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 08-21-2010, 11:16 PM
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 2D NMR of paramagnetic metalloenzymes: cyanide-inhibited horseradish peroxidase.

2D NMR of paramagnetic metalloenzymes: cyanide-inhibited horseradish peroxidase.

Related Articles 2D NMR of paramagnetic metalloenzymes: cyanide-inhibited horseradish peroxidase.

J Biomol NMR. 1991 Jul;1(2):175-90

Authors: de Ropp JS, Yu LP, La Mar GN

Two-dimensional (2D) proton NMR correlation spectroscopy, COSY, and nuclear Overhauser spectroscopy, NOESY, have been used to explore the applicability of these methods for the moderately large (42 KDa), paramagnetic cyanide-inhibited derivative of horseradish peroxidase, HRP-CN. The target resonances are those in the active site of HRP-CN which experience substantial hyperfine shifts and paramagnetic relaxation. The magnitude COSY experiment was found to yield cross peaks for all known spin-coupled heme substituents, as well as for the majority of non-heme hyperfine shifted protons, in spite of line widths of the order of approximately 100 Hz. Moreover, the rapid relaxation of the hyperfine-shifted resonances allows the extremely rapid collection of useful 2D NMR data sets without the loss of information. For the heme, the combination of COSY cross peaks for the vinyl and propionate substituents, and NOESY cross peaks among these substituent protons and heme methyls, allows assignment of heme resonances without recourse to deuterium labeling of the heme. A seven-proton coupled spin system was identified in the upfield region that is consistent with originating from the proposed catalytic Arg38 residue in the distal heme pocket, with orientation relative to the heme similar to that found in cytochrome c peroxidase. The upfield hyperfine-shifted methyl group in the substrate binding pocket previously proposed to arise from Leu237 is shown to arise instead from an as yet unidentified Ile. NOESY spectra collected at very short (3 ms) and intermediate (20 ms) mixing times indicate that build-up curves can be obtained that should yield estimates of distances in the heme cavity. It is concluded that 2D NMR studies should be able to provide the heme assignments, aid in identifying the catalytic residues, and provide information on the spatial disposition of such residues in the active site for cyanide complexes of a number of intermediate to large paramagnetic heme peroxidases, as well as for other paramagnetic metalloenzymes with line widths of approximately 100 Hz. Moreover, paramagnetic-induced hyperfine shifts and linewidths to approximately 100 Hz need not interfere with the complete solution structure determination of a small paramagnetic protein solely on the basis of 2D NMR data.

