NMR paper Epitope mapping of sialyl Lewis(x) bound to E-selectin using saturation transfer diff

		BioNMR > Educational resources > Journal club
[NMR paper] Epitope mapping of sialyl Lewis(x) bound to E-selectin using saturation transfer diff

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

11-24-2010, 09:01 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,191

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

Epitope mapping of sialyl Lewis(x) bound to E-selectin using saturation transfer diff

Epitope mapping of sialyl Lewis(x) bound to E-selectin using saturation transfer difference NMR experiments.

Related Articles Epitope mapping of sialyl Lewis(x) bound to E-selectin using saturation transfer difference NMR experiments.

Glycobiology. 2003 Jun;13(6):435-43

Authors: Rinnbauer M, Ernst B, Wagner B, Magnani J, Benie AJ, Peters T

A complex between sialyl Lewisx (alpha-D-Neu5Ac-[2-->3]- beta-D-Gal-[1-->4]-[alpha-L-Fuc-(1-->3)]-beta-D-GlcNAc-O-[CH2]8 COOMe) and E-selectin was studied using saturation transfer difference (STD) nuclear magnetic resonance (NMR) experiments. These experiments allow the identification of the binding epitope of a ligand at atomic resolution. A semiquantitative analysis of STD total correlation spectroscopy spectra provides clear evidence that the galactose residue receives the largest saturation transfer. The protons H4 and H6 of the galactose residue are in especially close contact to the amino acids of the E-selectin binding pocket. The fucose residue also receives a significant saturation transfer. The GlcNAc and Neu5Ac residues, with the exception of H3 and H3' of Neu5Ac, were found to interact weakly with the protein surface. These findings are in excellent agreement with a recently published X-ray structure and with the earlier findings from syntheses and activity assays. To further characterize the binding pocket of E-selectin, an inhibitory peptide, Ac-TWDQLWDLMK-CONH2, was synthesized and the binding to E-selectin studied utilizing transfer nuclear Overhauser effect spectroscopy (trNOESY) experiments. Finally, competitive trNOESY experiments were performed, showing that the synthetic peptide is a competitive inhibitor of sialyl Lewisx.

