of a second transmembrane protein tyrosine phosphatase, IA-2beta, as an autoantigen in insulin-dependent diabetes mellitus: precursor of the 37-kDa tryptic fragment. Proc Natl Acad Sci U S A. 1996;93:2307-11 pubmed..We conclude that IA-2beta and IA-2 are the precursors of the 37-kDa and 40-kDa islet cell autoantigens, respectively, and that both IA-2 and IA-2beta are major autoantigens in IDDM. ..
- Li W, Zhang J, Bottaro D, Pierce J. Identification of serine 643 of protein kinase C-delta as an important autophosphorylation site for its enzymatic activity. J Biol Chem. 1997;272:24550-5 pubmed..Taken together, our results demonstrate that serine 643 of PKC-delta is a major autophosphorylation site, and phosphorylation of this site plays an important role in controlling its enzymatic activity and biological function. ..
- Anantharaman V, Aravind L. New connections in the prokaryotic toxin-antitoxin network: relationship with the eukaryotic nonsense-mediated RNA decay system. Genome Biol. 2003;4:R81 pubmed..The core of the eukaryotic nonsense-mediated RNA decay system has probably evolved from a post-segregational cell killing-related system. ..
- Yu Y, Wootton J, Altschul S. The compositional adjustment of amino acid substitution matrices. Proc Natl Acad Sci U S A. 2003;100:15688-93 pubmed..Composition-specific substitution matrix adjustment is shown to be of utility for comparing compositionally biased proteins, including those of organisms with nucleotide-biased, and therefore codon-biased, genomes or isochores. ..
- Boissinot S, Roos C, Furano A. Different rates of LINE-1 (L1) retrotransposon amplification and evolution in New World monkeys. J Mol Evol. 2004;58:122-30 pubmed..In contrast, we found no evidence for a species-specific subfamily in Ateles, a result consistent with the low L1 activity in this species for the last approximately 25 My. ..
- Dyer K, Rosenberg H. The mouse RNase 4 and RNase 5/ang 1 locus utilizes dual promoters for tissue-specific expression. Nucleic Acids Res. 2005;33:1077-86 pubmed
- Taraporewala Z, Jiang X, Vasquez Del Carpio R, Jayaram H, Prasad B, Patton J. Structure-function analysis of rotavirus NSP2 octamer by using a novel complementation system. J Virol. 2006;80:7984-94 pubmed
- Makarova K, Aravind L, Wolf Y, Koonin E. Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems. Biol Direct. 2011;6:38 pubmed publisher..This article was reviewed by Malcolm White (nominated by Purficacion Lopez-Garcia), Frank Eisenhaber and Igor Zhulin. For the full reviews, see the Reviewers' Comments section. ..
- Biggar R, Whitby D, Marshall V, Linhares A, Black F. Human herpesvirus 8 in Brazilian Amerindians: a hyperendemic population with a new subtype. J Infect Dis. 2000;181:1562-8 pubmed..Transmission is probably oral rather than sexual. The limited genetic pool in isolated groups may permit more frequent transmission of a virus with a low prevalence in heterogeneous populations. ..
- Ponomarev V, Makarova K, Aravind L, Koonin E. Gene duplication with displacement and rearrangement: origin of the bacterial replication protein PriB from the single-stranded DNA-binding protein Ssb. J Mol Microbiol Biotechnol. 2003;5:225-9 pubmed
- Jeong S, Gaume B, Lee Y, Hsu Y, Ryu S, Yoon S, et al. Bcl-x(L) sequesters its C-terminal membrane anchor in soluble, cytosolic homodimers. EMBO J. 2004;23:2146-55 pubmed..The C-terminal tail of Bcl-x(L) is also required to mediate Bcl-x(L)/Bax heterodimer formation. Both mitochondrial import and antiapoptotic activity of different Bcl-x(L) mutants correlate with their ability to form homodimers. ..
