Genomes and Genes
Experts and Doctors on binding sites in United States
Locale: United States
Topic: binding sites
Publications608 found, 100 shown here
- Lee H, Neumann P, Macas J, Jiang J. Transcription and evolutionary dynamics of the centromeric satellite repeat CentO in rice. Mol Biol Evol. 2006;23:2505-20 pubmed..We detected transcripts derived from both strands of the CentO repeats. The CentO transcripts are processed into siRNA, suggesting a potential role of this satellite repeat family in epigenetic chromatin modification. ..
- Adkins M, Carson J, English C, Ramey C, Tyler J. The histone chaperone anti-silencing function 1 stimulates the acetylation of newly synthesized histone H3 in S-phase. J Biol Chem. 2007;282:1334-40 pubmed..These results demonstrate that Asf1 does not affect the stability of the newly synthesized histones per se, but instead histone binding by Asf1 promotes the efficient acetylation of specific residues of newly synthesized histone H3. ..
- Grunewald G, Seim M, Regier R, Criscione K. Exploring the active site of phenylethanolamine N-methyltransferase with 1,2,3,4-tetrahydrobenz[h]isoquinoline inhibitors. Bioorg Med Chem. 2007;15:1298-310 pubmed..22mM), which has a lipophilic 7-substituent that cannot hydrogen bond to the enzyme, is twice as potent at PNMT than 11. This once again illustrates the limitations of docking studies for lead optimization. ..
- Nelson G, Ahlborn G, Delker D, Kitchin K, O Brien T, Chen Y, et al. Folate deficiency enhances arsenic effects on expression of genes involved in epidermal differentiation in transgenic K6/ODC mouse skin. Toxicology. 2007;241:134-45 pubmed
- Zou S, Jha S, Kim E, Dryer S. A novel actin-binding domain on Slo1 calcium-activated potassium channels is necessary for their expression in the plasma membrane. Mol Pharmacol. 2008;73:359-68 pubmed
- Mohr G, Del Campo M, Mohr S, Yang Q, Jia H, Jankowsky E, et al. Function of the C-terminal domain of the DEAD-box protein Mss116p analyzed in vivo and in vitro. J Mol Biol. 2008;375:1344-64 pubmed
- McDaniell R, Lee B, Song L, Liu Z, Boyle A, Erdos M, et al. Heritable individual-specific and allele-specific chromatin signatures in humans. Science. 2010;328:235-9 pubmed publisher..Our study shows that heritable chromatin status and transcription factor binding differ as a result of genetic variation and may underlie phenotypic variation in humans. ..
- Wang L, Qin Y, Ilchenko S, Bohon J, Shi W, Cho M, et al. Structural analysis of a highly glycosylated and unliganded gp120-based antigen using mass spectrometry. Biochemistry. 2010;49:9032-45 pubmed publisher..In addition, the data illustrate interactions between specific sugar moieties and amino acid side chains potentially important to the gp120-OD8 structure. ..
- Tavares X, Blum A, Nakamura D, Puskar N, Shanata J, Lester H, et al. Variations in binding among several agonists at two stoichiometries of the neuronal, ?4?2 nicotinic receptor. J Am Chem Soc. 2012;134:11474-80 pubmed publisher..In addition, we see interesting variations in hydrogen bonding interactions with cytisine that provide a rationalization for the stoichiometry selectivity seen with this compound. ..
- Mellor L, Knudson C, Hida D, Askew E, Knudson W. Intracellular domain fragment of CD44 alters CD44 function in chondrocytes. J Biol Chem. 2013;288:25838-50 pubmed publisher..The data suggest that release of the CD44 intracellular domain into the cytoplasm of cells such as chondrocytes exerts a competitive or dominant-negative effect on the function of full-length CD44. ..
- Maldonado A, Burz D, Reverdatto S, Shekhtman A. Fate of pup inside the Mycobacterium proteasome studied by in-cell NMR. PLoS ONE. 2013;8:e74576 pubmed publisher..This suggests a mechanism by which transient binding of Mpa to the proteasome CP controls the fate of Pup. ..