PMID: 12626392 [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] Can anyone help me with Saturation Transfer NMR Can anyone help me with Saturation Transfer NMR Hi I am working on a Varian 500MHz NMR. I am attempting to use the pulse sequence satxfer1D to measure the rate constant of an exchanging system. I am not using solvent suppression and I am having trouble understanding the physics behind the "mixing time" after the 90 pulse. I also do not know how many iterations the selective pulse should go through because it seems that if I turn the mixing time off and just use a selective pulse, and then a pw90, I will still obtain the same spectrum no matter how many iterations the selective pulse train...	nmrlearner	News from other NMR forums	0	09-29-2011 07:36 PM
Mapping residue-specific contacts of polymyxin B with lipopolysaccharide by saturation transfer difference NMR: insights into outer-membrane disruption and endotoxin neutralization. Mapping residue-specific contacts of polymyxin B with lipopolysaccharide by saturation transfer difference NMR: insights into outer-membrane disruption and endotoxin neutralization. Mapping residue-specific contacts of polymyxin B with lipopolysaccharide by saturation transfer difference NMR: insights into outer-membrane disruption and endotoxin neutralization. Biopolymers. 2011;96(3):273-87 Authors: Bhunia A, Bhattacharjya S Abstract High-resolution interactions studies of molecules with lipopolysaccharide (LPS) or endotoxin are...	nmrlearner	Journal club	0	09-21-2011 03:31 PM
[NMR paper] Epitope mapping of the phosphorylation motif of the HIV-1 protein Vpu bound to the se Epitope mapping of the phosphorylation motif of the HIV-1 protein Vpu bound to the selective monoclonal antibody using TRNOESY and STD NMR spectroscopy. Related Articles Epitope mapping of the phosphorylation motif of the HIV-1 protein Vpu bound to the selective monoclonal antibody using TRNOESY and STD NMR spectroscopy. Biochemistry. 2004 Nov 23;43(46):14555-65 Authors: Gharbi-Benarous J, Bertho G, Evrard-Todeschi N, Coadou G, Megy S, Delaunay T, Benarous R, Girault JP The conformational preferences of a 22-amino acid peptide...	nmrlearner	Journal club	0	11-24-2010 10:03 PM
[NMR paper] Group epitope mapping by saturation transfer difference NMR to identify segments of a Group epitope mapping by saturation transfer difference NMR to identify segments of a ligand in direct contact with a protein receptor. Related Articles Group epitope mapping by saturation transfer difference NMR to identify segments of a ligand in direct contact with a protein receptor. J Am Chem Soc. 2001 Jun 27;123(25):6108-17 Authors: Mayer M, Meyer B A protocol based on saturation transfer difference (STD) NMR spectra was developed to characterize the binding interactions at an atom level, termed group epitope mapping (GEM). As an example...	nmrlearner	Journal club	0	11-19-2010 08:32 PM
[NMR paper] NMR studies on the flexibility of the poliovirus C3 linear epitope inserted into diff NMR studies on the flexibility of the poliovirus C3 linear epitope inserted into different sites of the maltose-binding protein. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--highwire.stanford.edu-icons-externalservices-pubmed-standard-jbc_full_free.gif Related Articles NMR studies on the flexibility of the poliovirus C3 linear epitope inserted into different sites of the maltose-binding protein. J Biol Chem. 1997 Jan 3;272(1):362-8 Authors: Lecroisey A, Martineau P, Hofnung M, Delepierre M A set of permissive positions that tolerate...	nmrlearner	Journal club	0	08-22-2010 03:31 PM
[NMR paper] NMR studies on the flexibility of the poliovirus C3 linear epitope inserted into diff NMR studies on the flexibility of the poliovirus C3 linear epitope inserted into different sites of the maltose-binding protein. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--highwire.stanford.edu-icons-externalservices-pubmed-standard-jbc_full_free.gif Related Articles NMR studies on the flexibility of the poliovirus C3 linear epitope inserted into different sites of the maltose-binding protein. J Biol Chem. 1997 Jan 3;272(1):362-8 Authors: Lecroisey A, Martineau P, Hofnung M, Delepierre M A set of permissive positions that tolerate...	nmrlearner	Journal club	0	08-22-2010 03:03 PM
[NMR paper] Studies on the three-dimensional behaviour of the selectin ligands Lewis(a) and sulph Studies on the three-dimensional behaviour of the selectin ligands Lewis(a) and sulphated Lewis(a) using NMR spectroscopy and molecular dynamics simulations. Related Articles Studies on the three-dimensional behaviour of the selectin ligands Lewis(a) and sulphated Lewis(a) using NMR spectroscopy and molecular dynamics simulations. Glycobiology. 1994 Feb;4(1):49-57 Authors: Kogelberg H, Rutherford TJ Sulphated blood group Lewis(a)/Lewis(x) (Le(a)/Le(x)) type sequences, with sulphate at the 3-position of galactose, have emerged as potent ligands...	nmrlearner	Journal club	0	08-22-2010 03:33 AM
[NMR paper] Studies on the three-dimensional behaviour of the selectin ligands Lewis(a) and sulph Studies on the three-dimensional behaviour of the selectin ligands Lewis(a) and sulphated Lewis(a) using NMR spectroscopy and molecular dynamics simulations. Related Articles Studies on the three-dimensional behaviour of the selectin ligands Lewis(a) and sulphated Lewis(a) using NMR spectroscopy and molecular dynamics simulations. Glycobiology. 1994 Feb;4(1):49-57 Authors: Kogelberg H, Rutherford TJ Sulphated blood group Lewis(a)/Lewis(x) (Le(a)/Le(x)) type sequences, with sulphate at the 3-position of galactose, have emerged as potent ligands...	nmrlearner	Journal club	0	08-22-2010 03:33 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