Related ArticlesSecondary and tertiary structural effects on protein NMR chemical shifts: an ab initio approach.
Science. 1993 Jun 4;260(5113):1491-6
Authors: de Dios AC, Pearson JG, Oldfield E
Recent theoretical developments permit the prediction of 1H, 13C, 15N, and 19F nuclear magnetic resonance chemical shifts in proteins and offer new ways of analyzing secondary and tertiary structure as well as for probing protein electrostatics. For 13C, phi, psi torsion angles dominate shielding for C alpha and C beta, but the addition of hydrogen bonding and electrostatics gives even better accord with experiment. For 15NH, side chain (chi 1) torsion angles are also important, as are nearest neighbor sequence effects, whereas for 1HN, hydrogen bonding is particularly significant. For 19F, weak or long-range electrostatic fields dominate 19F shielding nonequivalencies. The ability to predict chemical shifts in proteins from known or test structures opens new avenues to structure refinement or determination, especially for condensed systems.
[NMR paper] Secondary structural effects on protein NMR chemical shifts.
Secondary structural effects on protein NMR chemical shifts.
Related Articles Secondary structural effects on protein NMR chemical shifts.
J Biomol NMR. 2004 Nov;30(3):233-44
Authors: Wang Y
For an amino acid in protein, its chemical shift, delta(phi, psi)(s), is expressed as a function of its backbone torsion angles (phi and psi) and secondary state (s): delta(phi, psi)(s=deltaphi, psi)_coil+Deltadelta(phi, psi)_s), where delta(phi, psi)(coil) represents its chemical shift at coil state (s=coil); Delta delta(phi, psi)(s) (s=sheet or helix) is...
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[NMR paper] Reexamination of the secondary and tertiary structure of histidine-containing protein
Reexamination of the secondary and tertiary structure of histidine-containing protein from Escherichia coli by homonuclear and heteronuclear NMR spectroscopy.
Related Articles Reexamination of the secondary and tertiary structure of histidine-containing protein from Escherichia coli by homonuclear and heteronuclear NMR spectroscopy.
Biochemistry. 1991 Dec 24;30(51):11842-50
Authors: Hammen PK, Waygood EB, Klevit RE
Analysis of the histidine-containing protein (HPr) from Escherichia coli by two-dimensional homonuclear and heteronuclear nuclear...
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08-21-2010 11:12 PM
[NMR paper] Reexamination of the secondary and tertiary structure of histidine-containing protein
Reexamination of the secondary and tertiary structure of histidine-containing protein from Escherichia coli by homonuclear and heteronuclear NMR spectroscopy.
Related Articles Reexamination of the secondary and tertiary structure of histidine-containing protein from Escherichia coli by homonuclear and heteronuclear NMR spectroscopy.
Biochemistry. 1991 Dec 24;30(51):11842-50
Authors: Hammen PK, Waygood EB, Klevit RE
Analysis of the histidine-containing protein (HPr) from Escherichia coli by two-dimensional homonuclear and heteronuclear nuclear...
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08-21-2010 11:12 PM
Mapping of protein structural ensembles by chemical shifts
Abstract Applying the chemical shift prediction programs SHIFTX and SHIFTS to a data base of protein structures with known chemical shifts we show that the averaged chemical shifts predicted from the structural ensembles explain better the experimental data than the lowest energy structures. This is in agreement with the fact that proteins in solution occur in multiple conformational states in fast exchange on the chemical shift time scale. However, in contrast to the real conditions in solution at ambient temperatures, the standard NMR structural calculation methods as well chemical shift...
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08-14-2010 04:19 AM
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...
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08-14-2010 04:19 AM
The predictive accuracy of secondary chemical shifts is more affected by protein seco
Abstract Biomolecular NMR spectroscopy frequently employs estimates of protein secondary structure using secondary chemical shift (Î?δ) values, measured as the difference between experimental and random coil chemical shifts (RCCS). Most published random coil data have been determined in aqueous conditions, reasonable for non-membrane proteins, but potentially less relevant for membrane proteins. Two new RCCS sets are presented here, determined in dimethyl sulfoxide (DMSO) and chloroform:methanol:water (4:4:1 by volume) at 298 K. A web-based program, CS-CHEMeleon, has been implemented to...
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PSSI: secondary structure from chemical shifts
Link to PSSI program
Reference and abstract:
Probability-based protein secondary structure identification using combined NMR chemical-shift data.
Wang Y, Jardetzky O.
Division of Chemical Biology, Department of Molecular Pharmacology, Stanford University, Stanford, California 94305, USA.
Secondary and tertiary structural effects on protein NMR chemical shifts: an ab initi
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