Related ArticlesProline-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 random-coil chemical shift values and their dependence on the presence of a proline residue in the (i+1) position can successfully be exploited to assign all proline-directed phosphorylation sites. This is a first step toward the study of the phosphorylation of Tau by NMR spectroscopy.
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...
markber
NMR software
0
02-02-2012 11:36 PM
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] 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
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