Abstract:
:The fidelity of the poliovirus RNA-dependent RNA polymerase (3D(pol)) plays a direct role in the genomic evolution and pathogenesis of the virus. A single site mutation (Gly64Ser) that is remote from the catalytic center results in a higher fidelity polymerase. NMR studies with [methyl-(13)C]methionine-labeled protein were used to compare the solution structure and dynamics of wild-type and Gly64Ser 3D(pol). The chemical shifts for the Met6 resonance were significantly different between wild-type and Gly64Ser 3D(pol) when bound in ternary complexes with RNA and incorrect, but not with correct, nucleotide, suggesting that the Gly64Ser mutation induces structural changes in the N-terminal β-strand when the enzyme is bound to incorrect but not correct nucleotide. We also observe changes in the transverse relaxation times for methionines near regions important for nucleotide and RNA binding and catalysis. Our strategy to assign the [methyl-(13)C]methionine resonances involved separately mutating each of the 17 methionines. Several substitutions produced additional resonances for both Met6 and Met187, a reporter for RNA binding, and conformational changes in the highly conserved motif B loop, even though these methionines are greater than 20 Å apart. The results for Gly64Ser and the other mutants are intriguing considering that they can result in structural and/or dynamic changes to methionines distant from the site of mutation. We propose that there is a long-distance network operating throughout 3D(pol) that coordinates ligand binding, conformational changes, and catalysis. Mutation of Gly64 results in structural and/or dynamic changes to the network that may affect polymerase fidelity.
journal_name
Biochemistryjournal_title
Biochemistryauthors
Yang X,Welch JL,Arnold JJ,Boehr DDdoi
10.1021/bi100833rsubject
Has Abstractpub_date
2010-11-02 00:00:00pages
9361-71issue
43eissn
0006-2960issn
1520-4995journal_volume
49pub_type
杂志文章相关文献
BIOCHEMISTRY文献大全abstract::The characterization of cod somatolactin (SL), a new pituitary protein belonging to the growth hormone/prolactin family, is described. Cod SL has a molecular weight of 26 kDa and consists of 209 amino acids, of which eight are Cys. The protein has three disulfide bonds between residues Cys5-Cys15, Cys65-Cys181, and Cy...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00220a010
更新日期:1991-02-12 00:00:00
abstract::We have examined the conformational behavior under various unfolding conditions of a predominantly beta-sheet protein, cellular retinoic acid binding protein (CRABP). Urea unfolding-refolding of CRABP is a highly cooperative process that can be approximated by a two-state model. Acid denaturation is also cooperative a...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00167a017
更新日期:1994-01-11 00:00:00
abstract::Although there is considerable evidence that signaling by the erythropoietin (EPO) receptor is initiated when it is dimerized by binding EPO, it has been previously reported that the soluble extracellular domains of the EPO receptor (sEPOR) are not dimerized in the presence of EPO and are able to form only 1:1 complex...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9524272
更新日期:1996-02-06 00:00:00
abstract::We have synthesized a series of N-propylamino-substituted benzazepinones (NPSBs) as specific probes for the benzothiazepinone (BTZ) binding domain of muscle L-type calcium channels (LTCCs). NPSBs were identified which possess high affinity for the channel after purification. We synthesized a fluorescent NPSB, DMBODIPY...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00010a039
更新日期:1995-03-14 00:00:00
abstract::We obtained a novel carbohydrate-binding peptide having a helix-loop-helix scaffold from a random peptide library. The helix-loop-helix peptide library randomized at five amino acid residues was displayed on the major coat protein of a filamentous phage. Affinity selection with a ganglioside, Galbeta1-3GalNAcbeta1-4(N...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi8000837
更新日期:2008-07-01 00:00:00
abstract::AppA, a transcriptional antirepressor, regulates the steady expression of photosynthesis genes in Rhodobacter sphaeroides in response to high-intensity blue light and to redox signals. Its blue-light sensing is mediated by an N-terminal BLUF domain, a member of a novel flavin fold. The photocycle of this domain (AppA(...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi051367p
更新日期:2006-01-10 00:00:00
abstract::CDPKs are a family of calcium (Ca2+)-dependent protein kinases which are defined by a carboxyl-terminal calmodulin-like domain. Mutational analysis indicates that the junction domain, which joins the kinase and calmodulin-like domains, contains an autoinhibitor. CDPK isoform AK1 from Arabidopsis was expressed in Esche...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00189a031