- Blanco F, Sanduja S, Deane N, Blackshear P, Dixon D. Transforming growth factor ? regulates P-body formation through induction of the mRNA decay factor tristetraprolin. Mol Cell Biol. 2014;34:180-95 pubmed publisher..These results provide new insight into TGF-?'s antiproliferative properties and identify TGF-? as a novel mRNA stability regulator in intestinal epithelium through its ability to promote TTP expression and subsequent P-body formation. ..
- David L, Gokhale A, Jois S, Johnson A, Behrens M, Luthra H, et al. CD74/DQA1 dimers predispose to the development of arthritis in humanized mice. Immunology. 2016;147:204-11 pubmed publisher..The present data provide a possible explanation by which the DQA1 molecule contributes to susceptibility to develop arthritis. ..
- Sihag R, Nixon R. Identification of Ser-55 as a major protein kinase A phosphorylation site on the 70-kDa subunit of neurofilaments. Early turnover during axonal transport. J Biol Chem. 1991;266:18861-7 pubmed
- Coghlan V, Perrino B, Howard M, Langeberg L, Hicks J, Gallatin W, et al. Association of protein kinase A and protein phosphatase 2B with a common anchoring protein. Science. 1995;267:108-11 pubmed..These results suggest that both PKA and CaN are targeted to subcellular sites by association with a common anchor protein and thereby regulate the phosphorylation state of key neuronal substrates. ..
- Yuan W, Stromhaug P, Dunn W. Glucose-induced autophagy of peroxisomes in Pichia pastoris requires a unique E1-like protein. Mol Biol Cell. 1999;10:1353-66 pubmed..Our results suggest that this unique E1-like enzyme is required for homotypic membrane fusion, a late event in the sequestration of peroxisomes by the vacuole. ..
- Meacham G, Browne B, Zhang W, Kellermayer R, Bedwell D, Cyr D. Mutations in the yeast Hsp40 chaperone protein Ydj1 cause defects in Axl1 biogenesis and pro-a-factor processing. J Biol Chem. 1999;274:34396-402 pubmed..This study is the first to suggest a role for Ydj1p in RNA metabolism and identifies Axl1p as an in vivo substrate of the Hsp70/Ydj1p chaperone system...
- Thoden J, Phillips G, Neal T, Raushel F, Holden H. Molecular structure of dihydroorotase: a paradigm for catalysis through the use of a binuclear metal center. Biochemistry. 2001;40:6989-97 pubmed..The ensuing tetrahedral intermediate collapses with C-O bond cleavage and expulsion of the hydroxide which then bridges the binuclear metal center. ..
- Lin F, Fukuoka Y, Spicer A, Ohta R, Okada N, Harris C, et al. Tissue distribution of products of the mouse decay-accelerating factor (DAF) genes. Exploitation of a Daf1 knock-out mouse and site-specific monoclonal antibodies. Immunology. 2001;104:215-25 pubmed..The results have relevance for studies of in vivo murine DAF function and of murine DAF structure. ..
- Takata Y, Yamada T, Huang Y, Komoto J, Gomi T, Ogawa H, et al. Catalytic mechanism of S-adenosylhomocysteine hydrolase. Site-directed mutagenesis of Asp-130, Lys-185, Asp-189, and Asn-190. J Biol Chem. 2002;277:22670-6 pubmed..His-54 and His-300 hold and polarize a water molecule, which nucleophilically attacks the C5'- of 3'-keto-4',5'-dehydroadenosine to produce 3'-keto-Ado. ..
- Shi Q, Singh K, Srivastava A, Kaushik N, Modak M. Lysine 152 of MuLV reverse transcriptase is required for the integrity of the active site. Biochemistry. 2002;41:14831-42 pubmed..These results further indicate that the catalytic mechanism of MuLV RT is significantly different from that of HIV-1 RT, despite the presence of a number of conserved motifs and amino acid residues. ..
- Yu B, Pan Y, Janssen M, Bahnson B, Jain M. Kinetic and structural properties of disulfide engineered phospholipase A2: insight into the role of disulfide bonding patterns. Biochemistry. 2005;44:3369-79 pubmed..This in turn influences the coupling of the catalytic cycle to the calcium binding and the interfacial binding event. ..