- Venkova Canova T, Saha A, Chattoraj D. A 29-mer site regulates transcription of the initiator gene as well as function of the replication origin of Vibrio cholerae chromosome II. Plasmid. 2012;67:102-10 pubmed publisher..The 29-mer thus appears to play a dual role in regulating chrII replication: one independent of the cell cycle, the other dependent upon iteron methylation, hence responsive to the cell cycle. ..
- Miki T, Bottaro D, Fleming T, Smith C, Burgess W, Chan A, et al. Determination of ligand-binding specificity by alternative splicing: two distinct growth factor receptors encoded by a single gene. Proc Natl Acad Sci U S A. 1992;89:246-50 pubmed..Thus, two growth factor receptors with different ligand-binding specificities and expression patterns are encoded by alternative transcripts of the same gene. ..
- Buonanno A, Apone L, Morasso M, Beers R, Brenner H, Eftimie R. The MyoD family of myogenic factors is regulated by electrical activity: isolation and characterization of a mouse Myf-5 cDNA. Nucleic Acids Res. 1992;20:539-44 pubmed..Using extracellular electrodes to directly stimulate in situ the soleus muscle of rats, we found that 'electrical activity' per se, in absence of the nerve, represses the increases of myogenic factor mRNAs associated with denervation. ..
- Neuwald A, Green P. Detecting patterns in protein sequences. J Mol Biol. 1994;239:698-712 pubmed..In a search of a large set of sequences for internal repeats, the method detected novel ankyrin-like repeats in an Escherichia coli protein. ..
- Tachibana M, Perez Jurado L, Nakayama A, Hodgkinson C, Li X, Schneider M, et al. Cloning of MITF, the human homolog of the mouse microphthalmia gene and assignment to chromosome 3p14.1-p12.3. Hum Mol Genet. 1994;3:553-7 pubmed..These studies will help to verify if any of the hereditary pigment disturbances in humans are due to mutations in this gene. ..
- Tan D, Shao X, Pu L, Guo V, Nirenberg M. Sequence and expression of the murine Hoxd-3 homeobox gene. Proc Natl Acad Sci U S A. 1996;93:8247-52 pubmed
- Hellmich H, Kos L, Cho E, Mahon K, Zimmer A. Embryonic expression of glial cell-line derived neurotrophic factor (GDNF) suggests multiple developmental roles in neural differentiation and epithelial-mesenchymal interactions. Mech Dev. 1996;54:95-105 pubmed..Our results suggest multiple roles for GDNF during early stages of neuronal development and in epithelial-mesenchymal interactions. ..
- Kajava A, Cheng N, Cleaver R, Kessel M, Simon M, Willery E, et al. Beta-helix model for the filamentous haemagglutinin adhesin of Bordetella pertussis and related bacterial secretory proteins. Mol Microbiol. 2001;42:279-92 pubmed..Finally, we applied the same profile search method to the sequence database and found several other proteins--all large secreted proteins of bacterial provenance--that have similar repeats and probably also similar structures. ..
- Zhang A, Wassarman K, Ortega J, Steven A, Storz G. The Sm-like Hfq protein increases OxyS RNA interaction with target mRNAs. Mol Cell. 2002;9:11-22 pubmed..We also show that Hfq increases the OxyS RNA interaction with its target messages and propose that the enhancement of RNA-RNA pairing may be a general function of Hfq, Sm, and Sm-like proteins...
- Anantharaman V, Aravind L. Application of comparative genomics in the identification and analysis of novel families of membrane-associated receptors in bacteria. BMC Genomics. 2003;4:34 pubmed
- Laeyendecker O, Zhang G, Quinn T, Garten R, Ray S, Lai S, et al. Molecular epidemiology of HIV-1 subtypes in southern China. J Acquir Immune Defic Syndr. 2005;38:356-62 pubmed
- Bi X, Jones T, Abbasi F, Lee H, Stultz B, Hursh D, et al. Drosophila caliban, a nuclear export mediator, can function as a tumor suppressor in human lung cancer cells. Oncogene. 2005;24:8229-39 pubmed..We suggest that Sdccag1 inactivation contributes to the transformed state of human lung cancer cells and that Caliban should be considered a candidate for use in lung cancer gene therapy. ..
