Related ArticlesEvaluation of backbone proton positions and dynamics in a small protein by liquid crystal NMR spectroscopy.
J Am Chem Soc. 2003 Jul 30;125(30):9179-91
Authors: Ulmer TS, Ramirez BE, Delaglio F, Bax A
NMR measurements of a large set of protein backbone one-bond dipolar couplings have been carried out to refine the structure of the third IgG-binding domain of Protein G (GB3), previously solved by X-ray crystallography at a resolution of 1.1 A. Besides the commonly used bicelle, poly(ethylene glycol), and filamentous phage liquid crystalline media, dipolar couplings were also measured when the protein was aligned inside either positively or negatively charged stretched acrylamide gels. Refinement of the GB3 crystal structure against the (13)C(alpha)-(13)C' and (13)C'-(15)N dipolar couplings improves the agreement between experimental and predicted (15)N-(1)H(N) as well as (13)C(alpha)-(1)H(alpha) dipolar couplings. Evaluation of the peptide bond N-H orientations shows a weak anticorrelation between the deviation of the peptide bond torsion angle omega from 180 degrees and the angle between the N-H vector and the C'-N-C(alpha) plane. The slope of this correlation is -1, indicating that, on average, pyramidalization of the peptide N contributes to small deviations from peptide bond planarity ( = 179.3 +/- 3.1 degrees ) to the same degree as true twisting around the C'-N bond. Although hydrogens are commonly built onto crystal structures assuming the N-H vector orientation falls on the line bisecting the C'-N-C(alpha) angle, a better approximation adjusts the C(alpha)-C'-N-H torsion angle to -2 degrees. The (15)N-(1)H(N) dipolar data do not contradict the commonly accepted motional model where angular fluctuations of the N-H bond orthogonal to the peptide plane are larger than in-plane motions, but the amplitude of angular fluctuations orthogonal the C(alpha)(i-1)-N(i)-C(alpha)(i) plane exceeds that of in-plane motions by at most 10-15 degrees. Dipolar coupling analysis indicates that for most of the GB3 backbone, the amide order parameters, S, are highly homogeneous and vary by less than +/-7%. Evaluation of the H(alpha) proton positions indicates that the average C(alpha)-H(alpha) vector orientation deviates by less than 1 degrees from the direction that makes ideal tetrahedral angles with the C(alpha)-C(beta) and C(alpha)-N vectors.
[NMR paper] Assignment of amide proton signals by combined evaluation of HN, NN and HNCA MAS-NMR
Assignment of amide proton signals by combined evaluation of HN, NN and HNCA MAS-NMR correlation spectra.
Related Articles Assignment of amide proton signals by combined evaluation of HN, NN and HNCA MAS-NMR correlation spectra.
J Biomol NMR. 2003 Mar;25(3):217-23
Authors: van Rossum BJ, Castellani F, Pauli J, Rehbein K, Hollander J, de Groot HJ, Oschkinat H
In this paper, we present a strategy for the (1)H(N) resonance assignment in solid-state magic-angle spinning (MAS) NMR, using the alpha-spectrin SH3 domain as an example. A novel 3D...
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[NMR paper] Backbone dynamics of the human MIA protein studied by (15)N NMR relaxation: implicati
Backbone dynamics of the human MIA protein studied by (15)N NMR relaxation: implications for extended interactions of SH3 domains.
Related Articles Backbone dynamics of the human MIA protein studied by (15)N NMR relaxation: implications for extended interactions of SH3 domains.
Protein Sci. 2003 Mar;12(3):510-9
Authors: Stoll R, Renner C, Buettner R, Voelter W, Bosserhoff AK, Holak TA
The melanoma inhibitory activity (MIA) protein is a clinically valuable marker in patients with malignant melanoma as enhanced values diagnose metastatic...
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[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...
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[NMR paper] Backbone dynamics of the calcium-signaling protein apo-S100B as determined by 15N NMR
Backbone dynamics of the calcium-signaling protein apo-S100B as determined by 15N NMR relaxation.
Related Articles Backbone dynamics of the calcium-signaling protein apo-S100B as determined by 15N NMR relaxation.
Biochemistry. 2001 Mar 27;40(12):3439-48
Authors: Inman KG, Baldisseri DM, Miller KE, Weber DJ
Backbone dynamics of homodimeric apo-S100B were studied by (15)N nuclear magnetic resonance relaxation at 9.4 and 14.1 T. Longitudinal relaxation (T(1)), transverse relaxation (T(2)), and the (15)N- NOE were measured for 80 of 91 backbone...
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[NMR paper] 15N NMR relaxation studies of the FK506 binding protein: backbone dynamics of the unc
15N NMR relaxation studies of the FK506 binding protein: backbone dynamics of the uncomplexed receptor.
Related Articles 15N NMR relaxation studies of the FK506 binding protein: backbone dynamics of the uncomplexed receptor.
Biochemistry. 1993 Sep 7;32(35):9000-10
Authors: Cheng JW, Lepre CA, Chambers SP, Fulghum JR, Thomson JA, Moore JM
Backbone dynamics of the major tacrolimus (FK506) binding protein (FKBP-12, 107 amino acids) have been studied using 15N relaxation data derived from proton-detected two-dimensional 1H-15N NMR spectroscopy....
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[NMR paper] Backbone dynamics of calcium-loaded calbindin D9k studied by two-dimensional proton-d
Backbone dynamics of calcium-loaded calbindin D9k studied by two-dimensional proton-detected 15N NMR spectroscopy.
Related Articles Backbone dynamics of calcium-loaded calbindin D9k studied by two-dimensional proton-detected 15N NMR spectroscopy.
Biochemistry. 1992 May 26;31(20):4856-66
Authors: Kördel J, Skelton NJ, Akke M, Palmer AG, Chazin WJ
Backbone dynamics of calcium-loaded calbindin D9k have been investigated by two-dimensional proton-detected heteronuclear nuclear magnetic resonance spectroscopy, using a uniformly 15N enriched...