- Whittaker J, Whittaker L. Characterization of the functional insulin binding epitopes of the full-length insulin receptor. J Biol Chem. 2005;280:20932-6 pubmed..They had no effect on the maximal response to insulin but produced an increase in the EC50 commensurate with their effect on the affinity of the receptor for insulin. ..
- Misquitta S, Colman R. Communication between the two active sites of glutathione S-transferase A1-1, probed using wild-type-mutant heterodimers. Biochemistry. 2005;44:8608-19 pubmed..Modeling studies show that key amino acid residues and water molecules connect the two active sites. This connectivity is responsible for the cross-talk between the active sites. ..
- Plummer L, Hildebrandt E, Porter S, Rogers V, McCracken J, Schmidt W. Mutational analysis of the ras converting enzyme reveals a requirement for glutamate and histidine residues. J Biol Chem. 2006;281:4596-605 pubmed
- Zaitseva J, Lu J, Olechoski K, Lamb A. Two crystal structures of the isochorismate pyruvate lyase from Pseudomonas aeruginosa. J Biol Chem. 2006;281:33441-9 pubmed
- Campbell D, Bouchard P, Desjardins G, Legault P. NMR structure of varkud satellite ribozyme stem-loop V in the presence of magnesium ions and localization of metal-binding sites. Biochemistry. 2006;45:10591-605 pubmed..These studies improve our understanding of the role of Mg(2+) in U-turn structures and in substrate recognition by the VS ribozyme...
- Tusell S, Schittone S, Holmes K. Mutational analysis of aminopeptidase N, a receptor for several group 1 coronaviruses, identifies key determinants of viral host range. J Virol. 2007;81:1261-73 pubmed..Therefore, entry and host range of these group 1 coronaviruses depend on the ability of the viral spike glycoproteins to recognize small, species-specific amino acid differences in the APN proteins of different species. ..
- Tyler R, Bitto E, Berndsen C, Bingman C, Singh S, Lee M, et al. Structure of Arabidopsis thaliana At1g77540 protein, a minimal acetyltransferase from the COG2388 family. Biochemistry. 2006;45:14325-36 pubmed..This work establishes that the domain family COG2388 represents a novel class of acetyltransferase and provides insight into possible mechanistic roles of the conserved Cys76 and His41 residues of this family. ..
- Froehlich A, Chen C, Belden W, Madeti C, Roenneberg T, Merrow M, et al. Genetic and molecular characterization of a cryptochrome from the filamentous fungus Neurospora crassa. Eukaryot Cell. 2010;9:738-50 pubmed publisher..Whole-genome microarray experiments failed to identify substantive transcriptional regulatory activity of cry under our laboratory conditions. ..
- Byrne S, Steere A, Chasteen N, Mason A. Identification of a kinetically significant anion binding (KISAB) site in the N-lobe of human serum transferrin. Biochemistry. 2010;49:4200-7 pubmed publisher..This is the first identification of an authentic KISAB site in the N-lobe of hTF. The effect of the single R143A mutation on the kinetic profile of iron release provides a dramatic illustration of the dynamic nature of hTF. ..
- Durrant J, McCammon J. BINANA: a novel algorithm for ligand-binding characterization. J Mol Graph Model. 2011;29:888-93 pubmed publisher..We are hopeful that BINANA will be useful to computational chemists and structural biologists who wish to automatically characterize many ligand-receptor complexes for key binding characteristics. ..
- Peng C, Shi W, Lutz J, Kunze K, Liu J, Nelson W, et al. Stereospecific metabolism of itraconazole by CYP3A4: dioxolane ring scission of azole antifungals. Drug Metab Dispos. 2012;40:426-35 pubmed publisher..These data suggest that the dioxolane ring scission is a metabolic pathway for drugs that contain this moiety. ..
- Akdemir K, Jain A, Allton K, Aronow B, Xu X, Cooney A, et al. Genome-wide profiling reveals stimulus-specific functions of p53 during differentiation and DNA damage of human embryonic stem cells. Nucleic Acids Res. 2014;42:205-23 pubmed publisher..Our findings expand the registry of p53-regulated genes to define p53-regulated opposition to pluripotency during early differentiation, a process highly distinct from stress-induced p53 response in hESCs. ..