- Lee J, Gordiyenko N, Marchetti M, Tserentsoodol N, Sagher D, Alam S, et al. Gene structure, localization and role in oxidative stress of methionine sulfoxide reductase A (MSRA) in the monkey retina. Exp Eye Res. 2006;82:816-27 pubmed..Collectively these data suggest MSRA may play an important role in protecting macular RPE from oxidative damage. ..
- Goila Gaur R, Khan M, Miyagi E, Kao S, Strebel K. Targeting APOBEC3A to the viral nucleoprotein complex confers antiviral activity. Retrovirology. 2007;4:61 pubmed..Our results suggest that the A3G N-terminal domain carries determinants important for targeting the protein to viral NPCs. Transfer of this domain to A3A results in A3A targeting to viral NPCs and confers antiviral activity. ..
- Zhang Z, Alpert D, Francis R, Chatterjee B, Yu Q, Tansey T, et al. Massively parallel sequencing identifies the gene Megf8 with ENU-induced mutation causing heterotaxy. Proc Natl Acad Sci U S A. 2009;106:3219-24 pubmed publisher..Overall, through the recovery of an ENU-induced mutation, we uncovered Megf8 as an essential regulator of left-right patterning. ..
- Yan Y, Buckler White A, Wollenberg K, Kozak C. Origin, antiviral function and evidence for positive selection of the gammaretrovirus restriction gene Fv1 in the genus Mus. Proc Natl Acad Sci U S A. 2009;106:3259-63 pubmed publisher..This analysis suggests that Fv1 has had an antiviral role throughout Mus evolution predating exposure of mice to the MLVs restricted by laboratory mouse Fv1, and suggests a mechanism for Fv1 restriction...
- Boratyn G, Schäffer A, Agarwala R, Altschul S, Lipman D, Madden T. Domain enhanced lookup time accelerated BLAST. Biol Direct. 2012;7:12 pubmed publisher..DELTA-BLAST is a useful program for the detection of remote protein homologs. It is available under the "Protein BLAST" link at http://blast.ncbi.nlm.nih.gov. ..
- Raben N, Borriello F, Amin J, Horwitz R, Fraser D, Plotz P. Human histidyl-tRNA synthetase: recognition of amino acid signature regions in class 2a aminoacyl-tRNA synthetases. Nucleic Acids Res. 1992;20:1075-81 pubmed
- Nichols R, Raben N, Boerkoel C, Plotz P. Human isoleucyl-tRNA synthetase: sequence of the cDNA, alternative mRNA splicing, and the characteristics of an unusually long C-terminal extension. Gene. 1995;155:299-304 pubmed..Because human IRS has previously been shown to be the target of antibodies in autoimmune disease, we discuss the role of protein structural features in the development of an autoimmune response to IRS. ..
- Hough R, Avivi A, Davis J, Joel A, Nevo E, Piatigorsky J. Adaptive evolution of small heat shock protein/alpha B-crystallin promoter activity of the blind subterranean mole rat, Spalax ehrenbergi. Proc Natl Acad Sci U S A. 2002;99:8145-50 pubmed..We speculate that selective pressures on metabolic economy may have contributed to these tissue-specific modifications of promoter/enhancer function during adaptation to life underground. ..
- Bera T, Das S, Maeda H, Beers R, Wolfgang C, Kumar V, et al. NGEP, a gene encoding a membrane protein detected only in prostate cancer and normal prostate. Proc Natl Acad Sci U S A. 2004;101:3059-64 pubmed..Because of its selective expression in prostate cancer and its presence on the cell surface, NGEP-L is a promising target for the antibody-based therapies of prostate cancer. ..
