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 set of five disordered proteins. Inspection of the coil library confirms that nearest-neighbor effects significantly impact the ?/? distribution of residues in the coil state. Importantly, 3JHN-H? coupling constants derived from the nearest-neighbor modulated backbone ? distribution in the coil library show improved agreement to experimental values, thereby providing a better way to predict 3JHN-H? coupling constants for IDPs, and for identifying locations that deviate from fully random behavior.
[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] MERA: a webserver for evaluating backbone torsion angle distributions in dynamic and disordered proteins from NMR data.
MERA: a webserver for evaluating backbone torsion angle distributions in dynamic and disordered proteins from NMR data.
Related Articles MERA: a webserver for evaluating backbone torsion angle distributions in dynamic and disordered proteins from NMR data.
J Biomol NMR. 2015 Jul 29;
Authors: Mantsyzov AB, Shen Y, Lee JH, Hummer G, Bax A
Abstract
MERA (Maximum Entropy Ramachandran map Analysis from NMR data) is a new webserver that generates residue-by-residue Ramachandran map distributions for disordered proteins or...
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07-30-2015 01:34 PM
MERA: a webserver for evaluating backbone torsion angle distributions in dynamic and disordered proteins from NMR data
MERA: a webserver for evaluating backbone torsion angle distributions in dynamic and disordered proteins from NMR data
Abstract
MERA (Maximum Entropy Ramachandran map Analysis from NMR data) is a new webserver that generates residue-by-residue Ramachandran map distributions for disordered proteins or disordered regions in proteins on the basis of experimental NMR parameters. As input data, the program currently utilizes up to 12 different parameters. These include three different types of short-range NOEs, three types of backbone chemical shifts...
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07-28-2015 04:51 PM
[NMR paper] Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks.
Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks.
Related Articles Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks.
J Biomol NMR. 2013 Jun 2;
Authors: Shen Y, Bax A
Abstract
A new program, TALOS-N, is introduced for predicting protein backbone torsion angles from NMR chemical shifts. The program relies far more extensively on the use of trained artificial neural networks than its predecessor, TALOS+....
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06-04-2013 06:31 PM
[NMR paper] Analysis of main chain torsion angles in proteins: prediction of NMR coupling constan
Analysis of main chain torsion angles in proteins: prediction of NMR coupling constants for native and random coil conformations.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Analysis of main chain torsion angles in proteins: prediction of NMR coupling constants for native and random coil conformations.
J Mol Biol. 1996 Jan 26;255(3):494-506
Authors: Smith LJ, Bolin KA, Schwalbe H, MacArthur MW, Thornton JM, Dobson CM
Using a data base of 85 high resolution protein...
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08-22-2010 02:27 PM
Sequential nearest-neighbor effects on computed 13Cα chemical shifts
Abstract To evaluate sequential nearest-neighbor effects on quantum-chemical calculations of 13Cα chemical shifts, we selected the structure of the nucleic acid binding (NAB) protein from the SARS coronavirus determined by NMR in solution (PDB id 2K87). NAB is a 116-residue α/β protein, which contains 9 prolines and has 50% of its residues located in loops and turns. Overall, the results presented here show that sizeable nearest-neighbor effects are seen only for residues preceding proline, where Pro introduces an overestimation, on average, of 1.73 ppm in the computed 13Cα chemical...
Prediction of nearest neighbor effects on backbone torsion angles and NMR scalar coupling constants in disordered proteins
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