- Kasinathan S, Orsi G, Zentner G, Ahmad K, Henikoff S. High-resolution mapping of transcription factor binding sites on native chromatin. Nat Methods. 2014;11:203-9 pubmed publisher..Our results suggest that ORGANIC profiling is a widely applicable high-resolution method for sensitive and specific profiling of direct protein-DNA interactions. ..
- Singh S, Bandi S, Winder S, Mallela K. The actin binding affinity of the utrophin tandem calponin-homology domain is primarily determined by its N-terminal domain. Biochemistry. 2014;53:1801-9 pubmed publisher..These results indicate that the actin binding affinity of the utrophin tandem CH domain is primarily determined by its CH1 domain, when compared to that of its CH2 domain or the cooperativity between the two CH domains. ..
- Koen Y, Yue W, Galeva N, Williams T, Hanzlik R. Site-specific arylation of rat glutathione s-transferase A1 and A2 by bromobenzene metabolites in vivo. Chem Res Toxicol. 2006;19:1426-34 pubmed..No evidence for the presence of any putative BB-adducts in GST M1, M2, or A3 was obtained. This work highlights the challenges involved in the unambiguous identification of reactive metabolite adducts formed in vivo. ..
- Bray J, Goddard W. The structure of human serotonin 2c G-protein-coupled receptor bound to agonists and antagonists. J Mol Graph Model. 2008;27:66-81 pubmed publisher..We also compare a preliminary prediction for 5-HT(2B) with our prediction for 5-HT(2C) and find a difference in TM5 that contributes to different serotonin binding modes in 5-HT(2B) and 5-HT(2C). ..
- Whitney G, Starling G, Bowen M, Modrell B, Siadak A, Aruffo A. The membrane-proximal scavenger receptor cysteine-rich domain of CD6 contains the activated leukocyte cell adhesion molecule binding site. J Biol Chem. 1995;270:18187-90 pubmed..These results demonstrate that the membrane-proximal SRCR domain of CD6 is necessary for CD6 binding to ALCAM and provide the first direct evidence for the interaction of an SRCR domain with a ligand. ..
- Weiler M, Smith J, Masters J. CR16, a novel proline-rich protein expressed in rat brain neurons, binds to SH3 domains and is a MAP kinase substrate. J Mol Neurosci. 1996;7:203-15 pubmed..These data strongly suggest that the function of CR16 is to mediate one or more signal transduction pathways in CNS neurons, in addition to being a glucocorticoid-regulated gene. ..
- Alam M, Steveson T, Johnson R, Back N, Abraham B, Mains R, et al. Signaling mediated by the cytosolic domain of peptidylglycine alpha-amidating monooxygenase. Mol Biol Cell. 2001;12:629-44 pubmed..Consistent with this, mutation of its P-CIP2 phosphorylation site alters the ability of PAM to affect regulated secretion. ..
- Arndt J, Hao B, Ramakrishnan V, Cheng T, Chan S, Chan M. Crystal structure of a novel carboxypeptidase from the hyperthermophilic archaeon Pyrococcus furiosus. Structure. 2002;10:215-24 pubmed..The roles for these conserved residues in the catalytic mechanism are inferred based on modeling and their location. ..
- Xu B, Hua Q, Nakagawa S, Jia W, Chu Y, Katsoyannis P, et al. Chiral mutagenesis of insulin's hidden receptor-binding surface: structure of an allo-isoleucine(A2) analogue. J Mol Biol. 2002;316:435-41 pubmed..We propose that the Ile(A2) side-chain inserts within a chiral pocket of the receptor as part of insulin's hidden functional surface. ..
- Thoden J, Firestine S, Benkovic S, Holden H. PurT-encoded glycinamide ribonucleotide transformylase. Accommodation of adenosine nucleotide analogs within the active site. J Biol Chem. 2002;277:23898-908 pubmed
- Smith K, Ingram Smith C, Ferry J. Roles of the conserved aspartate and arginine in the catalytic mechanism of an archaeal beta-class carbonic anhydrase. J Bacteriol. 2002;184:4240-5 pubmed..Imidazole was unable to rescue the k(cat) of the R36A variant; however, partial rescue of the kinetic parameter was obtained with guanidine-HCl indicating that the guanido group of this residue is important. ..
