Synthesis and Molecular Recognition Studies of the HNK-1 Trisaccharide and Related Oligosaccharides. The Specificity of Monoclonal Anti-HNK-1 Antibodies as Assessed by Surface Plasmon Resonance and STD NMR

		BioNMR > Educational resources > Journal club
Synthesis and Molecular Recognition Studies of the HNK-1 Trisaccharide and Related Oligosaccharides. The Specificity of Monoclonal Anti-HNK-1 Antibodies as Assessed by Surface Plasmon Resonance and STD NMR

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

12-20-2011, 04:09 AM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,777

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

Synthesis and Molecular Recognition Studies of the HNK-1 Trisaccharide and Related Oligosaccharides. The Specificity of Monoclonal Anti-HNK-1 Antibodies as Assessed by Surface Plasmon Resonance and STD NMR

Yury E. Tsvetkov, Monika Burg-Roderfeld, Gabriele Loers, Ana Arda?, Elena V. Sukhova, Elena A. Khatuntseva, Alexey A. Grachev, Alexander O. Chizhov, Hans-Christian Siebert, Melitta Schachner, Jesu?s Jime?nez-Barbero and Nikolay E. Nifantiev

Journal of the American Chemical Society
DOI: 10.1021/ja2083015

Source: Journal of the American Chemical Society

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Structure and lipid interactions of an anti-inflammatory and anti-atherogenic 10-residue class G() apolipoprotein J peptide using solution NMR. Structure and lipid interactions of an anti-inflammatory and anti-atherogenic 10-residue class G() apolipoprotein J peptide using solution NMR. Structure and lipid interactions of an anti-inflammatory and anti-atherogenic 10-residue class G(*) apolipoprotein J peptide using solution NMR. Biochim Biophys Acta. 2011 Jan;1808(1):498-507 Authors: Mishra VK, Palgunachari MN, Hudson JS, Shin R, Keenum TD, Krishna NR, Anantharamaiah GM The surprising observation that a 10-residue class G(?) peptide from apolipoprotein J, apoJ, possesses...	nmrlearner	Journal club	0	03-08-2011 01:40 PM
[NMR paper] Molecular insight into the electrostatic membrane surface potential by 14n/31p MAS NM Molecular insight into the electrostatic membrane surface potential by 14n/31p MAS NMR spectroscopy: nociceptin-lipid association. Related Articles Molecular insight into the electrostatic membrane surface potential by 14n/31p MAS NMR spectroscopy: nociceptin-lipid association. J Am Chem Soc. 2005 May 11;127(18):6610-6 Authors: Lindström F, Williamson PT, Gröbner G Exploiting naturally abundant (14)N and (31)P nuclei by high-resolution MAS NMR (magic angle spinning nuclear magnetic resonance) provides a molecular view of the electrostatic...	nmrlearner	Journal club	0	11-25-2010 08:21 PM
[NMR paper] Design of a functional protein for molecular recognition: specificity of ligand bindi Design of a functional protein for molecular recognition: specificity of ligand binding in a metal-assembled protein cavity probed by 19f NMR. Related Articles Design of a functional protein for molecular recognition: specificity of ligand binding in a metal-assembled protein cavity probed by 19f NMR. J Am Chem Soc. 2004 Apr 7;126(13):4192-8 Authors: Doerr AJ, Case MA, Pelczer I, McLendon GL A metal-assembled homotrimeric coiled coil based on the GCN4-p1 sequence has been designed that noncovalently binds hexafluorobenzene and other similar...	nmrlearner	Journal club	0	11-24-2010 09:51 PM
[NMR paper] Epitope mapping of gibberellin to the anti-gibberellin A(4) monoclonal antibody by sa Epitope mapping of gibberellin to the anti-gibberellin A(4) monoclonal antibody by saturation transfer difference NMR spectroscopy. Related Articles Epitope mapping of gibberellin to the anti-gibberellin A(4) monoclonal antibody by saturation transfer difference NMR spectroscopy. Biochem Biophys Res Commun. 2003 Aug 1;307(3):498-502 Authors: Murata T, Hemmi H, Nakajima M, Yoshida M, Yamaguchi I Saturation transfer difference (STD) NMR spectroscopy is a promising tool for rapid screening, identifying ligands that interact with a target protein,...	nmrlearner	Journal club	0	11-24-2010 09:16 PM
[NMR paper] Heteronuclear NMR studies of the specificity of the post-translational modification o Heteronuclear NMR studies of the specificity of the post-translational modification of biotinyl domains by biotinyl protein ligase. Related Articles Heteronuclear NMR studies of the specificity of the post-translational modification of biotinyl domains by biotinyl protein ligase. FEBS Lett. 2000 Aug 18;479(3):93-8 Authors: Reche PA, Howard MJ, Broadhurst RW, Perham RN The lipoyl domains of 2-oxo acid dehydrogenase multienzyme complexes and the biotinyl domains of biotin-dependent enzymes have homologous structures, but the target lysine...	nmrlearner	Journal club	0	11-19-2010 08:29 PM
[NMR paper] NMR structure of an anti-gp120 antibody complex with a V3 peptide reveals a surface i NMR structure of an anti-gp120 antibody complex with a V3 peptide reveals a surface important for co-receptor binding. Related Articles NMR structure of an anti-gp120 antibody complex with a V3 peptide reveals a surface important for co-receptor binding. Structure. 2000 Apr 15;8(4):385-95 Authors: Tugarinov V, Zvi A, Levy R, Hayek Y, Matsushita S, Anglister J BACKGROUND: The protein 0.5beta is a potent strain-specific human immunodeficiency virus type 1 (HIV-1) neutralizing antibody raised against the entire envelope glycoprotein (gp120) of...	nmrlearner	Journal club	0	11-18-2010 09:15 PM
[NMR paper] NMR identification of epitopes of Lyme disease antigen OspA to monoclonal antibodies. NMR identification of epitopes of Lyme disease antigen OspA to monoclonal antibodies. Related Articles NMR identification of epitopes of Lyme disease antigen OspA to monoclonal antibodies. J Mol Biol. 1998 Aug 7;281(1):61-7 Authors: Huang X, Yang X, Luft BJ, Koide S Outer surface protein A (OspA) from the Lyme disease spirochete Borrelia burgdorferi has been a focus of vaccine development. We have identified epitopes of OspA to two monoclonal antibodies (mAbs) by comparing NMR chemical shifts of free OspA and those in Fab complexes....	nmrlearner	Journal club	0	11-17-2010 11:15 PM
[NMR paper] Structure and dynamics of oligosaccharides: NMR and modeling studies. Structure and dynamics of oligosaccharides: NMR and modeling studies. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Structure and dynamics of oligosaccharides: NMR and modeling studies. Curr Opin Struct Biol. 1996 Oct;6(5):710-20 Authors: Peters T, Pinto BM Recent advances in the conformational analysis of oligosaccharides have focused on protein-bound oligosaccharides, glycopeptides, and glycoproteins, as well as on the conformational dynamics about glycosidic...	nmrlearner	Journal club	0	08-22-2010 02:20 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