BioNMR
NMR aggregator & online community since 2003
BioNMR    
Learn or help to learn NMR - get free NMR books!
 

Go Back   BioNMR > Educational resources > Journal club
Advanced Search



Jobs Groups Conferences Literature Pulse sequences Software forums Programs Sample preps Web resources BioNMR issues


Webservers
NMR processing:
MDD
NMR assignment:
Backbone:
Autoassign
MARS
UNIO Match
PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
UNIO ATNOS-Candid
UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
UNIO Candid
Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
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:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
NOEs, other restraints:
PROSESS
PSVS
RPF scores
iCing
Chemical shifts:
PROSESS
CheShift2
Vasco
iCing
RDCs:
DC
Anisofit
Pseudocontact shifts:
Anisofit
Protein geomtery:
Resolution-by-Proxy
PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
PSQS
Eval123D
STAN
Ramachandran Plot
Rampage
ERRAT
Verify_3D
Harmony
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:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


Reply
Thread Tools Search this Thread Rate Thread Display Modes
  #1  
Unread 08-22-2010, 02:27 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 17,577
Points: 193,617, Level: 100
Points: 193,617, Level: 100 Points: 193,617, Level: 100 Points: 193,617, Level: 100
Level up: 0%, 0 Points needed
Level up: 0% Level up: 0% Level up: 0%
Activity: 50.7%
Activity: 50.7% Activity: 50.7% Activity: 50.7%
Last Achievements
Award-Showcase
NMR Credits: 0
NMR Points: 193,617
Downloads: 0
Uploads: 0
Default 1H-NMR studies on association of mRNA cap-analogues with tryptophan-containing peptid

1H-NMR studies on association of mRNA cap-analogues with tryptophan-containing peptides.

Related Articles 1H-NMR studies on association of mRNA cap-analogues with tryptophan-containing peptides.

Biochim Biophys Acta. 1996 Mar 7;1293(1):97-105

Authors: Stolarski R, Sitek A, StepiĹ?ski J, Jankowska M, Oksman P, Temeriusz A, Darzynkiewicz E, Lönnberg H, Shugar D

1H-NMR spectroscopy was applied to a study of the mode of interaction, in aqueous medium in the pH range 5.2-8.5 and at low and high temperatures, between several mono- and dinucleotide analogues of the mRNA cap m7GpppG and a selected tripeptide Trp-Leu-Glu, and a tetrapeptide Trp-Glu-Asp-Glu, the sequence of which corresponds to one of the suspected binding sites in the mRNA cap-binding protein (CBP). A program, GEOSHIFT, was developed, based on ring-current anisotropy theory, for analysis of experimentally observed changes in chemical shifts accompanying interactions between aromatic heterocyclic rings. This permitted quantitative evaluation of stacking interactions between the m7G cap and the tryptophan indole ring, and the relative orientations of the planes of the two rings, spaced about 3.2 angstroms apart. The structures of the stacked complexes were determined. In particular, stacking between m(2,2,7)3G (which has no free amino group for hydrogen bonding) and the indole ring is weaker and quite different from that between m7G and m(2,7)2G and indole. With the dinucleotide cap-analogues, only the m7G component stacks with the indole ring, without disruption of intramolecular stacking. In contrast to numerous earlier reports, the calculated stacking interactions are quantitatively in accord with the values derived from fluorescence measurements. It also has been shown that the positively charged (cationic) form of m7G stacks much more efficiently with the indole ring than the zwitterionic form resulting from dissociation of the guanine ring N1H (pKa approximately 7.3).

PMID: 8652634 [PubMed - indexed for MEDLINE]