- Roberts A, Bar Or D, Winkler J, Rael L. Copper-induced oxidation of epinephrine: protective effect of D-DAHK, a synthetic analogue of the high affinity copper binding site of human albumin. Biochem Biophys Res Commun. 2003;304:755-7 pubmed..These in vitro results indicate that copper-induced epinephrine oxidation is greatest at the physiological pH 7.4 as well as in severe acidosis, pH 7.0, and that D-DAHK completely inhibits this oxidation. ..
- Zhu Y, Wang Y, Gorman M, Jiang H, Kanost M. Manduca sexta serpin-3 regulates prophenoloxidase activation in response to infection by inhibiting prophenoloxidase-activating proteinases. J Biol Chem. 2003;278:46556-64 pubmed..Kinetic analysis of PAP-serpin-3 association strongly suggests that serpin-3 is a physiological regulator of the pro-PO activation reaction. ..
- Beck D, Bukys M, Singh L, Szabo K, Kalafatis M. The contribution of amino acid region ASP695-TYR698 of factor V to procofactor activation and factor Va function. J Biol Chem. 2004;279:3084-95 pubmed..These data provide functional evidence for an essential and productive contribution of factor Va to the activity of prothrombinase. ..
- Deng X, Gao F, Flagg T, May W. Mono- and multisite phosphorylation enhances Bcl2's antiapoptotic function and inhibition of cell cycle entry functions. Proc Natl Acad Sci U S A. 2004;101:153-8 pubmed
- Wang Z, Wei C, Sharma M, Pant K, Crane B, Stuehr D. A conserved Val to Ile switch near the heme pocket of animal and bacterial nitric-oxide synthases helps determine their distinct catalytic profiles. J Biol Chem. 2004;279:19018-25 pubmed..Our data suggest that a greater shielding of the heme pocket caused by the Val/Ile switch slows down NO synthesis and NO release in NOS, and thus identifies a structural basis for regulating these kinetic variables. ..
- Zhang Y, Sperry A. Comparative analysis of two C-terminal kinesin motor proteins: KIFC1 and KIFC5A. Cell Motil Cytoskeleton. 2004;58:213-30 pubmed..The KIFC5A tail contains a 43 amino acid sequence with both nuclear localization and microtubule binding activity while KIFC1 contains a 19 amino acid sequence sufficient to target this motor to membrane-bounded organelles. ..
- Gewin L, Myers H, Kiyono T, Galloway D. Identification of a novel telomerase repressor that interacts with the human papillomavirus type-16 E6/E6-AP complex. Genes Dev. 2004;18:2269-82 pubmed..We propose that the induction of telomerase by the HPV-16 E6/E6-AP complex involves targeting of NFX1-91, a newly identified repressor of telomerase, for ubiquitination and degradation. ..
- Czarnecka Verner E, Pan S, Salem T, Gurley W. Plant class B HSFs inhibit transcription and exhibit affinity for TFIIB and TBP. Plant Mol Biol. 2004;56:57-75 pubmed..In vitro binding studies were consistent with this pattern of activity since the BD region alone interacted strongly with TFIIB, and the presence of RD had an inhibitory effect on TFIIB binding and transcriptional activation. ..
- Gonzalez Bosc L, Layne J, Nelson M, Hill Eubanks D. Nuclear factor of activated T cells and serum response factor cooperatively regulate the activity of an alpha-actin intronic enhancer. J Biol Chem. 2005;280:26113-20 pubmed..These data provide the first evidence that NFAT and SRF may interact to cooperatively regulate SMC-specific gene expression and support a role for NFAT in the phenotypic maintenance of smooth muscle. ..
- Chang A, McDermott J, Frazier Z, Guerquin M, Samudrala R. INTEGRATOR: interactive graphical search of large protein interactomes over the Web. BMC Bioinformatics. 2006;7:146 pubmed..The interface provides animated local network views, rapid subgraph manipulation, and cross-referencing of functional annotations. Integrator is available at http://bioverse.compbio.washington.edu/integrator. ..
