NMR paper Epitope mapping by solution NMR spectroscopy.

		BioNMR > Educational resources > Journal club
[NMR paper] Epitope mapping by solution NMR spectroscopy.

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

03-03-2015, 08:34 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,734

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 by solution NMR spectroscopy.

Epitope mapping by solution NMR spectroscopy.

Epitope mapping by solution NMR spectroscopy.

J Mol Recognit. 2015 Feb 27;

Authors: Bardelli M, Livoti E, Simonelli L, Pedotti M, Moraes A, Valente AP, Varani L

Abstract
Antibodies play an ever more prominent role in basic research as well as in the biotechnology and pharmaceutical sectors. Characterizing their epitopes, that is, the region that they recognize on their target molecule, is useful for purposes ranging from molecular biology research to vaccine design and intellectual property protection. Solution NMR spectroscopy is ideally suited to the atomic level characterization of intermolecular interfaces and, as a consequence, to epitope discovery. Here, we illustrate how NMR epitope mapping can be used to rapidly and accurately determine protein antigen epitopes. The basic concept is that differences in the NMR signal of an antigen free or bound by an antibody will identify epitope residues. NMR epitope mapping provides more detailed information than mutagenesis or peptide mapping and can be much more rapid than X-ray crystallography. Advantages and drawbacks of this technique are discussed together with practical considerations. Copyright © 2015 John Wiley & Sons, Ltd.

PMID: 25726811 [PubMed - as supplied by publisher]

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Fragment-based discovery of novel thymidylate synthase leads by NMR screening and group epitope mapping. Fragment-based discovery of novel thymidylate synthase leads by NMR screening and group epitope mapping. Fragment-based discovery of novel thymidylate synthase leads by NMR screening and group epitope mapping. Chem Biol Drug Des. 2010 Sep 1;76(3):218-33 Authors: Begley DW, Zheng S, Varani G Solution-state nuclear magnetic resonance (NMR) is a versatile tool for the study of binding interactions between small molecules and macromolecular targets. We applied ligand-based NMR techniques to the study of human thymidylate synthase (hTS) using known...	nmrlearner	Journal club	0	01-05-2011 09:51 PM
[NMR paper] Precise epitope mapping of malaria parasite inhibitory antibodies by TROSY NMR cross- Precise epitope mapping of malaria parasite inhibitory antibodies by TROSY NMR cross-saturation. Related Articles Precise epitope mapping of malaria parasite inhibitory antibodies by TROSY NMR cross-saturation. Biochemistry. 2005 Jan 18;44(2):518-23 Authors: Morgan WD, Frenkiel TA, Lock MJ, Grainger M, Holder AA We have applied NMR cross-saturation with TROSY detection to the problem of precisely mapping conformational epitopes on complete protein antigen molecules. We have investigated complexes of the Fab fragments of two antibodies that...	nmrlearner	Journal club	0	11-24-2010 11:14 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] Epitope mapping and competitive binding of HSA drug site II ligands by NMR diffusion Epitope mapping and competitive binding of HSA drug site II ligands by NMR diffusion measurements. Related Articles Epitope mapping and competitive binding of HSA drug site II ligands by NMR diffusion measurements. J Am Chem Soc. 2004 Nov 3;126(43):14258-66 Authors: Lucas LH, Price KE, Larive CK It is important to characterize drug-albumin binding during drug discovery and lead optimization as strong binding may reduce bioavailability and/or increase the drug's in vivo half-life. Despite knowing about the location of human serum albumin (HSA)...	nmrlearner	Journal club	0	11-24-2010 10:03 PM
[NMR paper] 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-- beta-D-Gal---beta-D-GlcNAc-O-8 COOMe) and E-selectin was studied using saturation transfer difference (STD) nuclear magnetic resonance (NMR) experiments....	nmrlearner	Journal club	0	11-24-2010 09:01 PM
[NMR paper] Epitope mapping of ligand-receptor interactions by diffusion NMR. Epitope mapping of ligand-receptor interactions by diffusion NMR. Related Articles Epitope mapping of ligand-receptor interactions by diffusion NMR. J Am Chem Soc. 2002 Aug 28;124(34):9984-5 Authors: Yan J, Kline AD, Mo H, Zartler ER, Shapiro MJ A novel method based on diffusion NMR for the epitope mapping of ligand binding is presented. The intermolecular NOE builds up during a long diffusion period and creates a deviation from the linearity. The ligand proton nearest the protein generates the strongest NOE from protein during the diffusion...	nmrlearner	Journal club	0	11-24-2010 08:58 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
Simultaneous detection of amide and methyl correlations using a time shared NMR experiment: application to binding epitope mapping Simultaneous detection of amide and methyl correlations using a time shared NMR experiment: application to binding epitope mapping Peter Würtz, Olli Aitio, Maarit Hellman and Perttu Permi Journal of Biomolecular NMR; 2007; 39(2) pp 97 - 105 Abstract: Simultaneous recording of different NMR parameters is an efficient way to reduce the overall experimental time and speed up structural studies of biological macromolecules. This can especially be beneficial in the case of fast NMR-based drug screening applications or for collecting NOE restraints, where prohibitively long data collection...	stewart	Journal club	0	08-05-2008 01:41 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