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, 11:45 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 17,583
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 Complete sequence-specific 1H NMR resonance assignment of hyperfine-shifted residues

Complete sequence-specific 1H NMR resonance assignment of hyperfine-shifted residues in the active site of a paramagnetic protein: application to Aplysia cyano-metmyoglobin.

Related Articles Complete sequence-specific 1H NMR resonance assignment of hyperfine-shifted residues in the active site of a paramagnetic protein: application to Aplysia cyano-metmyoglobin.

J Biomol NMR. 1992 Nov;2(6):597-618

Authors: Qin J, La Mar GN

Two-dimensional sequence-specific 1H NMR resonance assignment methodology (Wüthrich, 1986) has been applied for the first time to a 18-kDa paramagnetic hemoprotein (cyano-met Aplysia Mb) to identify all the hyperfine-shifted residues. The assignment was greatly facilitated by the fact that hyperfine shifts of residues impart a strong temperature dependence to the cross peaks, which aids location and identification, and provides improved spectral dispersion, particularly in the fingerprint region. 2D COSY and TOCSY were found to be surprisingly effective in locating the complete spin connectivities of all of the hyperfine-shifted residues, with the exception of the axially coordinated His95 imidazole ring, whose proton resonances were found to exhibit severe line broadening (> 400 Hz). Conventional 1D NOE and NOESY with short mixing times, combined with paramagnetic-induced relaxation effects, led to the successful assignment of even extremely broad proton signals. Three helical stretches and two loop regions were identified as the source of all hyperfine-shifted residues: the F helical residues 3-9, the E-helix residues 6-14, the G-helix residues 5-9, the FG-loop residues 1-4 and the CD-loop residues 1-4. These segments comprise all the residues that make contact with the heme and modulate the reactivity of the prosthetic group. The sequence-specific identifications of the active-site residues revealed that the solution structure of Aplysia metMbCN is fully consistent with that observed by X-ray diffraction in single crystals for a variety of other derivatives, except for the distal Arg66 (E10), which is turned into the heme pocket, as found only in the metMbF crystal structure (Bolognesi et al., 1990). The ready identification, by their temperature sensitivity, and the complete assignments of all hyperfine-shifted residues of Aplysia metMbCN demonstrate that sequence-specific assignment can be profitably applied to paramagnetic proteins, and that it should be possible to determine the solution structures of paramagnetic proteins, at least for low-spin complexes, by using NMR techniques used for diamagnetic proteins.