- Xiao J, Dai R, Negyessy L, Bergson C. Calcyon, a novel partner of clathrin light chain, stimulates clathrin-mediated endocytosis. J Biol Chem. 2006;281:15182-93 pubmed..Collectively, these data indicate a role for calcyon in clathrin-mediated endocytosis in brain. ..
- Keramisanou D, Biris N, Gelis I, Sianidis G, Karamanou S, Economou A, et al. Disorder-order folding transitions underlie catalysis in the helicase motor of SecA. Nat Struct Mol Biol. 2006;13:594-602 pubmed..The intrinsic plasticity and functional disorder-order folding transitions coupled to ligand binding seem to provide a precise control of the catalytic activation process and simple regulation of allosteric mechanisms. ..
- Tang Z, Shangguan D, Wang K, Shi H, Sefah K, Mallikratchy P, et al. Selection of aptamers for molecular recognition and characterization of cancer cells. Anal Chem. 2007;79:4900-7 pubmed
- Jordan D. Beta-D-xylosidase from Selenomonas ruminantium: catalyzed reactions with natural and artificial substrates. Appl Biochem Biotechnol. 2008;146:137-49 pubmed publisher..4-Nitrophenol competitively inhibits SXA-catalyzed hydrolysis of 4NPX. SXA steady-state kinetic parameters account for complete progress curves of SXA-catalyzed hydrolysis reactions. ..
- Zhu M, Ma J, Parrington J, Calcraft P, Galione A, Evans A. Calcium signaling via two-pore channels: local or global, that is the question. Am J Physiol Cell Physiol. 2010;298:C430-41 pubmed publisher..This may call for a revision of current views on the mechanisms of intracellular calcium signaling. The purpose of this review is, therefore, to provide an appropriate framework for future studies in this area. ..
- Li H, Greene L. Sequence and structural analysis of the chitinase insertion domain reveals two conserved motifs involved in chitin-binding. PLoS ONE. 2010;5:e8654 pubmed publisher..Furthermore, evolutionary studies propose a link between the appearance of the chitinase insertion domain and the function of family 18 chitinases in the subfamily A. ..
- Hsu P, Hsu H, Singer G, Yan P, Rodriguez B, Liu J, et al. Estrogen-mediated epigenetic repression of large chromosomal regions through DNA looping. Genome Res. 2010;20:733-44 pubmed publisher..Together with the acquisition of DNA methylation and repressive chromatin modifications at the 16p11.2 loci, an inflexible DNA scaffold may be a novel determinant used by breast cancer cells to reinforce estrogen-mediated repression. ..
- Tsai M, Jih K, Shimizu H, Li M, Hwang T. Optimization of the degenerated interfacial ATP binding site improves the function of disease-related mutant cystic fibrosis transmembrane conductance regulator (CFTR) channels. J Biol Chem. 2010;285:37663-71 pubmed publisher..Thus, our results demonstrated that the degenerated site 1 can be rebuilt to complement or support site 2 for CFTR function. Possible approaches for developing CFTR potentiators targeting site 1 will be discussed. ..
- Füzéry A, Oh J, Ta D, Vickery L, Markley J. Three hydrophobic amino acids in Escherichia coli HscB make the greatest contribution to the stability of the HscB-IscU complex. BMC Biochem. 2011;12:3 pubmed publisher..We propose that this triple mutant could provide a more definitive test of the functional importance of the HscB-IscU interaction in vivo than those used previously that yielded inconclusive results. ..
- Davis N, Viollier P. Probing flagellar promoter occupancy in wild-type and mutant Caulobacter crescentus by chromatin immunoprecipitation. FEMS Microbiol Lett. 2011;319:146-52 pubmed publisher..We deduce that TipF contributes to proper expression of flagellar genes in C. crescentus by acting both within and outside of the canonical flagellar gene expression hierarchy. ..
