Abstract：
:SHAPE-MaP is unique among RNA structure probing strategies in that it both measures flexibility at single-nucleotide resolution and quantifies the uncertainties in these measurements. We report a straightforward analytical framework that incorporates these uncertainties to allow detection of RNA structural differences between any two states, and we use it here to detect RNA-protein interactions in healthy mouse trophoblast stem cells. We validate this approach by analysis of three model cytoplasmic and nuclear ribonucleoprotein complexes, in 2 min in-cell probing experiments. In contrast, data produced by alternative in-cell SHAPE probing methods correlate poorly (r = 0.2) with those generated by SHAPE-MaP and do not yield accurate signals for RNA-protein interactions. We then examine RNA-protein and RNA-substrate interactions in the RNase MRP complex and, by comparing in-cell interaction sites with disease-associated mutations, characterize these noncoding mutations in terms of molecular phenotype. Together, these results reveal that SHAPE-MaP can define true interaction sites and infer RNA functions under native cellular conditions with limited preexisting knowledge of the proteins or RNAs involved.
journal_name
Biochemistryjournal_title
Biochemistryauthors
Smola MJ,Calabrese JM,Weeks KMdoi
10.1021/acs.biochem.5b00977subject
Has Abstractpub_date
2015-11-24 00:00:00pages
6867-75issue
46eissn
0006-2960issn
1520-4995journal_volume
54pub_type
杂志文章相关文献
BIOCHEMISTRY文献大全abstract：:The chemical shifts of all the aromatic proton and anomeric proton resonances of NADP+, NADPH, and several structural analogues have been determined in their complexes with Lactobacillus casei dihydrofolate reductase by double-resonance (saturation transfer) experiments. The binding of NADP+ to the enzyme leads to lar...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00557a015
更新日期：1980-08-05 00:00:00
abstract：:Purine nucleoside phosphorylase (PNP) catalyzes the reversible phosphorolysis of purine ribonucleosides and 2'-deoxyribonucleosides, yielding the purine base and (2'-deoxy)ribose 1-phosphate as products. While this enzyme has been extensively studied, several questions with respect to the catalytic mechanism have rema...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/acs.biochem.5b01347
更新日期：2016-04-12 00:00:00
abstract：:The three-dimensional conformation of a 24-nucleotide variant of the RNA binding sequence for the coat protein of bacteriophage R17 has been analyzed using NMR, molecular dynamics, and energy minimization. The imino proton spectrum is consistent with base pairing requirements for coat protein binding known from bioche...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00019a030
更新日期：1995-05-16 00:00:00
abstract：:Kinesin-5 proteins are essential for formation of a bipolar mitotic spindle in most and, perhaps all, eukaryotic cells. Several Kinesin-5 proteins, notably the human version, HsEg5, are targets of a constantly expanding group of small-molecule inhibitors, which hold promise both as tools for probing mechanochemical tr...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi801291q
更新日期：2009-03-03 00:00:00
abstract：:We have characterized the importance of size, sulfation, and anticoagulant activity of heparin in release of basic fibroblast growth factor (bFGF) from the subendothelial extracellular matrix (ECM) and the luminal surface of the vascular endothelium. For this purpose, 125I-bFGF was first incubated with ECM and conflue...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00122a027
更新日期：1992-02-25 00:00:00
abstract：:The fluorophore 4-heptadecyl-7-hydroxycoumarin was used as a probe to study the properties of phospholipid bilayers at the lipid-water interface. To this end, the steady-state fluorescence anisotropy, the differential polarized phase fluorometry, and the emission lifetime of the fluorophore were measured in isotropic ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00324a005
更新日期：1985-01-29 00:00:00
abstract：:Reconstitution of highly purified aquaporin CHIP (channel-forming integral protein) into proteoliposomes was previously shown to confer high osmotic water permeability (Pf) to the membranes [Zeidel et al. (1992) Biochemistry 31, 7436-7440]. Here we report detailed ultrastructural, pharmacologic, and transport studies ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00172a042
更新日期：1994-02-15 00:00:00
abstract：:Reaction center (RC) complexes isolated from a Zn-bacteriochlorophyll (BChl) a-containing purple bacterium, Acidiphilium rubrum, were characterized by absorption, circular dichroism, and magnetic circular dichroism (MCD) spectroscopy. The oxidized-minus-reduced difference spectra indicated that, in this RC, the Zn-BCh...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi991444e
