Chemical shifts contain important site-specific information on the structure and dynamics of proteins. Deviations from statistical average values, known as random coil chemical shifts (RCCSs), are extensively used to infer these relationships. Unfortunately, the use of imprecise reference RCCSs leads to biased inference and obstructs the detection of subtle structural features. Here we present a new method, POTENCI, for the prediction of RCCSs that outperforms the currently most authoritative methods. POTENCI is parametrized using a large curated database of chemical shifts for protein segments with validated disorder; It takes pH and temperature explicitly into account, and includes sequence-dependent nearest and next-nearest neighbor corrections as well as second-order corrections. RCCS predictions with POTENCI show root-mean-square values that are lower by 25â??78%, with the largest improvements observed for 1Hα and 13Câ?². It is demonstrated how POTENCI can be applied to analyze subtle deviations from RCCSs to detect small populations of residual structure in intrinsically disorder proteins that were not discernible before. POTENCI source code is available for download, or can be deployed from the URL http://www.protein-nmr.org.
Prediction of nearest neighbor effects on backbone torsion angles and NMR scalar coupling constants in disordered proteins
Prediction of nearest neighbor effects on backbone torsion angles and NMR scalar coupling constants in disordered proteins
Abstract
Using fine-tuned hydrogen bonding criteria, a library of coiled peptide fragments has been generated from a large set of high-resolution protein X-ray structures. This library is shown to be an improved representation of ?/? torsion angles seen in intrinsically disordered proteins (IDPs). The ?/? torsion angle distribution of the library, on average, provides good agreement with experimentally observed chemical shifts and 3JHN-H? coupling constants for a...
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10-25-2017 10:14 PM
[NMR paper] Prediction of nearest neighbor effects on backbone torsion angles and NMR scalar coupling constants in disordered proteins.
Prediction of nearest neighbor effects on backbone torsion angles and NMR scalar coupling constants in disordered proteins.
Prediction of nearest neighbor effects on backbone torsion angles and NMR scalar coupling constants in disordered proteins.
Protein Sci. 2017 Sep 08;:
Authors: Shen Y, Roche J, Grishaev A, Bax A
Abstract
Using fine-tuned hydrogen bonding criteria, a library of coiled peptide fragments has been generated from a large set of high-resolution protein X-ray structures. This library is shown to be an improved...
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09-09-2017 06:59 PM
Prediction of nearest neighbor effects on backbone torsion angles and NMR scalar coupling constants in disordered proteins
Prediction of nearest neighbor effects on backbone torsion angles and NMR scalar coupling constants in disordered proteins
Abstract
Using fine-tuned hydrogen bonding criteria, a library of coiled peptide fragments has been generated from a large set of high-resolution protein X-ray structures. This library is shown to be an improved representation of ?/? torsion angles seen in intrinsically disordered proteins (IDPs). The ?/? torsion angle distribution of the library, on average, provides good agreement with experimentally observed chemical shifts and 3JHN-H? coupling constants for a...
[NMR paper] Conformational Propensities of Intrinsically Disordered Proteins from NMR Chemical Shifts.
Conformational Propensities of Intrinsically Disordered Proteins from NMR Chemical Shifts.
Related Articles Conformational Propensities of Intrinsically Disordered Proteins from NMR Chemical Shifts.
Chemphyschem. 2013 Jun 21;
Authors: Kragelj J, Ozenne V, Blackledge M, Jensen MR
Abstract
The realization that a protein can be fully functional even in the absence of a stable three-dimensional structure has motivated a large number of studies describing the conformational behaviour of these proteins at atomic resolution. Here, we review...
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06-26-2013 09:39 AM
Disordered proteins studied by chemical shifts
Disordered proteins studied by chemical shifts
January 2012
Publication year: 2012
Source:Progress in Nuclear Magnetic Resonance Spectroscopy, Volume 60</br>
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12-01-2012 06:10 PM
Structure-based prediction of methyl chemical shifts in proteins
Structure-based prediction of methyl chemical shifts in proteins
Abstract Protein methyl groups have recently been the subject of much attention in NMR spectroscopy because of the opportunities that they provide to obtain information about the structure and dynamics of proteins and protein complexes. With the advent of selective labeling schemes, methyl groups are particularly interesting in the context of chemical shift based protein structure determination, an approach that to date has exploited primarily the mapping between protein structures and backbone chemical shifts. In order to...
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07-15-2011 09:10 PM
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...
POTENCI: prediction of temperature, neighbor and pH-corrected chemical shifts for intrinsically disordered proteins
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