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 08-14-2010, 04:19 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 17,586
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 Analysis of and chemical shifts of cysteine and cystine residues in proteins: a quant

Abstract Cysteines possess a unique property among the 20 naturally occurring amino acids: it can be present in proteins in either the reduced or oxidized form, and can regulate the activity of some proteins. Consequently, to augment our previous treatment of the other types of residues, the
13\textC\upalpha and
13\textC\upbeta chemical shifts of 837 cysteines in disulfide-bonded cystine from a set of seven non-redundant proteins, determined by X-ray crystallography and NMR spectroscopy, were computed at the DFT level of theory. Our results indicate that the errors between observed and computed
13\textC\upalpha chemical shifts of such oxidized cysteines can be attributed to several effects such as: (a) the quality of the NMR-determined models, as evaluated by the conformational-average (ca) rmsd value; (b) the existence of high B-factor or crystal-packing effects for the X-ray-determined structures; (c) the dynamics of the disulfide bonds in solution; and (d) the differences in the experimental conditions under which the observed
13\textC\upalpha chemical shifts and the protein models were determined by either X-ray crystallography or NMR-spectroscopy. These quantum-chemical-based calculations indicate the existence of two, almost non-overlapped, basins for the oxidized and reduced ‚??SH
13\textC\upbeta , but not for the
13\textC\upalpha , chemical shifts, in good agreement with the observation of 375
13\textC\upalpha and 337
13\textC\upbeta resonances from 132 proteins by Sharma and Rajarathnam (2000). Overall, our results indicate that explicit consideration of the disulfide bonds is a necessary condition for an accurate prediction of
13\textC\upalpha and
13\textC\upbeta chemical shifts of cysteines in cystines.
  • Content Type Journal Article
  • DOI 10.1007/s10858-010-9396-x
  • Authors
    • Osvaldo A. Martin, Universidad Nacional de San Luis Instituto de Matem√°tica Aplicada San Luis CONICET, Ej√©rcito de Los Andes 950 5700 San Luis Argentina
    • Myriam E. Villegas, Universidad Nacional de San Luis Instituto de Matem√°tica Aplicada San Luis CONICET, Ej√©rcito de Los Andes 950 5700 San Luis Argentina
    • Jorge A. Vila, Universidad Nacional de San Luis Instituto de Matem√°tica Aplicada San Luis CONICET, Ej√©rcito de Los Andes 950 5700 San Luis Argentina
    • Harold A. Scheraga, Cornell University Baker Laboratory of Chemistry and Chemical Biology Ithaca NY 14853-1301 USA

Source: Journal of Biomolecular NMR
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Disordered proteins studied by chemical shifts
Disordered proteins studied by chemical shifts Publication year: 2011 Source: Progress in Nuclear Magnetic Resonance Spectroscopy, Available online 12 October 2011</br> Magnus*Kjaergaard, Flemming M.*Poulsen</br> More...
nmrlearner Journal club 0 10-14-2011 07:16 AM
Mapping allostery through the covariance analysis of NMR chemical shifts [Biophysics and Computational Biology]
Mapping allostery through the covariance analysis of NMR chemical shifts Selvaratnam, R., Chowdhury, S., VanSchouwen, B., Melacini, G.... Date: 2011-04-12 Allostery is a fundamental mechanism of regulation in biology. The residues at the end points of long-range allosteric perturbations are commonly identified by the comparative analyses of structures and dynamics in apo and effector-bound states. However, the networks of interactions mediating the propagation of allosteric signals between the end points often remain elusive. Here we show that the covariance analysis of NMR chemical...
nmrlearner Journal club 0 04-13-2011 01:15 AM
Mapping allostery through the covariance analysis of NMR chemical shifts.
Mapping allostery through the covariance analysis of NMR chemical shifts. Mapping allostery through the covariance analysis of NMR chemical shifts. Proc Natl Acad Sci U S A. 2011 Mar 28; Authors: Selvaratnam R, Chowdhury S, Vanschouwen B, Melacini G Allostery is a fundamental mechanism of regulation in biology. The residues at the end points of long-range allosteric perturbations are commonly identified by the comparative analyses of structures and dynamics in apo and effector-bound states. However, the networks of interactions mediating the...
nmrlearner Journal club 0 03-31-2011 06:24 PM
[NMR paper] Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its us
Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements. Related Articles Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements. J Biomol NMR. 2005 May;32(1):71-81 Authors: Eghbalnia HR, Wang L, Bahrami A, Assadi A, Markley JL We present an energy model that combines information from the amino acid sequence of a protein and available NMR chemical shifts for the purposes of identifying low...
nmrlearner Journal club 0 11-25-2010 08:21 PM
[NMR paper] Analysis of the 1H-NMR chemical shifts of Cu(I)-, Cu(II)- and Cd-substituted pea plas
Analysis of the 1H-NMR chemical shifts of Cu(I)-, Cu(II)- and Cd-substituted pea plastocyanin. Metal-dependent differences in the hydrogen-bond network around the copper site. 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 Analysis of the 1H-NMR chemical shifts of Cu(I)-, Cu(II)- and Cd-substituted pea plastocyanin. Metal-dependent differences in the hydrogen-bond network around the copper site. Eur J Biochem. 1996 Nov 15;242(1):132-47 ...
nmrlearner Journal club 0 08-22-2010 02:20 PM
[NMR paper] NMR chemical shifts and structure refinement in proteins.
NMR chemical shifts and structure refinement in proteins. Related Articles NMR chemical shifts and structure refinement in proteins. J Biomol NMR. 1993 Sep;3(5):607-12 Authors: Laws DD, de Dios AC, Oldfield E Computation of the 13C alpha chemical shifts (or shieldings) of glycine, alanine and valine residues in bovine and Drosophila calmodulins and Staphylococcal nuclease, and comparison with experimental values, is reported using a gauge-including atomic orbital quantum-chemical approach. The full approximately 24 ppm shielding range is...
nmrlearner Journal club 0 08-22-2010 03:01 AM
[NMR paper] 1H-NMR structural studies of a cystine-linked peptide containing residues 71-93 of tr
1H-NMR structural studies of a cystine-linked peptide containing residues 71-93 of transthyretin and effects of a Ser84 substitution implicated in familial amyloidotic polyneuropathy. 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 1H-NMR structural studies of a cystine-linked peptide containing residues 71-93 of transthyretin and effects of a Ser84 substitution implicated in familial amyloidotic polyneuropathy. Eur J Biochem. 1999 Jun;262(2):586-94 ...
nmrlearner Journal club 0 08-21-2010 04:03 PM
Analysis of NMR Chemical Shifts in Peptide & Protein Structure Determination-Wang '08
Analysis of NMR Chemical Shifts in Peptide and Protein Structure Determination By Liya Wang (2008) Amazon book description Chemical shifts provide detailed information about non-covalent structure, solvent interactions, ionization constants, ring orientations, hydrogen bond interactions, and other phenomena. Since different chemical shift data sets are not necessarily comparable without corrections or adjustments, the applicability of statistical analysis of NMR chemical shifts to biomolecules has so far been limited. We use the term "congruent" to describe data sets that can be...
Nikolai Books 0 08-20-2008 09:38 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 - 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 01:57 AM.


Map