- Keeffe J, Gnanapragasam P, Gillespie S, Yong J, Bjorkman P, Mayo S. Designed oligomers of cyanovirin-N show enhanced HIV neutralization. Proc Natl Acad Sci U S A. 2011;108:14079-84 pubmed publisher..The improvement in activity and broad cross-strain HIV neutralization exhibited by these molecules holds promise for the future therapeutic utility of these and other engineered CV-N variants. ..
- Zhang F, Walcott B, Zhou D, Gustchina A, Lasanajak Y, Smith D, et al. Structural studies of the interaction of Crataeva tapia bark protein with heparin and other glycosaminoglycans. Biochemistry. 2013;52:2148-56 pubmed publisher..Studies using chemically modified heparin show that N-sulfo and 6-O-sulfo groups on heparin are essential for CrataBL-heparin interaction. ..
- Kumar R, Lovell S, Matsumura H, Battaile K, Moenne Loccoz P, Rivera M. The hemophore HasA from Yersinia pestis (HasAyp) coordinates hemin with a single residue, Tyr75, and with minimal conformational change. Biochemistry. 2013;52:2705-7 pubmed publisher..In agreement with the minimal reorganization between the apo- and holo-structures, the hemin on-rate is too fast to detect by conventional stopped-flow measurements. ..
- Mart nez A, Gordon E, Sengupta A, Shirole N, Klepacki D, Martinez Garriga B, et al. Interactions of the TnaC nascent peptide with rRNA in the exit tunnel enable the ribosome to respond to free tryptophan. Nucleic Acids Res. 2014;42:1245-56 pubmed publisher..These findings suggest that interactions between TnaC residue I19 and 23S rRNA nucleotide A2058 contribute to the creation of a regulatory L-Trp binding site within the translating ribosome...
- Maroney P, Hannon G, Denker J, Nilsen T. The nematode spliced leader RNA participates in trans-splicing as an Sm snRNP. EMBO J. 1990;9:3667-73 pubmed..Mutations within the Sm binding sequence that prevent immunoprecipitation by Sm antisera and prevent cap trimethylation abolish trans-splicing. The effect on trans-splicing is not due to undermethylation of the cap structure. ..
- Liang G, Wolfgang C, Chen B, Chen T, Hai T. ATF3 gene. Genomic organization, promoter, and regulation. J Biol Chem. 1996;271:1695-701 pubmed..A possible mechanism implicating the C-Jun NH2-terminal kinase/stress-activated protein kinase (JNK/SAPK) stress-inducible signaling pathway in the induction of the ATF3 gene is discussed. ..
- Dalton T, Li Q, Bittel D, Liang L, Andrews G. Oxidative stress activates metal-responsive transcription factor-1 binding activity. Occupancy in vivo of metal response elements in the metallothionein-I gene promoter. J Biol Chem. 1996;271:26233-41 pubmed..These studies indicate that metal-responsive transcription factor-1 plays a role in activating mouse metallothionein-I gene transcription in response to reactive oxygen species. ..
- Kota R, Runge K. The yeast telomere length regulator TEL2 encodes a protein that binds to telomeric DNA. Nucleic Acids Res. 1998;26:1528-35 pubmed..MBP-Tel2p did not bind duplex telomeric DNA repeats from vertebrates, Tetrahymena or Oxytricha. These results suggest that Tel2p is a DNA binding protein that recognizes yeast telomeric DNA. ..
- Bai Y, Salvadore C, Chiang Y, Collart M, Liu H, Denis C. The CCR4 and CAF1 proteins of the CCR4-NOT complex are physically and functionally separated from NOT2, NOT4, and NOT5. Mol Cell Biol. 1999;19:6642-51 pubmed..These results define the CCR4-NOT complex as consisting of at least two physically and functionally separated groups of proteins. ..
- Baker J, Yan X, Peng T, Kasten S, Roche T. Marked differences between two isoforms of human pyruvate dehydrogenase kinase. J Biol Chem. 2000;275:15773-81 pubmed..PDK2 was activated only by assembled E2, and this activated state beget high responsiveness to those effectors. ..
