BioNMR
NMR aggregator & online community since 2003
BioNMR    
Learn or help to learn NMR - get free NMR books!
 

Go Back   BioNMR > Software > NMR software
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 Rating: Thread Rating: 1 votes, 5.00 average. Display Modes
  #1  
Unread 02-02-2012, 11:36 PM
markber's Avatar
Administrator
 
Join Date: Oct 2008
Posts: 1,538
Points: 38,561, Level: 100
Points: 38,561, Level: 100 Points: 38,561, Level: 100 Points: 38,561, Level: 100
Level up: 0%, 0 Points needed
Level up: 0% Level up: 0% Level up: 0%
Activity: 0%
Activity: 0% Activity: 0% Activity: 0%
Last Achievements
NMR Credits: 1,550
NMR Points: 38,561
Downloads: 17
Uploads: 4
Default RCI - Random Coil Index for predicting protein flexibility from chemical shifts

RCI website

RCI method predicts protein flexibility by calculating the Random Coil Index from backbone chemical shifts and predicting values of model-free order parameters as well as per-residue RMSF of NMR and MD ensembles from the Random Coil Index.

The key advantages of this protocol over existing methods of studying protein flexibility are (i) it does not require prior knowledge of a protein's tertiary structure, (ii) it is not sensitive to the protein's overall tumbling and (iii) it does not require additional NMR measurements beyond the standard experiments for backbone assignments.

The application of secondary chemical shifts to characterize protein flexibility is based on an assumption that the close proximity of chemical shifts to random coil values is a manifestation of increased protein mobility, while significant differences from random coil values is an indication of a relatively rigid structure.

Even though chemical shifts of rigid residues may adopt random coil values due to specific values of torsion angles, combining the chemical shifts from multiple nuclei into a single parameter allows one to decrease the influence of these random coil false positives. The improved performance originates from the different probabilities of random coil chemical shifts from different nuclei being found among amino acid residues in flexible regions versus rigid regions. Typically, residues in rigid helices or rigid beta-strands are less likely to have more than one random coil chemical shift among their backbone shifts than residues in mobile regions.

The actual calculation of the RCI involves several additional steps including the smoothing of secondary shifts over several adjacent residues, the use of neighboring residue corrections, chemical shift re-referencing, gap filling, chemical shift scaling and numeric adjustments to prevent divide-by-zero problems. 13C, 15 N and 1H secondary chemical shifts are then scaled to account for the characteristic resonance frequencies of these nuclei and to provide numeric consistency among different parts of the protocol. Once these scaling corrections have been done, the RCI is calculated. The ‘‘end-effect correction’’ can also be applied at this point. The last step of the protocol involves smoothing the initial set of RCI values by three-point averaging.

References:

1. Mark V. Berjanskii and David S. Wishart (2005) A Simple Method To Predict Protein Flexibility Using Secondary Chemical Shifts J. Am. Chem. Soc., 2005, 127 (43), pp 14970–14971

