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 08-21-2010, 11:16 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 Use of 2D NMR, protein engineering, and molecular modeling to study the hapten-bindin

Use of 2D NMR, protein engineering, and molecular modeling to study the hapten-binding site of an antibody Fv fragment against 2-phenyloxazolone.

Related Articles Use of 2D NMR, protein engineering, and molecular modeling to study the hapten-binding site of an antibody Fv fragment against 2-phenyloxazolone.

Biochemistry. 1991 Jun 18;30(24):5851-7

Authors: McManus S, Riechmann L

Two-dimensional (2D) 1H NMR spectroscopy was used to study the hapten-binding site of a recombinant antibody Fv fragment expressed in Escherichia coli. Point mutations of residues in the CDR loops of the Fv fragment were designed in order to investigate their influence on hapten binding and to make site-specific assignments of aromatic NMR proton signals. Two tyrosines giving NOEs to the ligand 2-phenyloxazolone were identified, residue 33 in CDR1 of the heavy chain and residue 32 in CDR1 of the light chain. The benzyl portion of 2-phenyloxazolone is located between these two residues. The binding site is close to the surface of the Fv fragment. Comparison with a different anti-2-phenyloxazolone antibody, the crystal structure of which has recently been solved, shows that the general location of the hapten-binding site in both antibodies is similar. However, in the crystallographically solved antibody, the hapten is bound farther from the surface in a pocket created by a short CDR3 loop of the heavy chain. In the binding site identified in the Fv fragment studied in this report, this space is probably filled by the extra seven residues of the CDR3.

PMID: 2043627 [PubMed - indexed for MEDLINE]



Source: PubMed
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Development of Non-Peptide Ligands of Growth Factor Receptor-Bound Protein 2-Src Homology 2 Domain Using Molecular Modeling and NMR Spectroscopy (†).
Development of Non-Peptide Ligands of Growth Factor Receptor-Bound Protein 2-Src Homology 2 Domain Using Molecular Modeling and NMR Spectroscopy (†). Development of Non-Peptide Ligands of Growth Factor Receptor-Bound Protein 2-Src Homology 2 Domain Using Molecular Modeling and NMR Spectroscopy (†). J Med Chem. 2011 Jan 27; Authors: Orcajo-Rinco?n AL, Ortega-Gutie?rrez S, Serrano P, Torrecillas IR, Wu?thrich K, Campillo M, Pardo L, Viso A, Benhamu? B, Lo?pez-Rodri?guez ML We report a novel series of non-peptide ligands that inhibit the growth...
nmrlearner Journal club 0 01-29-2011 12:35 PM
[NMR paper] NMR spectroscopic and molecular modeling studies of protein-carbohydrate and protein-
NMR spectroscopic and molecular modeling studies of protein-carbohydrate and protein-peptide interactions. Related Articles NMR spectroscopic and molecular modeling studies of protein-carbohydrate and protein-peptide interactions. Carbohydr Res. 2004 Apr 2;339(5):907-28 Authors: Johnson MA, Pinto BM Investigations of the conformations of carbohydrates, their analogues and their molecular mimics are described, with emphasis on structural and functional information that can be gained by NMR spectroscopic techniques in combination with molecular...
nmrlearner Journal club 0 11-24-2010 09:51 PM
[NMR paper] NMR and molecular modeling of complex carbohydrates and carbohydrate-protein interact
NMR and molecular modeling of complex carbohydrates and carbohydrate-protein interactions. Applications to anti-bacteria vaccines. Related Articles NMR and molecular modeling of complex carbohydrates and carbohydrate-protein interactions. Applications to anti-bacteria vaccines. Adv Exp Med Biol. 2001;491:543-50 Authors: Brisson JR, Jennings HJ In order to characterize the conformational epitope of the group B meningococcal polysaccharide and of the type III group B Streptococcus capsular polysaccharide NMR measurements were done on a wide...
nmrlearner Journal club 0 11-19-2010 08:32 PM
[NMR paper] DNA-XPA interactions: a (31)P NMR and molecular modeling study of dCCAATAACC associat
DNA-XPA interactions: a (31)P NMR and molecular modeling study of dCCAATAACC association with the minimal DNA-binding domain (M98-F219) of the nucleotide excision repair protein XPA. Related Articles DNA-XPA interactions: a (31)P NMR and molecular modeling study of dCCAATAACC association with the minimal DNA-binding domain (M98-F219) of the nucleotide excision repair protein XPA. Nucleic Acids Res. 2001 Jun 15;29(12):2635-43 Authors: Buchko GW, Tung CS, McAteer K, Isern NG, Spicer LD, Kennedy MA Recent NMR-based, chemical shift mapping...
nmrlearner Journal club 0 11-19-2010 08:32 PM
[NMR paper] A mini-protein designed by removing a module from barnase: molecular modeling and NMR
A mini-protein designed by removing a module from barnase: molecular modeling and NMR measurements of the conformation. Related Articles A mini-protein designed by removing a module from barnase: molecular modeling and NMR measurements of the conformation. Protein Eng. 1999 Aug;12(8):673-80 Authors: Takahashi K, Noguti T, Hojo H, Yamauchi K, Kinoshita M, Aimoto S, Ohkubo T, G? M A globular domain can be decomposed into compact modules consisting of contiguous 10-30 amino acid residues. The correlation between modules and exons observed in...
nmrlearner Journal club 0 11-18-2010 08:31 PM
[NMR paper] NMR and molecular modeling study of the conformations of taxol 2'-acetate in chlorofo
NMR and molecular modeling study of the conformations of taxol 2'-acetate in chloroform and aqueous dimethyl sulfoxide solutions. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles NMR and molecular modeling study of the conformations of taxol 2'-acetate in chloroform and aqueous dimethyl sulfoxide solutions. J Med Chem. 1996 Mar 29;39(7):1555-9 Authors: Williams HJ, Moyna G, Scott AI, Swindell CS, Chirlian LE, Heerding JM, Williams DK Taxol 2'-acetate, an analog of the antitumor drug...
nmrlearner Journal club 0 08-22-2010 02:27 PM
[NMR paper] NMR and molecular modeling studies on two glycopeptides from the carbohydrate-protein
NMR and molecular modeling studies on two glycopeptides from the carbohydrate-protein linkage region of connective tissue proteoglycans. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--highwire.stanford.edu-icons-externalservices-pubmed-custom-oxfordjournals_final_free.gif Related Articles NMR and molecular modeling studies on two glycopeptides from the carbohydrate-protein linkage region of connective tissue proteoglycans. Glycobiology. 1999 Jul;9(7):669-77 Authors: Agrawal PK, Jacquinet JC, Krishna NR Complete 1H and 13C NMR...
nmrlearner Journal club 0 08-21-2010 04:03 PM
Molecular Modeling
Molecular ModelingWHAT If Calculation AutoStructure: Automated Determination of Protein Structures from NMR Data GenCons Hyper Queen Analysis Database of Macromolecular Movements with Associated Tools for Geometric Analysis PDBStat Dynamics
ale51 BioNMR Wiki 2 08-23-2006 04:46 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 05:02 AM.


Map