PMID: 1490108 [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
[NMR paper] A modified strategy for sequence specific assignment of protein NMR spectra based on
A modified strategy for sequence specific assignment of protein NMR spectra based on amino acid type selective experiments. Related Articles A modified strategy for sequence specific assignment of protein NMR spectra based on amino acid type selective experiments. J Biomol NMR. 2005 Feb;31(2):115-28 Authors: Schubert M, Labudde D, Leitner D, Oschkinat H, Schmieder P The determination of the three-dimensional structure of a protein or the study of protein-ligand interactions requires the assignment of all relevant nuclei as an initial step....
nmrlearner Journal club 0 11-24-2010 11:14 PM
[NMR paper] Protein expression, selective isotopic labeling, and analysis of hyperfine-shifted NM
Protein expression, selective isotopic labeling, and analysis of hyperfine-shifted NMR signals of Anabaena 7120 vegetative ferredoxin. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Protein expression, selective isotopic labeling, and analysis of hyperfine-shifted NMR signals of Anabaena 7120 vegetative ferredoxin. Arch Biochem Biophys. 1995 Jan 10;316(1):619-34 Authors: Cheng H, Westler WM, Xia B, Oh BH, Markley JL Two alternative T7 RNA promoter/polymerase systems...
nmrlearner Journal club 0 08-22-2010 03:41 AM
[NMR paper] Comparison of native and mutant proteins provides a sequence-specific assignment of t
Comparison of native and mutant proteins provides a sequence-specific assignment of the cysteinyl ligand proton NMR resonances in the 2 ferredoxin from Clostridium pasteurianum. Related Articles Comparison of native and mutant proteins provides a sequence-specific assignment of the cysteinyl ligand proton NMR resonances in the 2 ferredoxin from Clostridium pasteurianum. Biochemistry. 1994 Dec 6;33(48):14486-95 Authors: Scrofani SD, Brereton PS, Hamer AM, Lavery MJ, McDowall SG, Vincent GA, Brownlee RT, Hoogenraad NJ, Sadek M, Wedd AG A...
nmrlearner Journal club 0 08-22-2010 03:29 AM
[NMR paper] Sequence-specific 1H-NMR assignment and determination of the secondary structure of b
Sequence-specific 1H-NMR assignment and determination of the secondary structure of bovine heart fatty-acid-binding protein. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif Related Articles Sequence-specific 1H-NMR assignment and determination of the secondary structure of bovine heart fatty-acid-binding protein. Eur J Biochem. 1992 Dec 15;210(3):901-10 Authors: Lücke C, Lassen D, Kreienkamp HJ, Spener F, Rüterjans H The nearly complete...
nmrlearner Journal club 0 08-21-2010 11:45 PM
[NMR paper] Sequence-specific 1H-NMR assignment and secondary structure of the Tyr41----His mutan
Sequence-specific 1H-NMR assignment and secondary structure of the Tyr41----His mutant of the single-stranded DNA binding protein, gene V protein, encoded by the filamentous bacteriophage M13. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif Related Articles Sequence-specific 1H-NMR assignment and secondary structure of the Tyr41----His mutant of the single-stranded DNA binding protein, gene V protein, encoded by the filamentous bacteriophage M13. Eur J Biochem. 1991 Dec...
nmrlearner Journal club 0 08-21-2010 11:12 PM
[NMR paper] Sequence-specific 1H-NMR assignment and secondary structure of the Tyr41----His mutan
Sequence-specific 1H-NMR assignment and secondary structure of the Tyr41----His mutant of the single-stranded DNA binding protein, gene V protein, encoded by the filamentous bacteriophage M13. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif Related Articles Sequence-specific 1H-NMR assignment and secondary structure of the Tyr41----His mutant of the single-stranded DNA binding protein, gene V protein, encoded by the filamentous bacteriophage M13. Eur J Biochem. 1991 Dec...
nmrlearner Journal club 0 08-21-2010 11:12 PM
[NMR paper] Complete sequence-specific 1H NMR assignments for human insulin.
Complete sequence-specific 1H NMR assignments for human insulin. Related Articles Complete sequence-specific 1H NMR assignments for human insulin. Biochemistry. 1990 Mar 27;29(12):2906-13 Authors: Kline AD, Justice RM Solvent conditions where human insulin could be studied by high-resolution NMR were determined. Both low pH and addition of acetonitrile were required to overcome the protein's self-association and to obtain useful spectra. Two hundred eighty-six 1H resonances were located and assigned to specific sites on the protein by using...
nmrlearner Journal club 0 08-21-2010 10:48 PM
Sequence specific resonance assignment via Multicanonical Monte Carlo search using an ABACUS approach
Sequence specific resonance assignment via Multicanonical Monte Carlo search using an ABACUS approach Alexander Lemak, Carlos A. Steren, Cheryl H. Arrowsmith and Miguel Llins Journal of Biomolecular NMR; 2008; 41(1); pp 29 - 41 Abstract: ABACUS is a novel protocol for automated protein structure determination via NMR. ABACUS starts from molecular fragments defined by unassigned J-coupled spin-systems and involves a Monte Carlo stochastic search in assignment space, probabilistic sequence selection, and assembly of fragments into structures that are used to guide the stochastic...
Mikey Journal club 0 08-14-2008 12:37 AM


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 - 2017, 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 05:24 PM.


Map