- Plumb M, Sodetz J. An indel within the C8 alpha subunit of human complement C8 mediates intracellular binding of C8 gamma and formation of C8 alpha-gamma. Biochemistry. 2000;39:13078-83 pubmed
- Pan B, Maciejewski M, Marintchev A, Mullen G. Solution structure of the catalytic domain of gammadelta resolvase. Implications for the mechanism of catalysis. J Mol Biol. 2001;310:1089-107 pubmed publisher..A mechanism for covalent catalysis by this class of recombinases is proposed that may be related to dimer interface dissociation...
- Takayama T, McMullen B, Nelson P, Matsumura M, Fujikawa K. Characterization of hK4 (prostase), a prostate-specific serine protease: activation of the precursor of prostate specific antigen (pro-PSA) and single-chain urokinase-type plasminogen activator and degradation of prostatic acid phosphatase. Biochemistry. 2001;40:15341-8 pubmed..These results indicate that hK4 may have a role in the physiologic processing of seminal plasma proteins such as pro-PSA, as well as in the pathogenesis of prostate cancer through its activation of pro-uPA. ..
- Lin Y, Hwang W, Basavappa R. Structural and functional analysis of the human mitotic-specific ubiquitin-conjugating enzyme, UbcH10. J Biol Chem. 2002;277:21913-21 pubmed..The structure provides additional insight into UbcH10 function including possible sites of interaction with the anaphase promoting complex/cyclosome and the disposition of a putative destruction box motif in the structure. ..
- Zhang Y, Wu X, Guo D, Rechkoblit O, Taylor J, Geacintov N, et al. Lesion bypass activities of human DNA polymerase mu. J Biol Chem. 2002;277:44582-7 pubmed..These results provide new insights into the biochemistry of human Polmu and show that efficient translesion synthesis activity is not strictly confined to the Y family polymerases. ..
- Singh L, Bukys M, Beck D, Kalafatis M. Amino acids Glu323, Tyr324, Glu330, and Val331 of factor Va heavy chain are essential for expression of cofactor activity. J Biol Chem. 2003;278:28335-45 pubmed..Our data demonstrate that amino acid residues Glu323, Tyr324, Glu330, and Val331 of factor Va heavy chain are critical for expression of factor Va cofactor activity. ..
- Nyborg A, Jansen K, Ladd T, Fauq A, Golde T. A signal peptide peptidase (SPP) reporter activity assay based on the cleavage of type II membrane protein substrates provides further evidence for an inverted orientation of the SPP active site relative to presenilin. J Biol Chem. 2004;279:43148-56 pubmed..This assay should prove useful for additional functional studies of SPP as well as evaluation of SPP and gamma-secretase inhibitors. ..
- Xu L, Appell M, Kennedy S, Momany F, Price N. Conformational analysis of chirally deuterated tunicamycin as an active site probe of UDP-N-acetylhexosamine:polyprenol-P N-acetylhexosamine-1-P translocases. Biochemistry. 2004;43:13248-55 pubmed..Our data support the hypothesis that tunicamycin is a structural analogue of the UDP-D-HexNAc substrate and is reversibly coordinated to the divalent metal cofactor in the D-HexNAc-1-P translocase active site. ..
- Matson S, Pare G, Kapiloff M. A novel isoform of Cbl-associated protein that binds protein kinase A. Biochim Biophys Acta. 2005;1727:145-9 pubmed..CAP is a scaffold protein implicated in insulin signaling and cytoskeleton regulation. The protein kinase A binding site is encoded by a previously unidentified, alternatively spliced exon. ..
- Miller M, Palmer B, Ruch S, Martin L, Farman G, Wang Y, et al. The essential light chain N-terminal extension alters force and fiber kinetics in mouse cardiac muscle. J Biol Chem. 2005;280:34427-34 pubmed..Our results strongly suggest that an interaction between residues 5-14 of the ELC N terminus and the C-terminal residues of actin enhances cardiac performance. ..
- Thompson J, Ryan Z, Salisbury J, Kumar R. The structure of the human centrin 2-xeroderma pigmentosum group C protein complex. J Biol Chem. 2006;281:18746-52 pubmed..The interface between centrin-2 and each peptide is predominantly nonpolar, and key hydrophobic residues of XPC have been identified that lead us to propose a novel binding motif for centrin...