NMR paper Rapid and simple approach for the NMR resonance assignment of the carbohydrate chains

		BioNMR > Educational resources > Journal club
[NMR paper] Rapid and simple approach for the NMR resonance assignment of the carbohydrate chains

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:

Thread Tools

Search this Thread

Rate Thread

Display Modes

08-22-2010, 03:29 AM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,732

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

Rapid and simple approach for the NMR resonance assignment of the carbohydrate chains

Rapid and simple approach for the NMR resonance assignment of the carbohydrate chains of an intact glycoprotein. Application of gradient-enhanced natural abundance 1H-13C HSQC and HSQC-TOCSY to the alpha-subunit of human chorionic gonadotropin.

Related Articles Rapid and simple approach for the NMR resonance assignment of the carbohydrate chains of an intact glycoprotein. Application of gradient-enhanced natural abundance 1H-13C HSQC and HSQC-TOCSY to the alpha-subunit of human chorionic gonadotropin.

FEBS Lett. 1994 Jul 4;348(1):1-6

Authors: de Beer T, van Zuylen CW, HÃ¥rd K, Boelens R, Kaptein R, Kamerling JP, Vliegenthart JF

The structure assessment of an intact glycoprotein in solution requires an extensive assignment of the carbohydrate NMR resonances. However, assignment of homonuclear spectra is very complicated because of the severe overlap of protein and carbohydrate signals. Application of pulsed field gradients allowed high quality natural abundance 1H-13C HSQC and HSQC-TOCSY spectra to be recorded of the alpha-subunit of human chorionic gonadotropin. Most carbohydrate 1H-13C correlations appear in a distinct region between the aromatic region and the protein C alpha-H alpha region. The enormous reduction in overlap led to fast and unambiguous assignment of the anomeric 1H-13C correlations. Subsequently, correlations of the monosaccharide skeleton atoms were readily assigned in the HSQC-TOCSY spectrum.

PMID: 8026573 [PubMed - indexed for MEDLINE]

Source: PubMed

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[Question from NMRWiki Q&A forum] Simple 1H-NMR Assignment Query Simple 1H-NMR Assignment Query Hi guys, sorry to be really cheeky and sign up simply to ask for help, but here goes. I've done a simple Grignard addition of isopropyl magnesium bromide to 3-methoxy benzaldehyde and I'm just assigning the peaks, but I've come up stumped on one issue. Concerning the isopropyl -CH(CH3)2 proton (at approximately d=1.95p.p.m.), it's observed as a septet, but the integration is 2.14 and I'm stuck as to why. This Grignard addition should occur non-preferentially at either the Re-/Si- face of the aldehyde, so can it be explained by some form of entiomeric...	nmrlearner	News from other NMR forums	0	10-15-2011 08:16 PM
4D APSY-HBCB(CG)CDHD experiment for automated assignment of aromatic amino acid side chains in proteins 4D APSY-HBCB(CG)CDHD experiment for automated assignment of aromatic amino acid side chains in proteins Abstract A four-dimensional (4D) APSY (automated projection spectroscopy)-HBCB(CG)CDHD experiment is presented. This 4D experiment correlates aromatic with aliphatic carbon and proton resonances from the same amino acid side chain of proteins in aqueous solution. It thus allows unambiguous sequence-specific assignment of aromatic amino acid ring signals based on backbone assignments. Compared to conventional 2D approaches, the inclusion of evolution periods on 1HÎ² and 13CÎ´...	nmrlearner	Journal club	0	09-30-2011 08:01 PM
A simple biosynthetic method for stereospecific resonance assignment of prochiral methyl groups in proteins A simple biosynthetic method for stereospecific resonance assignment of prochiral methyl groups in proteins Abstract A new method for stereospecific assignment of prochiral methyl groups in proteins is presented in which protein samples are produced using U-glucose and subsaturating amounts of 2-methyl-acetolactate. The resulting non-uniform labeling pattern allows proR and proS methyl groups to be easily distinguished by their different phases in a constant-time two-dimensional 1H-13C correlation spectra. Protein samples are conveniently prepared using the same media composition as the...	nmrlearner	Journal club	0	02-06-2011 07:42 PM
[NMR paper] NMR assignment of protein side chains using residue-correlated labeling and NOE spect NMR assignment of protein side chains using residue-correlated labeling and NOE spectra. Related Articles NMR assignment of protein side chains using residue-correlated labeling and NOE spectra. J Magn Reson. 2003 Dec;165(2):237-47 Authors: Mueller GA, Kirby TW, DeRose EF, London RE A new approach for the isotopic labeling of proteins is proposed that aims to facilitate side chain resonance assignments. Residue-correlated (RC) labeling is achieved by the expression of a protein on a medium containing a mixture of labeled, e.g., amino acids,...	nmrlearner	Journal club	0	11-24-2010 09:16 PM
Rapid, Accurate and Simple Model to Predict NMR Chemical Shifts for Biological Molecu Rapid, Accurate and Simple Model to Predict NMR Chemical Shifts for Biological Molecules. Rapid, Accurate and Simple Model to Predict NMR Chemical Shifts for Biological Molecules. J Phys Chem B. 2010 Nov 18; Authors: Atieh Z, Aubert-Fre?con M, Allouche AR We present a new model to predict chemical shifts for biological molecules. It is simple, fast, and involves a limited number of parameters. It is particularly adapted to be used in molecular dynamics studies with a molecular mechanic potential. We test the model for polyamines, which are rather...	nmrlearner	Journal club	0	11-20-2010 06:01 PM
[NMR paper] Dynamics of the carbohydrate chains attached to the Fc portion of immunoglobulin G as Dynamics of the carbohydrate chains attached to the Fc portion of immunoglobulin G as studied by NMR spectroscopy assisted by selective 13C labeling of the glycans. Related Articles Dynamics of the carbohydrate chains attached to the Fc portion of immunoglobulin G as studied by NMR spectroscopy assisted by selective 13C labeling of the glycans. J Biomol NMR. 1998 Oct;12(3):385-94 Authors: Yamaguchi Y, Kato K, Shindo M, Aoki S, Furusho K, Koga K, Takahashi N, Arata Y, Shimada I A systematic method for 13C labeling of the glycan of...	nmrlearner	Journal club	0	11-17-2010 11:15 PM
[NMR paper] A simple approach to analyzing protein side-chain dynamics from 13C NMR relaxation da A simple approach to analyzing protein side-chain dynamics from 13C NMR relaxation data. Related Articles A simple approach to analyzing protein side-chain dynamics from 13C NMR relaxation data. J Magn Reson. 1998 Feb;130(2):329-34 Authors: Daragan VA, Mayo KH A simple approach to deriving motional dynamics information of protein and peptide side chains by using 13C NMR relaxation data is presented. By using linear approximation of internal rotational correlation functions, simple equations for relating side-chain conformation, bond rotational...	nmrlearner	Journal club	0	11-17-2010 11:06 PM
Sequence specific resonance assignment via Multicanonical Monte Carlo search using an ABACUS approach Sequence specific resonance assignment via Multicanonical Monte Carlo search using an ABACUS approach Alexander Lemak, Carlos A. Steren, Cheryl H. Arrowsmith and Miguel Llinás Journal of Biomolecular NMR; 2008; 41(1); pp 29 - 41 Abstract: ABACUS is a novel protocol for automated protein structure determination via NMR. ABACUS starts from molecular fragments defined by unassigned J-coupled spin-systems and involves a Monte Carlo stochastic search in assignment space, probabilistic sequence selection, and assembly of fragments into structures that are used to guide the stochastic...	Mikey	Journal club	0	08-14-2008 12:37 AM

« 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