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
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02-02-2012 11:36 PM
NMR Provides a Quantitative Description of Protein Conformational Flexibility on Physiologically Important Timescales.
NMR Provides a Quantitative Description of Protein Conformational Flexibility on Physiologically Important Timescales.
NMR Provides a Quantitative Description of Protein Conformational Flexibility on Physiologically Important Timescales.
Biochemistry. 2011 Mar 9;
Authors: Salmon L, Bouvignies G, Markwick PR, Blackledge M
A complete description of biomolecular activity requires an understanding of the nature and the role of protein conformational dynamics. In recent years novel NMR-based techniques have emerged that provide hitherto inaccessible...
nmrlearner
Journal club
0
03-11-2011 03:14 PM
[NMR paper] Increased rigidity of eglin c at acidic pH: evidence from NMR spin relaxation and MD
Increased rigidity of eglin c at acidic pH: evidence from NMR spin relaxation and MD simulations.
Related Articles Increased rigidity of eglin c at acidic pH: evidence from NMR spin relaxation and MD simulations.
Biochemistry. 2003 Dec 2;42(47):13856-68
Authors: Hu H, Clarkson MW, Hermans J, Lee AL
To gain physical insights into how proteins respond to changes in pH, the picosecond to nanosecond time scale dynamics of the small serine protease inhibitor eglin c have been studied by NMR spin relaxation experiments and MD simulations under two...
nmrlearner
Journal club
0
11-24-2010 09:16 PM
[NMR paper] Phosphorylation and flexibility of cyclic-AMP-dependent protein kinase (PKA) using (3
Phosphorylation and flexibility of cyclic-AMP-dependent protein kinase (PKA) using (31)P NMR spectroscopy.
Related Articles Phosphorylation and flexibility of cyclic-AMP-dependent protein kinase (PKA) using (31)P NMR spectroscopy.
Biochemistry. 2002 May 14;41(19):5968-77
Authors: Seifert MH, Breitenlechner CB, Bossemeyer D, Huber R, Holak TA, Engh RA
Cell signaling pathways rely on phosphotransfer reactions that are catalyzed by protein kinases. The protein kinases themselves are typically regulated by phosphorylation and concurrent structural...
nmrlearner
Journal club
0
11-24-2010 08:49 PM
[NMR paper] Simulated and NMR-derived backbone dynamics of a protein with significant flexibility
Simulated and NMR-derived backbone dynamics of a protein with significant flexibility: a comparison of spectral densities for the betaARK1 PH domain.
Related Articles Simulated and NMR-derived backbone dynamics of a protein with significant flexibility: a comparison of spectral densities for the betaARK1 PH domain.
J Am Chem Soc. 2001 Apr 4;123(13):3021-36
Authors: Pfeiffer S, Fushman D, Cowburn D
A 7.6 ns molecular dynamics trajectory of the betaARK1 PH domain in explicit water with appropriate ions was calculated at 300 K. Spectral densities...
nmrlearner
Journal club
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11-19-2010 08:32 PM
A quantitative NMR spectroscopic examination of the flexibility of the C-terminal ext
A quantitative NMR spectroscopic examination of the flexibility of the C-terminal extensions of the molecular chaperones, alphaA- and alphaB-crystallin.
Related Articles A quantitative NMR spectroscopic examination of the flexibility of the C-terminal extensions of the molecular chaperones, alphaA- and alphaB-crystallin.
Exp Eye Res. 2010 Aug 20;
Authors: Treweek TM, Rekas A, Walker MJ, Carver JA
The principal lens proteins alphaA- and alphaB-crystallin are members of the small heat-shock protein (sHsp) family of molecular chaperone proteins. Via...
nmrlearner
Journal club
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08-25-2010 02:04 PM
[NMR paper] Using neural network predicted secondary structure information in automatic protein N
Using neural network predicted secondary structure information in automatic protein NMR assignment.
Related Articles Using neural network predicted secondary structure information in automatic protein NMR assignment.
J Chem Inf Comput Sci. 1997 Nov-Dec;37(6):1086-94
Authors: Choy WY, Sanctuary BC, Zhu G
In CAPRI, an automated NMR assignment software package that was developed in our laboratory, both chemical shift values and coupling topologies of spin patterns are used in a procedure for amino acids recognition. By using a knowledge base of...
nmrlearner
Journal club
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08-22-2010 05:08 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...
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