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 06-19-2014, 10:21 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,135
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 NMR structure analysis of uniformly 13C-labeled carbohydrates

NMR structure analysis of uniformly 13C-labeled carbohydrates

Abstract

In this study, a set of nuclear magnetic resonance experiments, some of them commonly used in the study of 13C-labeled proteins and/or nucleic acids, is applied for the structure determination of uniformly 13C-enriched carbohydrates. Two model substances were employed: one compound of low molecular weight [(UL-13C)-sucrose, 342Â*Da] and one compound of medium molecular weight (13C-enriched O-antigenic polysaccharide isolated from Escherichia coli O142, ~10Â*kDa). The first step in this approach involves the assignment of the carbon resonances in each monosaccharide spin system using the anomeric carbon signal as the starting point. The 13C resonances are traced using 13Câ??13C correlations from homonuclear experiments, such as (H)CCâ??CTâ??COSY, (H)CCâ??NOESY, CCâ??CTâ??TOCSY and/or virtually decoupled (H)CCâ??TOCSY. Based on the assignment of the 13C resonances, the 1H chemical shifts are derived in a straightforward manner using one-bond 1Hâ??13C correlations from heteronuclear experiments (HCâ??CTâ??HSQC). In order to avoid the 1 J CC splitting of the 13C resonances and to improve the resolution, either constant-time (CT) in the indirect dimension or virtual decoupling in the direct dimension were used. The monosaccharide sequence and linkage positions in oligosaccharides were determined using either 13C or 1H detected experiments, namely CCâ??CTâ??COSY, band-selective (H)CCâ??TOCSY, HCâ??CTâ??HSQCâ??NOESY or long-range HCâ??CTâ??HSQC. However, due to the short T2 relaxation time associated with larger polysaccharides, the sequential information in the O-antigen polysaccharide from E. coli O142 could only be elucidated using the 1H-detected experiments. Exchanging protons of hydroxyl groups and N-acetyl amides in the 13C-enriched polysaccharide were assigned by using HCâ??H2BC spectra. The assignment of the N-acetyl groups with 15N at natural abundance was completed by using HNâ??SOFASTâ??HMQC, HNCA, HNCO and 13C-detected (H)CACO spectra.