- Duncan M, Haynes J, Piatigorsky J. The chicken beta A4- and beta B1-crystallin-encoding genes are tightly linked. Gene. 1995;162:189-96 pubmed
- Minoguchi K, Kihara H, Nishikata H, Hamawy M, Siraganian R. Src family tyrosine kinase Lyn binds several proteins including paxillin in rat basophilic leukemia cells. Mol Immunol. 1994;31:519-29 pubmed..Thus Fc epsilon RI mediated signal transduction in RBL-2H3 cells may result from the interaction of p53/56lyn with paxillin, pp72, pp110 and other proteins. ..
- Sadofsky M, Hesse J, Gellert M. Definition of a core region of RAG-2 that is functional in V(D)J recombination. Nucleic Acids Res. 1994;22:1805-9 pubmed..Thus all basic features of V(D)J joining are retained in a RAG-2 protein with only the first 75% of the sequence. ..
- Ellsworth R, Jamison D, Touchman J, Chissoe S, Braden Maduro V, Bouffard G, et al. Comparative genomic sequence analysis of the human and mouse cystic fibrosis transmembrane conductance regulator genes. Proc Natl Acad Sci U S A. 2000;97:1172-7 pubmed..Furthermore, the generated sequence reveals the precise architecture of genes residing near CFTR/Cftr, including one known gene (WNT2/Wnt2) and two previously unknown genes that immediately flank CFTR/Cftr. ..
- Zhang J, Dyer K, Rosenberg H. Evolution of the rodent eosinophil-associated RNase gene family by rapid gene sorting and positive selection. Proc Natl Acad Sci U S A. 2000;97:4701-6 pubmed publisher..The discovery of a large number of divergent EARs suggests the intriguing possibility that these proteins have been specifically tailored to fight against distinct rodent pathogens...
- Wolfgang C, Essand M, Vincent J, Lee B, Pastan I. TARP: a nuclear protein expressed in prostate and breast cancer cells derived from an alternate reading frame of the T cell receptor gamma chain locus. Proc Natl Acad Sci U S A. 2000;97:9437-42 pubmed..We have named this protein TCRgamma alternate reading frame protein (TARP). These results demonstrate that an alternative protein product is encoded by the TCRgamma locus in cells other than T lymphocytes. ..
- Dyer K, Rosenberg H, Zhang J. Isolation, characterization, and evolutionary divergence of mouse RNase 6: evidence for unusual evolution in rodents. J Mol Evol. 2004;59:657-65 pubmed..66. These data suggest that the ancestral rodent RNase 6 was subject to accelerated evolution, resulting in the conserved modern gene, which most likely plays an important role in mouse physiology. ..
- Wistow G, Wyatt K, David L, Gao C, Bateman O, Bernstein S, et al. gammaN-crystallin and the evolution of the betagamma-crystallin superfamily in vertebrates. FEBS J. 2005;272:2276-91 pubmed..Although well conserved throughout vertebrate evolution, gammaN in primates has apparently undergone major changes and possible loss of functional expression. ..
- Wolf Y, Madej T, Babenko V, Shoemaker B, Panchenko A. Long-term trends in evolution of indels in protein sequences. BMC Evol Biol. 2007;7:19 pubmed..Domains from several Gene Ontology categories also demonstrate certain tendencies for insertion or deletion events as inferred from the analysis of spacer sizes. ..
- Chernikova D, Motamedi S, Csuros M, Koonin E, Rogozin I. A late origin of the extant eukaryotic diversity: divergence time estimates using rare genomic changes. Biol Direct. 2011;6:26 pubmed publisher..This article was reviewed by William Martin, Herve Philippe (nominated by I. King Jordan), and Romain Derelle. ..
- Iyer L, Zhang D, Rogozin I, Aravind L. Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems. Nucleic Acids Res. 2011;39:9473-97 pubmed publisher..These observations greatly expand the distribution of possible unidentified mutagenic processes catalyzed by nucleic acid deaminases. ..
- Yao X, Zhang J, Zhou H, Wang E, Xiang X. In vivo roles of the basic domain of dynactin p150 in microtubule plus-end tracking and dynein function. Traffic. 2012;13:375-87 pubmed publisher..We suggest that the basic amino acids are required for the electrostatic interaction between p150 and MTs, which is important for kinesin-1-mediated plus-end targeting of dynactin and dynein in A. nidulans...