更新日期：2000-04-11 00:00:00
abstract：:GMP and native DNA were reacted with 7-iodo and 7-fluoro derivatives of N-acetoxy-N-2-acetylaminofluorene. It was shown that the 7-halogeno derivatives react on C-8 of guanine. Furthermore the respective amount of arylamidation (covalent linkage on the C-8 of guanine) and arylation (covalent linkage on 2-NH2 groups of...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00606a016
更新日期：1978-06-27 00:00:00
abstract：:The inhibitory effect of phosphorothioate residues, located within one strand of double-stranded DNA, on the hydrolytic activity of the restriction endonuclease EcoRV was investigated. Specific incorporation of a phosphorothioate group at the site of cleavage yielded the sequence 5'-GATsATC-3'. This modified sequence ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00493a008
更新日期：1990-10-16 00:00:00
abstract：:Two-dimensional homonuclear and heteronuclear NMR and minimized potential energy calculations have been combined to define the structure of the antitumor agent mitomycin C (MC) cross-linked to deoxyguanosines on adjacent base pairs in the d(T1-A2-C3-G4-T5-A6).d(T7-A8-C9-G10-T11-A12) duplex. The majority of the mitomyc...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00463a032
更新日期：1990-03-20 00:00:00
abstract：:Resonance energy transfer measurements provide a way to estimate distances between chromophores attached to different sites of macromolecules. There are two unknowns involved in resonance energy transfer measurements, the distance between two chromophores and their relative orientation. When static orientational disor...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00149a027
更新日期：1992-09-01 00:00:00
abstract：:Here we report that the Methanocaldococcus jannaschii enzyme derived from the MJ0309 gene is an Fe(II) dependent agmatinase (SpeB). This is the first report of an iron-dependent agmatinase. We demonstrate that aerobically isolated recombinant enzyme contains two disulfide bonds and only a trace amount of any metal and...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi300039f
更新日期：2012-04-10 00:00:00
abstract：:Natriuretic peptide receptor A (NPRA) is a noncovalent homodimeric receptor, composed of an extracellular domain (ECD) with a ligand-binding site, a single transmembrane domain (TM), and an intracellular domain (ICD) exhibiting guanylyl cyclase activity. NPRA activation by atrial natriuretic peptide (ANP) leads to cGM...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi901711w
更新日期：2010-06-08 00:00:00
abstract：:The unique structural properties of the ferritin protein cages have provided impetus to focus on the methodical study of these self-assembling nanosystems. Among these proteins, Escherichia coli bacterioferritin (EcBfr), although architecturally very similar to other members of the family, shows structural instability...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi200207w
更新日期：2011-05-17 00:00:00
abstract：:DB2277, a heterocyclic diamidine, is a successful design for mixed base pair (bp) DNA sequence recognition. The compound has a central aza-benzimidazole group that forms two H-bonds with a GC bp that has flanking AT bps. The nuclear magnetic resonance structure of the DB2277-DNA complex with an AAGATA recognition site...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/acs.biochem.8b00647
更新日期：2018-08-21 00:00:00
abstract：:The polysaccharide-rich cell walls (CWs) of plants perform essential functions such as maintaining tensile strength and allowing plant growth. Using two- and three-dimensional magic-angle-spinning (MAS) solid-state NMR and uniformly (13)C-labeled Arabidopsis thaliana, we have assigned the resonances of the major polys...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi101795q
更新日期：2011-02-15 00:00:00
abstract：:Manganese superoxide dismutase (MnSOD) cycles between the Mn(II) and Mn(III) states during the catalyzed disproportionation of O(2)(*-), a catalysis that is limited at micromolar levels of superoxide by a peroxide-inhibited complex with the metal. We have investigated the role in catalysis and inhibition of the conser...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi011047f
更新日期：2001-10-09 00:00:00
abstract：:It has been shown by genetic analysis that the external and internal invertases from Saccharomyces cerevisiae share a common structural gene [Taussig, R., & Carlson, M. (1983) Nucleic Acids Res. 11, 1943-1954]. However, the only amino acid composition of these two forms of invertase reported to date has revealed exten...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00343a014
