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
Home Forums Wiki NMR feeds Downloads Register Today's Posts



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  
Old 08-22-2010, 03:33 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,700
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 Structural and dynamic properties of the Fv fragment and the single-chain Fv fragment

Structural and dynamic properties of the Fv fragment and the single-chain Fv fragment of an antibody in solution investigated by heteronuclear three-dimensional NMR spectroscopy.

Related Articles Structural and dynamic properties of the Fv fragment and the single-chain Fv fragment of an antibody in solution investigated by heteronuclear three-dimensional NMR spectroscopy.

Biochemistry. 1994 Mar 22;33(11):3296-303

Authors: Freund C, Ross A, Plückthun A, Holak TA

Fv fragments, heterodimers of the variable light (VL) and variable heavy chain (VH) domains, are the smallest functional antibody units with molecular masses of approximately 26 kDa. The structural and dynamic properties of the Fv fragment and the corresponding single-chain Fv fragment (scFv: VH-linker-VL, 252 amino acids) of the phosphorylcholine-binding antibody McPC603 in the presence of hapten have been studied in solution by heteronuclear multidimensional NMR spectroscopy. Both 15N TOCSY-HMQC and triple-resonance experiments (HNCA and HN(CA)H, with 15N-13C-labeled protein) gave poor spectra, due to short T2 relaxation times for most of the backbone 1H, 15N, and 13C alpha atoms. The assignment procedure therefore relied upon the combination of amino acid and domain (VL) specifically labeled spectra and the 3D NOESY-HMQC spectrum of the uniformly 15N labeled Fv and scFv fragments. Approximately 80% of the 15N and 1H backbone and 60% of the 1H side-chain resonances have been assigned. Short- and long-range NOEs were used to determine the extent of beta-sheet structure and were compared to the X-ray crystallographic data. The 1H-15N NOE data indicate that the scFv backbone has a well-defined structure of limited conformational flexibility. However, the linker of the scFv fragment exhibits substantial fast internal motion (on the picosecond to nanosecond time scale) compared with the overall rotational correlation time of the whole molecule. Several residues in the CDRs, in turns, or at the C-terminal end of the protein have smaller NOEs, reflecting some degree of rapid motion in the protein backbone.