- Zhu J, Ofek G, Yang Y, Zhang B, Louder M, Lu G, et al. Mining the antibodyome for HIV-1-neutralizing antibodies with next-generation sequencing and phylogenetic pairing of heavy/light chains. Proc Natl Acad Sci U S A. 2013;110:6470-5 pubmed publisher..Altogether, our findings suggest that phylogenetic matching of heavy and light chains can provide a means to approximate natural pairings. ..
- Iyer L, Zhang D, Burroughs A, Aravind L. Computational identification of novel biochemical systems involved in oxidation, glycosylation and other complex modifications of bases in DNA. Nucleic Acids Res. 2013;41:7635-55 pubmed publisher..These results open opportunities for the investigation of the biology of these systems and their use in biotechnology. ..
- Parra G, Sosnovtsev S, Abente E, Sandoval Jaime C, Bok K, Dolan M, et al. Mapping and modeling of a strain-specific epitope in the Norwalk virus capsid inner shell. Virology. 2016;492:232-41 pubmed publisher..The S domain, like the P domain, contains strain-specific epitopes that contribute to the antigenic diversity among the noroviruses. ..
- Ney P, Andrews N, Jane S, Safer B, Purucker M, Weremowicz S, et al. Purification of the human NF-E2 complex: cDNA cloning of the hematopoietic cell-specific subunit and evidence for an associated partner. Mol Cell Biol. 1993;13:5604-12 pubmed..Thus, p18 appears to be the sole specific partner of p45 NF-E2 in erythroid cells. Cloning of human p45 NF-E2 should permit studies of the role of NF-E2 in globin gene regulation and erythroid differentiation. ..
- Chen C, Kim M, Soo Lyu M, Kozak C, Schwartz R, Flomerfelt F. Characterization of the mouse gene, human promoter and human cDNA of TSCOT reveals strong interspecies homology. Biochim Biophys Acta. 2000;1493:159-69 pubmed
- Di Francesco V, Garnier J, Munson P. Protein topology recognition from secondary structure sequences: application of the hidden Markov models to the alpha class proteins. J Mol Biol. 1997;267:446-63 pubmed..To illustrate the potential utility of our method, protein topology recognition is attempted on leptin, the obese gene product, and the human interleukin-6 sequence, for which fold predictions have been previously published. ..
- Lin T, Orrison B, Leahey A, Suchy S, Bernard D, Lewis R, et al. Spectrum of mutations in the OCRL1 gene in the Lowe oculocerebrorenal syndrome. Am J Hum Genet. 1997;60:1384-8 pubmed..Missense mutations that abolish enzyme activity but not expression of the protein will be useful for studying structure-function relationships in PtdIns(4,5)P2 5-phosphatases...
- Segovia L, Horwitz J, Gasser R, Wistow G. Two roles for mu-crystallin: a lens structural protein in diurnal marsupials and a possible enzyme in mammalian retinas. Mol Vis. 1997;3:9 pubmed..mu-crystallin may be an enzyme, possibly of amino acid metabolism, with particular importance for photoreceptors. ..
- Pouliot J, Yao K, Robertson C, Nash H. Yeast gene for a Tyr-DNA phosphodiesterase that repairs topoisomerase I complexes. Science. 1999;286:552-5 pubmed..The presence of this gene in humans may have implications for the effectiveness of topoisomerase I poisons, such as the camptothecins, in chemotherapy. ..
- Kaye F, Modi S, Ivanovska I, Koonin E, Thress K, Kubo A, et al. A family of ubiquitin-like proteins binds the ATPase domain of Hsp70-like Stch. FEBS Lett. 2000;467:348-55 pubmed..These findings extend the association between Hsp70 members and genes encoding UbL sequences and suggest a broader role for the Hsp70-like ATPase family in regulating cell cycle and cell death events. ..