更新日期：1985-10-22 00:00:00
abstract：:As part of a search for organic compounds that selectively target RNA, we found that specific diphenylfuran derivatives, which are related to compounds that bind to the DNA minor groove, bind very strongly to RNA in a manner very sensitive to the structure of the compounds. In extended development of the diphenylfuran...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi002338b
更新日期：2001-02-06 00:00:00
abstract：:The importance of a specific hydrogen bond between thermolysin and a phosphonamidate inhibitor, Z-NHCH2-PO(O-)-Leu-Leu (1) [Bartlett, P. A., & Marlowe, C. K. (1987) Science (Washington D.C.) 235, 569-571], has been reevaluated. We have determined the inhibition constants (binding free energies) for thermolysin of phos...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00438a006
更新日期：1989-06-13 00:00:00
abstract：:The synthesis of sphingomyelin was studied in baby hamster kidney cells and in subcellular fractions derived from rat liver. During pulse-chase experiments with [3H]choline in tissue culture cells, the specific radioactivity of sphingomyelin continued to increase after the specific activities of phosphocholine and cyt...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00540a027
更新日期：1982-05-25 00:00:00
abstract：:Numerous studies have been published stressing the importance of finding ligands that can bind specifically to DNA secondary structures. Several have identified ligands that are presented as having specific binding to the G-quadruplex; however, these were not originally tested on the complementary i-motif structure. T...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/acs.biochem.8b00968
更新日期：2019-01-29 00:00:00
abstract：:The complete primary structure of the major component myoglobin from the Arctic minke whale, Balaenoptera acutorostrata, was determined by specific cleavage of the protein to obtain large peptides which are readily degraded by the automatic sequencer. Over 80% of the amino acid sequence was established from the three ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00623a023
更新日期：1977-02-22 00:00:00
abstract：:Aminoglycoside 2''-phosphotransferase IVa [APH(2'')-IVa] is a member of a family of bacterial enzymes responsible for medically relevant resistance to antibiotics. APH(2'')-IVa confers high-level resistance against several clinically used aminoglycoside antibiotics in various pathogenic Enterococcus species by phospho...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi200747f
更新日期：2011-07-19 00:00:00
abstract：:The abnormal isoform of the scrapie prion protein PrPSc is both a host-derived protein and a component of the infectious agent causing scrapie. PrPSc and the normal cellular isoform PrPC have different physical properties that apparently arise from a posttranslational event. Both PrP isoforms are covalently modified a...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00474a028
更新日期：1990-06-05 00:00:00
abstract：:Linker histone H1 plays an essential role in chromatin organization. Proper deposition of linker histone H1 as well as its removal is essential for chromatin dynamics and function. Linker histone chaperones perform this important task during chromatin assembly and other DNA-templated phenomena in the cell. Our in vitr...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi101835j
更新日期：2011-04-12 00:00:00
abstract：:There is no complete understanding of how serine protease inhibitors of the serpin family inhibit their target enzymes. Structural and biochemical studies have suggested that serpins utilize a mechanism that is distinct from the standard mechanism of inhibition proposed for most small protein protease inhibitors. Prot...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi960233w
更新日期：1996-06-11 00:00:00
abstract：:Previous work from this laboratory has established that the NADPH-menadione oxidoreductase reaction catalyzed by methylenetetrahydrofolate reductase from pig liver proceeds by Ping Pong Bi Bi kinetics and that the reductive half-reaction is rate limiting in steady-state turnover. We have now shown that methylenetetrah...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00317a027
更新日期：1984-10-23 00:00:00
abstract：:The effects of cysteine modification and variations in pH on the equilibrium parameters for inducer and operator binding to the lactose repressor protein were examined. Operator binding affinity was minimally affected by increasing the pH from 7.5 to 9.2, whereas inducer binding was decreased for both the unliganded p...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00367a020
更新日期：1986-09-23 00:00:00
