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 08-22-2010, 03:31 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,134
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 paramagnetic NMR probes for structural analysis in cytochrome c3 from Desulfov

Use of paramagnetic NMR probes for structural analysis in cytochrome c3 from Desulfovibrio vulgaris.

Related Articles Use of paramagnetic NMR probes for structural analysis in cytochrome c3 from Desulfovibrio vulgaris.

Eur J Biochem. 1997 Mar 15;244(3):721-34

Authors: Salgueiro CA, Turner DL, Xavier AV

The dipolar field generated by each of the four haems in the tetrahaem ferricytochrome c3 from Desulfovibrio vulgaris (Hildenborough) (c3DvH) is determined by means of a novel procedure. In this method the 13C chemical shifts of the nuclei directly bound to the haems are used to determine the in-plane orientations of the rhombic perturbation in each of the four haems with respect to a model of molecular orbitals of e(g) symmetry which are subject to a rhombic perturbation [Turner, D. L., Salgueiro, C. A., Schenkels, P., LeGall, J. & Xavier, A. V. (1995) Biochim. Biophys. Acta 1246, 24-281. These orientations, together with the components of the magnetic susceptibility tensors obtained from the EPR g values and the crystal structure of c3DvH, can be used to calculate the dipolar shifts induced by each haem throughout the protein. Thus the observed 13C paramagnetic shifts of the c3DvH haem substituents were fitted considering both the pseudocontact and contact shifts of each haem simultaneously. The dipolar shifts calculated by this method were tested against the observed dipolar shifts for some amino acid residues strategically placed in the protein and also for the haem propionate groups. The effect of considering the calculated dipolar extrinsic shifts on the behaviour of the chemical shifts of the haem methyl groups in the intermediate stages of oxidation at different pH values was also analysed. The several tests applied to the calculated dipolar shifts have shown that the method is extremely useful for predicting chemical shifts as an aid to complete proton assignment, and to add further constraints in the refinement of solution structures of paramagnetic proteins and hence to probe subtle structural rearrangements around the haem pocket.

PMID: 9108240 [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
Narrowing the conformational space sampled by two-domain proteins with paramagnetic probes in both domains
Narrowing the conformational space sampled by two-domain proteins with paramagnetic probes in both domains Abstract Calmodulin is a two-domain protein which in solution can adopt a variety of conformations upon reorientation of its domains. The maximum occurrence (MO) of a set of calmodulin conformations that are representative of the overall conformational space possibly sampled by the protein, has been calculated from the paramagnetism-based restraints. These restraints were measured after inclusion of a lanthanide binding tag in the C-terminal domain to supplement the data obtained...
nmrlearner Journal club 0 08-13-2011 02:47 AM
[NMR paper] NMR analysis shows that a b-type variant of Hydrogenobacter thermophilus cytochrome c
NMR analysis shows that a b-type variant of Hydrogenobacter thermophilus cytochrome c552 retains its native structure. Related Articles NMR analysis shows that a b-type variant of Hydrogenobacter thermophilus cytochrome c552 retains its native structure. J Biol Chem. 2004 Apr 9;279(15):15177-82 Authors: Wain R, Redfield C, Ferguson SJ, Smith LJ Conversion of Hydrogenobacter thermophilus cytochrome c(552) into a b-type cytochrome by mutagenesis of both heme-binding cysteines to alanines significantly reduces the stability of the protein...
nmrlearner Journal club 0 11-24-2010 09:25 PM
[NMR paper] 19F NMR of trifluoroacetyl-labeled cysteine mutants of myoglobin: structural probes o
19F NMR of trifluoroacetyl-labeled cysteine mutants of myoglobin: structural probes of nitric oxide bound to the H93G cavity mutant. Related Articles 19F NMR of trifluoroacetyl-labeled cysteine mutants of myoglobin: structural probes of nitric oxide bound to the H93G cavity mutant. Biochemistry. 2001 Jul 24;40(29):8588-96 Authors: Thomas MR, Boxer SG Nitric oxide (NO) binds to the myoglobin (Mb) cavity mutant, H93G, forming either a 5- or 6-coordinate Fe--NO heme complex. The H93G mutation replaces the proximal histidine of Mb with glycine,...
nmrlearner Journal club 0 11-19-2010 08:44 PM
[NMR paper] Complex of plastocyanin and cytochrome c characterized by NMR chemical shift analysis
Complex of plastocyanin and cytochrome c characterized by NMR chemical shift analysis. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles Complex of plastocyanin and cytochrome c characterized by NMR chemical shift analysis. Biochemistry. 1997 May 27;36(21):6326-35 Authors: Ubbink M, Bendall DS The complexes of horse ferrous and ferric cytochrome c with Cd-substituted pea plastocyanin have been characterized by nuclear magnetic resonance, in order to determine the binding sites and to study...
nmrlearner Journal club 0 08-22-2010 03:31 PM
[NMR paper] Complex of plastocyanin and cytochrome c characterized by NMR chemical shift analysis
Complex of plastocyanin and cytochrome c characterized by NMR chemical shift analysis. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles Complex of plastocyanin and cytochrome c characterized by NMR chemical shift analysis. Biochemistry. 1997 May 27;36(21):6326-35 Authors: Ubbink M, Bendall DS The complexes of horse ferrous and ferric cytochrome c with Cd-substituted pea plastocyanin have been characterized by nuclear magnetic resonance, in order to determine the binding sites and to study...
nmrlearner Journal club 0 08-22-2010 03:03 PM
[NMR paper] Use of paramagnetic NMR probes for structural analysis in cytochrome c3 from Desulfov
Use of paramagnetic NMR probes for structural analysis in cytochrome c3 from Desulfovibrio vulgaris. 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 Use of paramagnetic NMR probes for structural analysis in cytochrome c3 from Desulfovibrio vulgaris. Eur J Biochem. 1997 Mar 15;244(3):721-34 Authors: Salgueiro CA, Turner DL, Xavier AV The dipolar field generated by each of the four haems in the tetrahaem ferricytochrome c3 from...
nmrlearner Journal club 0 08-22-2010 03:03 PM
[NMR paper] NMR identification of protein surfaces using paramagnetic probes.
NMR identification of protein surfaces using paramagnetic probes. Related Articles NMR identification of protein surfaces using paramagnetic probes. Biochemistry. 1990 Oct 30;29(43):10041-8 Authors: Petros AM, Mueller L, Kopple KD Paramagnetic agents produce line broadening and thus cancellation of anti phase cross-peak components in two-dimensional correlated nuclear magnetic resonance spectra. The specificity of this effect was examined to determine its utility for identifying surface residues of proteins. Ubiquitin and hen egg white...
nmrlearner Journal club 0 08-21-2010 11:04 PM
Paramagnetic tagging for protein structure and dynamics analysis
Paramagnetic tagging for protein structure and dynamics analysis Publication year: 2010 Source: Progress in Nuclear Magnetic Resonance Spectroscopy, In Press, Accepted Manuscript, Available online 12 August 2010</br> Peter H.J., Keizers , Marcellus, Ubbink</br> More...
nmrlearner Journal club 0 08-16-2010 03:29 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 - 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 02:37 PM.


Map