- Adya N, Castilla L, Liu P. Function of CBFbeta/Bro proteins. Semin Cell Dev Biol. 2000;11:361-8 pubmed..The ubiquitous expression pattern of the CBFB gene suggests that it may play important roles in many other organ systems. ..
- Aravind L, Dixit V, Koonin E. Apoptotic molecular machinery: vastly increased complexity in vertebrates revealed by genome comparisons. Science. 2001;291:1279-84 pubmed..A considerable repertoire of apoptotic protein domains was detected in Actinomycetes and Cyanobacteria, which suggests a major contribution of horizontal gene transfer to the early evolution of apoptosis. ..
- Koonin E. DnaC protein contains a modified ATP-binding motif and belongs to a novel family of ATPases including also DnaA. Nucleic Acids Res. 1992;20:1997 pubmed
- Epifano O, Liang L, Familari M, Moos M, Dean J. Coordinate expression of the three zona pellucida genes during mouse oogenesis. Development. 1995;121:1947-56 pubmed..Our data support the hypothesis that the transcription of the zona genes is controlled, in part, by shared regulatory element(s). ..
- Bharathi A, Ghosh A, Whalen W, Yoon J, Pu R, Dasso M, et al. The human RAE1 gene is a functional homologue of Schizosaccharomyces pombe rae1 gene involved in nuclear export of Poly(A)+ RNA. Gene. 1997;198:251-8 pubmed..An epitope tagged human Rae1p localizes to both the nucleus and the cytoplasm in transiently transfected HeLa cells. We discuss the potential role of Rae1p in nuclear cytoplasmic trafficking in yeast and higher eukaryotic cells. ..
- Dey B, Furlanetto R, Nissley S. Cloning of human p55 gamma, a regulatory subunit of phosphatidylinositol 3-kinase, by a yeast two-hybrid library screen with the insulin-like growth factor-I receptor. Gene. 1998;209:175-83 pubmed..Our findings suggest that hp55 gamma interacts with the IGFIR and IR and may be involved in PI 3-kinase activation by these receptors. ..
- Damon I, Murphy P, Moss B. Broad spectrum chemokine antagonistic activity of a human poxvirus chemokine homolog. Proc Natl Acad Sci U S A. 1998;95:6403-7 pubmed..The broad spectrum chemokine antagonistic activity of MC148 can explain the prolonged absence of an inflammatory response in skin tumors that harbor replicating molluscum contagiosum virus...
- Zhang Y, Chang C, Gehling D, Hemmati Brivanlou A, Derynck R. Regulation of Smad degradation and activity by Smurf2, an E3 ubiquitin ligase. Proc Natl Acad Sci U S A. 2001;98:974-9 pubmed
- Rayasam G, Wendling O, Angrand P, Mark M, Niederreither K, Song L, et al. NSD1 is essential for early post-implantation development and has a catalytically active SET domain. EMBO J. 2003;22:3153-63 pubmed..We have also examined the enzymatic potential of NSD1 and found that its SET domain possesses intrinsic histone methyltransferase activity with specificity for Lys36 of histone H3 (H3-K36) and Lys20 of histone H4 (H4-K20). ..
- Ribeiro J, Andersen J, Silva Neto M, Pham V, Garfield M, Valenzuela J. Exploring the sialome of the blood-sucking bug Rhodnius prolixus. Insect Biochem Mol Biol. 2004;34:61-79 pubmed..The electronic version of the complete tables is available at http://www.ncbi.nlm.nih.gov/projects/vectors/rhodnius_prolixus. ..
- Liu S, Milne G, Kuremsky J, Fink G, Leppla S. Identification of the proteins required for biosynthesis of diphthamide, the target of bacterial ADP-ribosylating toxins on translation elongation factor 2. Mol Cell Biol. 2004;24:9487-97 pubmed..The physiological function of diphthamide and the basis of its ubiquity remain a mystery, but evidence is presented that Dph1 to -3 function in vivo as a protein complex in multiple cellular processes. ..