PMID: 8136365 [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
Target immobilization as a strategy for NMR-based fragment screening: comparison of TINS, STD, and SPR for fragment hit identification.
Target immobilization as a strategy for NMR-based fragment screening: comparison of TINS, STD, and SPR for fragment hit identification. Target immobilization as a strategy for NMR-based fragment screening: comparison of TINS, STD, and SPR for fragment hit identification. J Biomol Screen. 2010 Sep;15(8):978-89 Authors: Kobayashi M, Retra K, Figaroa F, Hollander JG, Ab E, Heetebrij RJ, Irth H, Siegal G Fragment-based drug discovery (FBDD) has become a widely accepted tool that is complementary to high-throughput screening (HTS) in developing...
nmrlearner Journal club 0 01-13-2011 12:00 PM
[NMR paper] Interactions of a didomain fragment of the Drosophila sex-lethal protein with single-
Interactions of a didomain fragment of the Drosophila sex-lethal protein with single-stranded uridine-rich oligoribonucleotides derived from the transformer and Sex-lethal messenger RNA precursors: NMR with residue-selective uridine substitutions. Related Articles Interactions of a didomain fragment of the Drosophila sex-lethal protein with single-stranded uridine-rich oligoribonucleotides derived from the transformer and Sex-lethal messenger RNA precursors: NMR with residue-selective uridine substitutions. J Biomol NMR. 2000 Jun;17(2):153-65 Authors: Kim...
nmrlearner Journal club 0 11-18-2010 09:15 PM
[NMR paper] Structure and dynamic properties of the single disulfide-deficient alpha-amylase inhi
Structure and dynamic properties of the single disulfide-deficient alpha-amylase inhibitor tendamistat: an NMR study. Related Articles Structure and dynamic properties of the single disulfide-deficient alpha-amylase inhibitor tendamistat: an NMR study. Proteins. 1998 Nov 1;33(2):285-94 Authors: Balbach J, Seip S, Kessler H, Scharf M, Kashani-Poor N, Engels JW Covalent linkages such as disulfide bonds are important for the stabilization of proteins. In the present NMR study we compare the structure and the dynamics of the single...
nmrlearner Journal club 0 11-17-2010 11:15 PM
[NMR paper] Helix formation by the phospholipase A2 38-59 fragment: influence of chain shortening
Helix formation by the phospholipase A2 38-59 fragment: influence of chain shortening and dimerization monitored by nmr chemical shifts. Related Articles Helix formation by the phospholipase A2 38-59 fragment: influence of chain shortening and dimerization monitored by nmr chemical shifts. Biopolymers. 1994 May;34(5):647-61 Authors: Jiménez MA, Carreño C, Andreu D, Blanco FJ, Herranz J, Rico M, Nieto JL The solution structure of a peptide fragment corresponding to the 38-59 region of porcine phospholipase A2 has been investigated using CD,...
nmrlearner Journal club 0 08-22-2010 03:33 AM
[NMR paper] Structural analysis of peptide fragment 71-93 of transthyretin by NMR spectroscopy an
Structural analysis of peptide fragment 71-93 of transthyretin by NMR spectroscopy and electron microscopy: insight into amyloid fibril formation. Related Articles Structural analysis of peptide fragment 71-93 of transthyretin by NMR spectroscopy and electron microscopy: insight into amyloid fibril formation. Biochemistry. 1994 Jan 11;33(1):33-41 Authors: Jarvis JA, Munro SL, Craik DJ A peptide corresponding to the amino acid region 71-93 of the plasma protein transthyretin (TTR) has been synthesized to investigate its role in the native...
nmrlearner Journal club 0 08-22-2010 03:33 AM
[NMR paper] Helix formation by the phospholipase A2 38-59 fragment: influence of chain shortening
Helix formation by the phospholipase A2 38-59 fragment: influence of chain shortening and dimerization monitored by nmr chemical shifts. Related Articles Helix formation by the phospholipase A2 38-59 fragment: influence of chain shortening and dimerization monitored by nmr chemical shifts. Biopolymers. 1994 May;34(5):647-61 Authors: Jiménez MA, Carreño C, Andreu D, Blanco FJ, Herranz J, Rico M, Nieto JL The solution structure of a peptide fragment corresponding to the 38-59 region of porcine phospholipase A2 has been investigated using CD,...
nmrlearner Journal club 0 08-22-2010 03:33 AM
[NMR paper] Structural and dynamic properties of the Fv fragment and the single-chain Fv fragment
Structural and dynamic properties of the Fv fragment and the single-chain Fv fragment of an antibody in solution investigated by heteronuclear three-dimensional NMR spectroscopy. Related Articles Structural and dynamic properties of the Fv fragment and the single-chain Fv fragment of an antibody in solution investigated by heteronuclear three-dimensional NMR spectroscopy. Biochemistry. 1994 Mar 22;33(11):3296-303 Authors: Freund C, Ross A, Plückthun A, Holak TA Fv fragments, heterodimers of the variable light (VL) and variable heavy chain...
nmrlearner Journal club 0 08-22-2010 03:33 AM
[NMR paper] Structural analysis of peptide fragment 71-93 of transthyretin by NMR spectroscopy an
Structural analysis of peptide fragment 71-93 of transthyretin by NMR spectroscopy and electron microscopy: insight into amyloid fibril formation. Related Articles Structural analysis of peptide fragment 71-93 of transthyretin by NMR spectroscopy and electron microscopy: insight into amyloid fibril formation. Biochemistry. 1994 Jan 11;33(1):33-41 Authors: Jarvis JA, Munro SL, Craik DJ A peptide corresponding to the amino acid region 71-93 of the plasma protein transthyretin (TTR) has been synthesized to investigate its role in the native...
nmrlearner Journal club 0 08-22-2010 03:33 AM



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 03:56 AM.


Map