PMID: 1841693 [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] 13C NMR signal detection of iron-bound cyanide ions in ferric cyanide complexes of he
13C NMR signal detection of iron-bound cyanide ions in ferric cyanide complexes of heme proteins. Related Articles 13C NMR signal detection of iron-bound cyanide ions in ferric cyanide complexes of heme proteins. J Am Chem Soc. 2002 May 29;124(21):5936-7 Authors: Fujii H 13CN ion appears to have the greatest potential to probe the heme environment of the ferric heme proteins; however, a resonance of the iron-bound (13)CN ion in ferric heme proteins has not yet been located. We show here the first detection of (13)C NMR signals of the...
nmrlearner Journal club 0 11-24-2010 08:49 PM
[NMR paper] PASE (PAramagnetic signals enhancement): a new method for NMR study of paramagnetic p
PASE (PAramagnetic signals enhancement): a new method for NMR study of paramagnetic proteins. Related Articles PASE (PAramagnetic signals enhancement): a new method for NMR study of paramagnetic proteins. J Magn Reson. 1998 Sep;134(1):154-7 Authors: Bondon A, Mouro C A new method for NMR spectra acquisition of paramagnetic proteins is described, based on the simple use of homonuclear broadband decoupling of the diamagnetic region. Several advantages are associated with this method which was applied to one-dimensional spectra, to 1D...
nmrlearner Journal club 0 11-17-2010 11:15 PM
[NMR paper] Solution characterisation by NMR spectroscopy of two horseradish peroxidase isoenzyme
Solution characterisation by NMR spectroscopy of two horseradish peroxidase isoenzyme C mutants with alanine replacing either Phe142 or Phe143. 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 Solution characterisation by NMR spectroscopy of two horseradish peroxidase isoenzyme C mutants with alanine replacing either Phe142 or Phe143. Eur J Biochem. 1995 Oct 15;233(2):650-8 Authors: Veitch NC, Williams RJ, Bone NM, Burke JF, Smith AT ...
nmrlearner Journal club 0 08-22-2010 03:50 AM
[NMR paper] Structural studies by proton-NMR spectroscopy of plant horseradish peroxidase C, the
Structural studies by proton-NMR spectroscopy of plant horseradish peroxidase C, the wild-type recombinant protein from Escherichia coli and two protein variants, Phe41----Val and Arg38----Lys. 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 Structural studies by proton-NMR spectroscopy of plant horseradish peroxidase C, the wild-type recombinant protein from Escherichia coli and two protein variants, Phe41----Val and Arg38----Lys. Eur J Biochem. 1992 Jul...
nmrlearner Journal club 0 08-21-2010 11:45 PM
[NMR paper] NMR study of the active site of resting state and cyanide-inhibited lignin peroxidase
NMR study of the active site of resting state and cyanide-inhibited lignin peroxidase from Phanerochaete chrysosporium. Comparison with horseradish peroxidase. Related Articles NMR study of the active site of resting state and cyanide-inhibited lignin peroxidase from Phanerochaete chrysosporium. Comparison with horseradish peroxidase. J Biol Chem. 1991 Aug 15;266(23):15001-8 Authors: de Ropp JS, La Mar GN, Wariishi H, Gold MH One- and two-dimensional 1H NMR spectroscopy has been used to probe the active site of the high spin ferric resting...
nmrlearner Journal club 0 08-21-2010 11:12 PM
[NMR paper] NMR study of the active site of resting state and cyanide-inhibited lignin peroxidase
NMR study of the active site of resting state and cyanide-inhibited lignin peroxidase from Phanerochaete chrysosporium. Comparison with horseradish peroxidase. Related Articles NMR study of the active site of resting state and cyanide-inhibited lignin peroxidase from Phanerochaete chrysosporium. Comparison with horseradish peroxidase. J Biol Chem. 1991 Aug 15;266(23):15001-8 Authors: de Ropp JS, La Mar GN, Wariishi H, Gold MH One- and two-dimensional 1H NMR spectroscopy has been used to probe the active site of the high spin ferric resting...
nmrlearner Journal club 0 08-21-2010 11:12 PM
[NMR paper] Two-dimensional 1H-NMR studies of horseradish peroxidase C and its interaction with i
Two-dimensional 1H-NMR studies of horseradish peroxidase C and its interaction with indole-3-propionic acid. 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 Two-dimensional 1H-NMR studies of horseradish peroxidase C and its interaction with indole-3-propionic acid. Eur J Biochem. 1990 Apr 30;189(2):351-62 Authors: Veitch NC, Williams RJ The binding of aromatic donor molecules to plant peroxidases has been investigated by examining...
nmrlearner Journal club 0 08-21-2010 10:48 PM
[NMR paper] The interaction of the nitrate anion with cytochrome c peroxidase: a 15N-NMR study.
The interaction of the nitrate anion with cytochrome c peroxidase: a 15N-NMR study. Related Articles The interaction of the nitrate anion with cytochrome c peroxidase: a 15N-NMR study. Spectrochim Acta A Mol Biomol Spectrosc. 1999 Feb;55A(2):415-20 Authors: Banci L, Pierattelli R The interaction of the nitrate anion with cytochrome c peroxidase has been demonstrated by using 15N-NMR spectroscopy. The results indicate that the nitrate anion binds to the protein in a specific binding site and are consistent with the hypothesis of an interaction...
nmrlearner Journal club 0 08-21-2010 04:03 PM



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 02:34 PM.


Map