NMR paper Oxidation of guanines in the iron-responsive element RNA: similar structures from che

		BioNMR > Educational resources > Journal club
[NMR paper] Oxidation of guanines in the iron-responsive element RNA: similar structures from che

Webservers

NMR processing:

MDD

NMR assignment:

Backbone:

Side-chains:

NOEs:

Structure from NMR restraints:

Ab initio:

Fragment-based:

Rosetta-NMR (Robetta)

Template-based:

GeNMR

I-TASSER

Refinement:

Amber

Structure from chemical shifts:

Fragment-based:

Homology-based:

Torsion angles from chemical shifts:

Preditor

TALOS

Promega- Proline

Secondary structure from chemical shifts:

CSI (via RCI server)

TALOS

MICS caps, β-turns

d2D

PECAN

Flexibility from chemical shifts:

RCI

Interactions from chemical shifts:

HADDOCK

Chemical shifts re-referencing:

NMR model quality:

NOEs, other restraints:

Chemical shifts:

RDCs:

Pseudocontact shifts:

Protein geomtery:

SAVES2 or SAVES4

Quality Control Check

NMR spectrum prediction:

FANDAS

MestReS

V-NMR

Flexibility from structure:

Backbone S2

Methyl S2

B-factor

Molecular dynamics:

Gromacs

Amber

Antechamber

Chemical shifts prediction:

From structure:

Shiftx2

Sparta+

Camshift

CH3shift- Methyl

ArShift- Aromatic

ShiftS

Proshift

PPM

CheShift-2- Cα

From sequence:

Shifty

Camcoil

Poulsen_rc_CS

Disordered proteins:

MAXOCC

Format conversion & validation:

CCPN

From NMR-STAR 3.1

Validate NMR-STAR 3.1

NMR sample preparation:

Protein disorder:

DisMeta

Protein solubility:

Isotope labeling:

Solid-state NMR:

View First Unread

Thread Tools

Search this Thread

Rate Thread

Display Modes

11-17-2010, 11:15 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,175

Points: 193,617, Level: 100

Level up: 0%, 0 Points needed

Activity: 50.7%

Last Achievements

Award-Showcase

NMR Credits: 0

NMR Points: 193,617

Downloads: 0

Uploads: 0

Oxidation of guanines in the iron-responsive element RNA: similar structures from che

Oxidation of guanines in the iron-responsive element RNA: similar structures from chemical modification and recent NMR studies.

Related Articles Oxidation of guanines in the iron-responsive element RNA: similar structures from chemical modification and recent NMR studies.

Chem Biol. 1998 Dec;5(12):679-87

Authors: Ciftan SA, Theil EC, Thorp HH

BACKGROUND: The translation or stability of the mRNAs from ferritin, maconitase, erythroid aminoevulinate synthase and the transferrin receptor is controlled by the binding of two iron regulatory proteins to a family of hairpin-forming RNA sequences called iron-responsive elements (IREs). The determination of high-resolution nuclear magnetic resonance (NMR) structures of IRE variants suggests an unusual hexaloop structure, leading to an intra-loop G-C base pair and a highly exposed loop guanine, and a special internal loop/bulge in the ferritin IRE involving a shift in base pairing not predicted with standard algorithms. RESULTS: Cleavage of synthetic 55- and 30-mer RNA oligonucleotides corresponding to the ferritin IRE with complexes based on oxoruthenium(IV) shows enhanced reactivity at a hexaloop guanine and at a guanine adjacent to the internal loop/bulge with strong protection at a guanine in the internal loop/bulge. These results are consistent with the recent NMR structures. The synthetic 55-mer RNA binds the iron-regulatory protein from rabbit reticulocyte lysates. The DNA analogs of the 55- and 30-mers do not show the same reactivity pattern. CONCLUSIONS: The chemical reactivity of the guanines in the ferritin IRE towards oxoruthenium(IV) supports the published NMR structures and the known oxidation chemistry of the metal complexes. The results constitute progress towards developing stand-alone chemical nucleases that reveal significant structural properties and provide results that can ultimately be used to constrain molecular modeling.

PMID: 9862796 [PubMed - indexed for MEDLINE]