Source: PubMed
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Antimicrobial peptides and their superior fluorinated analogues: structure-activity relationships as revealed by NMR spectroscopy and MD calculations.
Antimicrobial peptides and their superior fluorinated analogues: structure-activity relationships as revealed by NMR spectroscopy and MD calculations. Antimicrobial peptides and their superior fluorinated analogues: structure-activity relationships as revealed by NMR spectroscopy and MD calculations. Chembiochem. 2010 Nov 22;11(17):2424-32 Authors: Díaz MD, Palomino-Schätzlein M, Corzana F, Andreu C, Carbajo RJ, del Olmo M, Canales-Mayordomo A, Pineda-Lucena A, Asensio G, Jiménez-Barbero J The conformations of two synthetic pentapeptides with...
nmrlearner Journal club 0 05-04-2011 04:14 PM
Modular protein-RNA interactions regulating mRNA metabolism: a role for NMR.
Modular protein-RNA interactions regulating mRNA metabolism: a role for NMR. Modular protein-RNA interactions regulating mRNA metabolism: a role for NMR. Eur Biophys J. 2011 Apr 7; Authors: Cukier CD, Ramos A Here we review the role played by transient interactions between multi-functional proteins and their RNA targets in the regulation of mRNA metabolism, and we describe the important function of NMR spectroscopy in the study of these systems. We place emphasis on a general approach for the study of different features of modular multi-domain...
nmrlearner Journal club 0 04-08-2011 10:00 AM
NMR structure of the let-7 miRNA interacting with the site LCS1 of lin-41 mRNA from Caenorhabditis elegans.
NMR structure of the let-7 miRNA interacting with the site LCS1 of lin-41 mRNA from Caenorhabditis elegans. NMR structure of the let-7 miRNA interacting with the site LCS1 of lin-41 mRNA from Caenorhabditis elegans. Nucleic Acids Res. 2010 Nov 1;38(21):7814-21 Authors: Cevec M, Thibaudeau C, Plavec J We have determined the 3D structure of a 34-nt RNA construct, herein named LCS1co, which mimics the interaction of let-7 microRNA (miRNA) to one of its complementary binding sites, LCS1, in the 3'-untranslated region of lin-41 mRNA by solution-state...
nmrlearner Journal club 0 01-14-2011 12:05 PM
[NMR paper] Joint X-ray and NMR refinement of the yeast L30e-mRNA complex.
Joint X-ray and NMR refinement of the yeast L30e-mRNA complex. Related Articles Joint X-ray and NMR refinement of the yeast L30e-mRNA complex. Structure. 2004 Jul;12(7):1165-76 Authors: Chao JA, Williamson JR L30e, a Saccharomyces cervisiae ribosomal protein, regulates its own expression by binding to a purine-rich asymmetric internal loop located in both its pre-mRNA and mature mRNA. A crystal structure of an MBP-L30e fusion protein in complex with an RNA containing the pre-mRNA regulatory site was solved at 3.24 A. Interestingly, the...
nmrlearner Journal club 0 11-24-2010 09:51 PM
[NMR paper] Conformational analysis of peptide analogues of silkmoth chorion protein segments usi
Conformational analysis of peptide analogues of silkmoth chorion protein segments using CD, NMR and molecular modelling. Related Articles Conformational analysis of peptide analogues of silkmoth chorion protein segments using CD, NMR and molecular modelling. J Pept Sci. 2004 Jun;10(6):381-92 Authors: Benaki DC, Mikros E, Hamodrakas SJ Silkmoth proteins secreted from the follicular cells that surround the oocyte form a large extracellular assembly which is important for protecting and sustaining the structure of the oocyte and the developing...
nmrlearner Journal club 0 11-24-2010 09:51 PM
[NMR paper] Real-time refolding studies of 6-19F-tryptophan labeled Escherichia coli dihydrofolat
Real-time refolding studies of 6-19F-tryptophan labeled Escherichia coli dihydrofolate reductase using stopped-flow NMR spectroscopy. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles Real-time refolding studies of 6-19F-tryptophan labeled Escherichia coli dihydrofolate reductase using stopped-flow NMR spectroscopy. Biochemistry. 1996 Dec 24;35(51):16843-51 Authors: Hoeltzli SD, Frieden C Escherichia coli dihydrofolate reductase (ecDHFR, EC1.5.1.3) contains 5 tryptophan residues that have...
nmrlearner Journal club 0 08-22-2010 02:20 PM
[NMR paper] Stopped-flow NMR spectroscopy: real-time unfolding studies of 6-19F-tryptophan-labele
Stopped-flow NMR spectroscopy: real-time unfolding studies of 6-19F-tryptophan-labeled Escherichia coli dihydrofolate reductase. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles Stopped-flow NMR spectroscopy: real-time unfolding studies of 6-19F-tryptophan-labeled Escherichia coli dihydrofolate reductase. Proc Natl Acad Sci U S A. 1995 Sep 26;92(20):9318-22 Authors: Hoeltzli SD, Frieden C Escherichia coli dihydrofolate reductase (DHFR; EC 1.5.1.3) contains...
nmrlearner Journal club 0 08-22-2010 03:50 AM
[NMR paper] Studies of protein-protein association between yeast cytochrome c peroxidase and yeas
Studies of protein-protein association between yeast cytochrome c peroxidase and yeast iso-1 ferricytochrome c by hydrogen-deuterium exchange labeling and proton NMR spectroscopy. Related Articles Studies of protein-protein association between yeast cytochrome c peroxidase and yeast iso-1 ferricytochrome c by hydrogen-deuterium exchange labeling and proton NMR spectroscopy. Biochemistry. 1994 Oct 11;33(40):12032-41 Authors: Yi Q, Erman JE, Satterlee JD Hydrogen-deuterium (H-D) exchange labeling and proton NMR have been applied to study the...
nmrlearner Journal club 0 08-22-2010 03:29 AM


Thread Tools Search this Thread
Search this Thread:

Advanced Search
Display Modes Rate This Thread
Rate This 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



BioNMR advertisements to pay for website hosting and domain registration. Nobody does it for us.



Powered by vBulletin® Version 3.7.3
Copyright ©2000 - 2017, Jelsoft Enterprises Ltd.
Copyright, BioNMR.com, 2003-2013
Search Engine Friendly URLs by vBSEO 3.6.0

All times are GMT. The time now is 01:27 AM.


Map