2. Mark V. Berjanskii and David S. Wishart (2008) Application of the random coil index to studying protein flexibility. J Biomol NMR. 2008 Jan;40(1):31-48. Epub 2007 Nov 6.
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Sequence correction of random coil chemical shifts: correlation between neighbor correction factors and changes in the Ramachandran distribution
Sequence correction of random coil chemical shifts: correlation between neighbor correction factors and changes in the Ramachandran distribution Abstract Random coil chemical shifts are necessary for secondary chemical shift analysis, which is the main NMR method for identification of secondary structure in proteins. One of the largest challenges in the determination of random coil chemical shifts is accounting for the effect of neighboring residues. The contributions from the neighboring residues are typically removed by using neighbor correction factors determined based on each...
nmrlearner Journal club 0 06-06-2011 12:53 AM
Random coil chemical shift for intrinsically disordered proteins: effects of temperature and pH
Random coil chemical shift for intrinsically disordered proteins: effects of temperature and pH Abstract Secondary chemical shift analysis is the main NMR method for detection of transiently formed secondary structure in intrinsically disordered proteins. The quality of the secondary chemical shifts is dependent on an appropriate choice of random coil chemical shifts. We report random coil chemical shifts and sequence correction factors determined for a GGXGG peptide series following the approach of Schwarzinger et al. (J Am Chem Soc 123(13):2970â??2978, 2001). The chemical shifts are...
nmrlearner Journal club 0 01-17-2011 02:40 AM
[NMR paper] Accepting its random coil nature allows a partial NMR assignment of the neuronal Tau
Accepting its random coil nature allows a partial NMR assignment of the neuronal Tau protein. Related Articles Accepting its random coil nature allows a partial NMR assignment of the neuronal Tau protein. Chembiochem. 2004 Dec 3;5(12):1639-46 Authors: Smet C, Leroy A, Sillen A, Wieruszeski JM, Landrieu I, Lippens G A combined strategy to obtain a partial NMR assignment of the neuronal Tau protein is presented. Confronted with the extreme spectral degeneracy that the spectrum of this 441 amino acid long unstructured protein presents, we have...
nmrlearner Journal club 0 11-24-2010 10:03 PM
[NMR paper] Proline-directed random-coil chemical shift values as a tool for the NMR assignment o
Proline-directed random-coil chemical shift values as a tool for the NMR assignment of the tau phosphorylation sites. Related Articles Proline-directed random-coil chemical shift values as a tool for the NMR assignment of the tau phosphorylation sites. Chembiochem. 2004 Jan 3;5(1):73-8 Authors: Lippens G, Wieruszeski JM, Leroy A, Smet C, Sillen A, Buée L, Landrieu I NMR spectroscopy of the full-length neuronal Tau protein has proved to be difficult due to the length of the protein and the unfavorable amino acid composition. We show that the...
nmrlearner Journal club 0 11-24-2010 09:25 PM
[NMR paper] Sequence-dependent correction of random coil NMR chemical shifts.
Sequence-dependent correction of random coil NMR chemical shifts. Related Articles Sequence-dependent correction of random coil NMR chemical shifts. J Am Chem Soc. 2001 Apr 4;123(13):2970-8 Authors: Schwarzinger S, Kroon GJ, Foss TR, Chung J, Wright PE, Dyson HJ Random coil chemical shifts are commonly used to detect secondary structure elements in proteins in chemical shift index calculations. While this technique is very reliable for folded proteins, application to unfolded proteins reveals significant deviations from measured random coil...
nmrlearner Journal club 0 11-19-2010 08:32 PM
[NMR paper] Side-chains in native and random coil protein conformations. Analysis of NMR coupling
Side-chains in native and random coil protein conformations. Analysis of NMR coupling constants and chi1 torsion angle preferences. Related Articles Side-chains in native and random coil protein conformations. Analysis of NMR coupling constants and chi1 torsion angle preferences. J Mol Biol. 1998 Jul 31;280(5):867-77 Authors: West NJ, Smith LJ The behaviour of amino acid side-chains in proteins in solution has been characterised by analysing NMR 3JHalphaH beta coupling constants and crystallographic chi1 torsion angles. Side-chains both in the...
nmrlearner Journal club 0 11-17-2010 11:15 PM
Application of the random coil index to studying protein flexibility
Application of the random coil index to studying protein flexibility Mark V. Berjanskii and David S. Wishart Journal of Biomolecular NMR; 2008; 40(1); pp 31-48 Abstract: Protein flexibility lies at the heart of many protein–ligand binding events and enzymatic activities. However, the experimental measurement of protein motions is often difficult, tedious and error-prone. As a result, there is a considerable interest in developing simpler and faster ways of quantifying protein flexibility. Recently, we described a method, called Random Coil Index (RCI), which appears to be able to...
matthias Journal club 0 08-14-2008 01:03 AM
Chemical shift prediction in random coil peptides
Please check this program and let me know if it does work for your random coil peptides. http://bloch.anu.edu.au/cgi-bin/shiftpred/shiftpred.cgi Thank you, Bogdan Bancia bbancia@yahoo.com
bbancia NMR software 2 04-13-2007 03:54 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 - 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 03:03 PM.


Map