更新日期:1994-06-14 00:00:00
abstract::Autophagy, an essential eukaryotic homeostasis pathway, allows the sequestration of unwanted, damaged, or harmful cytoplasmic components in vesicles called autophagosomes, permitting subsequent lysosomal degradation and nutrient recycling. Autophagosome nucleation is mediated by class III phosphatidylinositol-3-kinase...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.6b00246
更新日期:2016-08-02 00:00:00
abstract::Specific lysine residues on the ubiquitin surface were selected during the course of evolution to form different polyubiquitin chain structures that signal diverse cellular processes. A vast number of ubiquitin receptors specifically recognize and decode the signals conferred by these polyubiquitin chains. The mechani...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.5b00498
更新日期:2015-08-04 00:00:00
abstract::Calcium binding to triads isolated from rabbit skeletal muscle followed a single hyperbolic function in the pH range 5.5-8.0. Maximal binding was obtained at pH 8.0; decreasing the pH decreased the binding capacity and, at pH < or = 6.0, increased Kd 2-fold. These results indicate that lowering the pH diminished calci...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9616209
更新日期:1996-10-15 00:00:00
abstract::The effect of monoclonal anti-(DNA polymerase alpha) immunoglobulin G (IgG) and F(ab) fragments on DNA replication in lysolecithin-permeabilized human cells and on DNA polymerase alpha activity was determined. DNA polymerase alpha activity in vitro was inhibited equally by the same concentrations of monoclonal IgGs an...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00346a061
更新日期:1985-12-03 00:00:00
abstract::The diiron active sites of the purple acid phosphatases from porcine uterus (also called uteroferrin, Uf) and bovine spleen (BSPAP) and their complexes with tungstate are compared by 1H NMR and NOE techniques. The paramagnetically shifted features of the 1H NMR spectrum of reduced BSPAP are similar to those of reduced...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00138a004
更新日期:1992-06-16 00:00:00
abstract::UDP-glucose:glycoprotein glucosyltransferase (UGT) is a soluble protein of the endoplasmic reticulum (ER) that operates as a gatekeeper for quality control by preventing transport of improperly folded glycoproteins out of the ER. We report the isolation of two cDNAs encoding human UDP-glucose:glycoprotein glucosyltran...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9916473
更新日期:2000-03-07 00:00:00
abstract::Calcium protects a limited number of embryonic chick neural retina cell surface proteins from tryptic cleavage. One glycoprotein of Mr approximately 1.3 X 10(5) and pI approximately 4.8 (gp130) is present in intact retinas and, in the presence of Ca2+, is both resistant to tryptic cleavage and poorly iodinated. When c...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00300a016
更新日期:1984-02-28 00:00:00
abstract::The positions of single amino acids in the interhelical loop regions and the C-terminal tail of bacteriorhodopsin (bR) were investigated by X-ray diffraction using site-directed heavy-atom labeling. Since wild-type bR does not contain any cysteines, appropriate cysteine mutants were produced with a unique sulfhydryl g...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi971735s
更新日期:1998-07-21 00:00:00
abstract::The Iowa point mutation in apolipoprotein A-I (G26R) leads to a systemic amyloidosis condition, and the Milano mutation (R173C) is associated with hypoalphalipoproteinemia, a reduced plasma level of high-density lipoprotein. To probe the structural effects that lead to these outcomes, we used amide hydrogen-deuterium ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi300926j
更新日期:2012-11-06 00:00:00
abstract::The proprotein convertase furin is a highly specific serine protease modifying and thereby activating proteins in the secretory pathway by proteolytic cleavage. Its substrates are involved in many diseases, including cancer and infections caused by bacteria and viruses. Understanding furin's substrate specificity is c...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.7b01124
更新日期:2018-02-13 00:00:00
abstract::Activation of washed human platelets initiated with alpha-thrombin, SFLLRN, or AYPGKF invariably results in the generation of PAR-1-(1-41) and PAR-4-(1-47). PAR-1-(1-41) and PAR-4-(1-47) are amino-terminal peptides generated when PAR-1 and -4 are cleaved in their first extracellular domains after R(41) and R(47), resp...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi801399c
更新日期:2009-02-24 00:00:00