Source: Journal of Biomolecular NMR
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[NMR paper] NMR structure analysis of uniformly (13)C-labeled carbohydrates.
NMR structure analysis of uniformly (13)C-labeled carbohydrates. Related Articles NMR structure analysis of uniformly (13)C-labeled carbohydrates. J Biomol NMR. 2014 Apr 26; Authors: Fontana C, Kovacs H, Widmalm G Abstract In this study, a set of nuclear magnetic resonance experiments, some of them commonly used in the study of (13)C-labeled proteins and/or nucleic acids, is applied for the structure determination of uniformly (13)C-enriched carbohydrates. Two model substances were employed: one compound of low molecular weight ...
nmrlearner Journal club 0 04-29-2014 12:04 PM
A rigid lanthanide binding tag for NMR structural analysis of carbohydrates.
A rigid lanthanide binding tag for NMR structural analysis of carbohydrates. A rigid lanthanide binding tag for NMR structural analysis of carbohydrates. Chem Commun (Camb). 2011 May 23; Authors: Mallagaray A, Canales A, Domínguez G, Jiménez-Barbero J, Pérez-Castells J The first synthesis of a carbohydrate molecule covalently bound to a rigid lanthanide binding tag is reported. This derivative has been designed as a new tool to provide long-range restraints for structural elucidation and molecular recognition studies of carbohydrates, thus...
nmrlearner Journal club 0 05-25-2011 07:01 PM
[NMR paper] Towards high-resolution solid-state NMR on large uniformly 15N- and [13C,15N]-labeled
Towards high-resolution solid-state NMR on large uniformly 15N- and -labeled membrane proteins in oriented lipid bilayers. Related Articles Towards high-resolution solid-state NMR on large uniformly 15N- and -labeled membrane proteins in oriented lipid bilayers. J Biomol NMR. 2002 Mar;22(3):225-47 Authors: Vosegaard T, Nielsen NC Based on exact numerical simulations, taking into account isotropic and conformation-dependent anisotropic nuclear spin interactions, we systematically analyse the prospects for high-resolution solid-state NMR on...
nmrlearner Journal club 0 11-24-2010 08:49 PM
[NMR paper] Preparation and characterization of a uniformly 2 H/ 15 N-labeled RNA oligonucleotide
Preparation and characterization of a uniformly 2 H/ 15 N-labeled RNA oligonucleotide for NMR studies. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--highwire.stanford.edu-icons-externalservices-pubmed-custom-oxfordjournals_final_free.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles Preparation and characterization of a uniformly 2 H/ 15 N-labeled RNA oligonucleotide for NMR studies. Nucleic Acids Res. 1997 Apr 1;25(7):1390-6 Authors: Nikonowicz EP,...
nmrlearner Journal club 0 08-22-2010 03:31 PM
[NMR paper] Preparation and characterization of a uniformly 2 H/ 15 N-labeled RNA oligonucleotide
Preparation and characterization of a uniformly 2 H/ 15 N-labeled RNA oligonucleotide for NMR studies. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--highwire.stanford.edu-icons-externalservices-pubmed-custom-oxfordjournals_final_free.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles Preparation and characterization of a uniformly 2 H/ 15 N-labeled RNA oligonucleotide for NMR studies. Nucleic Acids Res. 1997 Apr 1;25(7):1390-6 Authors: Nikonowicz EP,...
nmrlearner Journal club 0 08-22-2010 03:03 PM
[NMR paper] Expression of human chorionic gonadotropin uniformly labeled with NMR isotopes in Chi
Expression of human chorionic gonadotropin uniformly labeled with NMR isotopes in Chinese hamster ovary cells: an advance toward rapid determination of glycoprotein structures. Related Articles Expression of human chorionic gonadotropin uniformly labeled with NMR isotopes in Chinese hamster ovary cells: an advance toward rapid determination of glycoprotein structures. J Biomol NMR. 1996 Jun;7(4):295-304 Authors: Lustbader JW, Birken S, Pollak S, Pound A, Chait BT, Mirza UA, Ramnarain S, Canfield RE, Brown JM Most secreted eukaryotic proteins...
nmrlearner Journal club 0 08-22-2010 02:27 PM
[NMR paper] 15N NMR assignments and chemical shift analysis of uniformly labeled 15N calbindin D9
15N NMR assignments and chemical shift analysis of uniformly labeled 15N calbindin D9k in the apo, (Cd2+)1 and (Ca2+)2 states. Related Articles 15N NMR assignments and chemical shift analysis of uniformly labeled 15N calbindin D9k in the apo, (Cd2+)1 and (Ca2+)2 states. FEBS Lett. 1992 Jun 1;303(2-3):136-40 Authors: Skelton NJ, Akke M, Kördel J, Thulin E, Forsén S, Chazin WJ 15N has been uniformly incorporated into the EF-hand Ca(2+)-binding protein calbindin D9k so that heteronuclear experiments can be used to further characterize the...
nmrlearner Journal club 0 08-21-2010 11:41 PM
[NMR paper] Two-dimensional 1H, 15N NMR investigation of uniformly 15N-labeled lac repressor head
Two-dimensional 1H, 15N NMR investigation of uniformly 15N-labeled lac repressor headpiece. Related Articles Two-dimensional 1H, 15N NMR investigation of uniformly 15N-labeled lac repressor headpiece. J Biomol Struct Dyn. 1992 Apr;9(5):921-33 Authors: Lancelot G, Gervais A, Maurizot JC 15N uniformly labeled lac repressor and lac repressor headpiece were prepared. 15N NMR spectra of lac repressor were shown resolution inadequate for detailed study while the data showed that the 15N labeled N-terminal part of the protein is quite suitable for...
nmrlearner Journal club 0 08-21-2010 11:41 PM


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 - 2024, 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 04:59 AM.


Map