Source: PubMed

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR paper] NMR structures reveal how oxidation inactivates thrombomodulin. NMR structures reveal how oxidation inactivates thrombomodulin. Related Articles NMR structures reveal how oxidation inactivates thrombomodulin. Biochemistry. 2003 Oct 21;42(41):11932-42 Authors: Wood MJ, Becvar LA, Prieto JH, Melacini G, Komives EA Oxidation of Met 388, one of the three linker residues connecting the fourth and fifth EGF-like domains of thrombomodulin (TM), is deleterious for TM activity. An NMR structure of the smallest active fragment of TM (TMEGF45) and a crystal structure of a larger fragment (TMEGF456) bound to thrombin...	nmrlearner	Journal club	0	11-24-2010 09:16 PM
[NMR paper] Bending and adaptability to proteins of the cAMP DNA-responsive element: molecular dy Bending and adaptability to proteins of the cAMP DNA-responsive element: molecular dynamics contrasted with NMR. Related Articles Bending and adaptability to proteins of the cAMP DNA-responsive element: molecular dynamics contrasted with NMR. Biophys J. 2000 Aug;79(2):656-69 Authors: Derreumaux S, Fermandjian S DNA bending is assumed to play a crucial role during recognition of the cAMP-responsive element (CRE) by transcription factors. However, diverging results have been obtained for the bending direction of the unbound double helix. The...	nmrlearner	Journal club	0	11-19-2010 08:29 PM
[NMR paper] Mechanism of neomycin and Rev peptide binding to the Rev responsive element of HIV-1 Mechanism of neomycin and Rev peptide binding to the Rev responsive element of HIV-1 as determined by fluorescence and NMR spectroscopy. Related Articles Mechanism of neomycin and Rev peptide binding to the Rev responsive element of HIV-1 as determined by fluorescence and NMR spectroscopy. Biochemistry. 2000 May 16;39(19):5630-41 Authors: Lacourciere KA, Stivers JT, Marino JP Rev is an essential HIV-1 regulatory protein that binds the Rev responsive element (RRE) within the env gene of the HIV-1 RNA genome and is involved in transport of...	nmrlearner	Journal club	0	11-18-2010 09:15 PM
[NMR paper] Iron uptake by ferritin: NMR relaxometry studies at low iron loads. Iron uptake by ferritin: NMR relaxometry studies at low iron loads. Related Articles Iron uptake by ferritin: NMR relaxometry studies at low iron loads. J Inorg Biochem. 1998 Sep;71(3-4):153-7 Authors: Vymazal J, Brooks RA, Bulte JW, Gordon D, Aisen P Twenty ferritin samples were prepared at pH 6.5 with average loadings of 0-89 Fe atoms per molecule. Nuclear magnetic relaxation times T1 and T2 were measured at 3 degrees C, 23 degrees C, and at 37 degrees C and at field strength from 0.025 to 1.5 T. The field dependence, temperature dependence,...	nmrlearner	Journal club	0	11-17-2010 11:15 PM
[NMR paper] Investigation of oxidation state-dependent conformational changes in Desulfovibrio vu Investigation of oxidation state-dependent conformational changes in Desulfovibrio vulgaris Hildenborough cytochrome c553 by two-dimensional H-NMR spectra. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Investigation of oxidation state-dependent conformational changes in Desulfovibrio vulgaris Hildenborough cytochrome c553 by two-dimensional H-NMR spectra. FEBS Lett. 1996 Jul 1;389(2):203-9 Authors: Blanchard L, Blackledge MJ, Marion D, Guerlesquin F Two-dimensional...	nmrlearner	Journal club	0	08-22-2010 02:27 PM
[NMR paper] A model of the iron responsive element RNA hairpin loop structure determined from NMR A model of the iron responsive element RNA hairpin loop structure determined from NMR and thermodynamic data. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles A model of the iron responsive element RNA hairpin loop structure determined from NMR and thermodynamic data. Biochemistry. 1996 Oct 22;35(42):13586-96 Authors: Laing LG, Hall KB The iron responsive element (IRE) is a conserved RNA structure that is found in the 5' UTR of ferritin mRNA and in the 3' UTR of transferrin receptor mRNA....	nmrlearner	Journal club	0	08-22-2010 02:20 PM
[NMR paper] The importance of a single G in the hairpin loop of the iron responsive element (IRE) The importance of a single G in the hairpin loop of the iron responsive element (IRE) in ferritin mRNA for structure: an NMR spectroscopy study. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles The importance of a single G in the hairpin loop of the iron responsive element (IRE) in ferritin mRNA for structure: an NMR spectroscopy study. Nucleic Acids Res. 1995 Jan 11;23(1):146-53 Authors: Sierzputowska-Gracz H, McKenzie RA, Theil EC Noncoding sequences...	nmrlearner	Journal club	0	08-22-2010 03:41 AM
[NMR paper] An intrinsic curvature towards the minor groove in the cAMP-responsive element DNA fo An intrinsic curvature towards the minor groove in the cAMP-responsive element DNA found by combined NMR and molecular modelling studies. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif Related Articles An intrinsic curvature towards the minor groove in the cAMP-responsive element DNA found by combined NMR and molecular modelling studies. Eur J Biochem. 1999 Feb;259(3):877-86 Authors: Chaoui M, Derreumaux S, Mauffret O, Fermandjian S The...	nmrlearner	Journal club	0	08-21-2010 04:03 PM

« Previous Thread | Next Thread »

Posting Rules
You may not post new threads You may not post replies You may not post attachments You may not edit your posts BB code is On Smilies are On [IMG] code is On HTML code is On Trackbacks are Off Pingbacks are Off Refbacks are Off