abstract::The inheritance of DNA methylation patterns may play an important role in the stability of the differentiated state. We have therefore studied the inhibitory effects of DNA binding proteins on DNA methylation in vitro. Mouse L1210 cells grown in the presence of 5-azacytidine acquire hemimethylated sites in their DNA. ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00326a021
更新日期:1985-02-26 00:00:00
abstract::The S-protein/vitronectin gene was isolated from a human genomic DNA library, and its sequence of about 5.3 kilobases including the adjacent 5' and 3' flanking regions was established. Alignment of the genomic DNA nucleotide sequence and the cDNA sequence indicated that the gene consisted of eight exons and seven intr...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00395a024
更新日期:1987-10-20 00:00:00
abstract::Extensive molecular modeling with molecular dynamics simulations and van der Waals energy analyses were used to elucidate the striking finding that a mutagenic benzo[a]pyrene-derived DNA lesion, the base-displaced intercalated 10R-(+)-cis-anti-B[a]P-N(2)-dG (G*), manifests large differences in nucleotide excision repa...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi4009177
更新日期:2013-08-20 00:00:00
abstract::The 18 kDa translocator protein (TSPO), formerly known as the peripheral-type benzodiazepine receptor, has been reported to be closely associated with the mitochondrial permeability transition pore (MPTP). TSPO is believed to exert pro-apoptotic functions via modulation of MPTP opening. Cobalt chloride (CoCl(2)), whic...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi900064t
更新日期:2009-06-02 00:00:00
abstract::The N-terminal region of alpha-spectrin is responsible for its association with beta-spectrin in a heterodimer, forming functional tetramers. Non-erythroid alpha-spectrin (alphaII-spectrin) has a significantly higher association affinity for beta-spectrin than the homologous erythroid alpha-spectrin (alphaI-spectrin)....
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi8013032
更新日期:2009-01-13 00:00:00
abstract::Interaction of affinity chromatographically purified antihistone H3 and antihistone H4 with isolated HeLa core particles, followed by separation of unreacted and reacted particles by sedimentation, demonstrates that every core particle contains these histones. Taken together with our previous data indicating the prese...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00643a033
更新日期:1977-11-29 00:00:00
abstract::Stopped-flow measurements have been employed to study the kinetics of the conformational changes in TetR (B) induced by tetracycline binding with and without Mg(2+) ions. Result of stopped-flow fluorometry measurements at pH 8.0 indicate conformational changes in the helix-turn-helix motif in the N-terminal domain and...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi048548w
更新日期:2005-01-25 00:00:00
abstract::The structural features of a chemically modified DNA template strand may promote error-prone DNA synthesis during replication. The resulting higher incidence of mutations, in turn, can eventually lead to tumor initiation. Structural insights into this process can be monitored by studying chemically modified base adduc...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00046a043
更新日期:1995-11-21 00:00:00
abstract::Pineapple stem bromelain was photooxidized in the presence of Methylene Blue used as a sensitizer. The essential sulfhydryl group of the enzyme protein rapidly became inaccessible to react with 5,5'-dithiobis(nitrobenzoic acid), but the reactivity was readily regained to the original level upon treatment with dithioth...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00673a009
更新日期:1975-01-28 00:00:00
abstract::Human angiotensin-converting enzyme (ACE) has two homologous domains, the N and C domains, with differing substrate preferences. X-ray crystal structures of the C and N domains complexed with various inhibitors have allowed identification of active site residues that might be important for the molecular basis of this ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi8002605
更新日期:2008-06-03 00:00:00
abstract::Proteolytic activation, oligomerization, and membrane insertion are three steps that precede channel formation by the bacterial toxin aerolysin. Using attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR) and hydrogen-deuterium exchange, the structural changes associated with each step were an...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi971216p
更新日期:1997-12-09 00:00:00
abstract::The carbon-13 (13C) nuclear magnetic resonance (NMR) behavior of the hyperactive analogue of luteinizing-hormone-releasing hormone (LH-RH), des-Gly-NH2(10)-[D-Leu6]LH-RH ethylamide, has been studied. The spectra are compared with those of the hypoactive des-Gly-NH2(10)-[L-Leu6]LH-RH ethylamide. Spin-lattice relaxation...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00666a020
更新日期:1976-10-19 00:00:00