Orientation of the rotational diffusion principal axis system determined by nuclear relaxation data

Dölle, Andreas; Bluhm, Th.

doi:10.1016/0079-6565(89)80003-2

Cited by 24 publications

(20 citation statements)

References 95 publications

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“…It should be noted that in this analysis only the independence of the internal and molecular motions is assumed. Anisotropy in molecular tumbling can be readily incorporated into the RR calculations using analysis in terms of symmetrical or asymmetrical ellipsoids of rotational diffusion (Dolle and Bluhm, 1989).…”

Section: Relaxation Analysis Via the (Sf S2n) (S/s~) And 2 2 2 ( Smentioning

confidence: 99%

Larmor frequency selective model free analysis of protein NMR relaxation

LeMaster

1995

J Biomol NMR

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The Lipari-Szabo dynamical formalism is extended by setting the time constants of the Lorentzian terms to [Formula: see text] and [Formula: see text]. This analysis is compared to the earlier proposed three-parameter [Formula: see text] extended model free formalism with regard to the range of equivalence and the advantages of the simplified two-parameter (S (inff) (sup2) ,S (infH) (sup2) ) and (S (inff) (sup2) ,S (infN) (sup2) ) representations. Spectral density components are calculated and compared to those obtained from the spectral density analysis formalism. Protein relaxation data, commonly analyzed in terms of the two-parameter [Formula: see text] representation, may correspond to a dynamically heterogeneous behaviour that is more appropriately represented in terms of a fast limit order parameter and a second, lower frequency order parameter.

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Section: Relaxation Analysis Via the (Sf S2n) (S/s~) And 2 2 2 ( Smentioning

confidence: 99%

Larmor frequency selective model free analysis of protein NMR relaxation

LeMaster

1995

J Biomol NMR

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“…In the case of the HMG1 A-domain, the ratio of the principal components of the moment of inertia tensor (2.5: 2.0:1.0) indicates that the symmetry of the protein is nearly axial. For lower symmetry, the principal axis system of the rotational diffusion tensor can be shifted from the moment of inertia axis system, especially for small molecules, due to interactions with solvent molecules (Dolle & Bluhm, 1989). However, the major axis of the rotational diffusion system coincides with that of the moment of inertia if the symmetry is axial or higher (Huntress, 1965).…”

Section: '5mentioning

confidence: 99%

Backbone Dynamics of the A-Domain of HMG1 As Studied by 15N NMR Spectroscopy

Broadhurst¹,

Ch²,

Jo³

et al. 1995

Biochemistry

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The HMG-box sequence motif (approximately 80 residues) occurs in a number of abundant eukaryotic chromosomal proteins such as HMG1, which binds DNA without sequence specificity, but with "structure specificity", as well as in several sequence-specific transcription factors. HMG1 has two such boxes, A and B, which show approximately 30% sequence identity, and an acidic C-terminal tail. The boxes are responsible for the ability of the protein to bend DNA and bind to bent or distorted DNA. The structure of the HMG box has been determined by NMR spectroscopy for the B-domain of HMG1 [Weir et al. (1993) EMBO J. 12, 1311-1319; Read et al. (1993) Nucleic Acids Res. 21, 3427-3436) and for Drosophila HMG-D (Jones et al. (1994) Structure 2, 609-627]. It has an unusual twisted L-shape, suggesting that the protein might tumble anisotropically in solution. In this paper we report studies of the A-domain from HMG1 using 15N NMR spectroscopy which show that the backbone dynamics of the protein can be described by two different rotational correlation times of 9.0 +/- 0.5 and 10.8 +/- 0.5 ns. We show that the relaxation data can be analyzed by assuming that the protein is a rigid, axially symmetric ellipsoid undergoing anisotropic rotational diffusion; the global rotational diffusion constants, D parallel and D perpendicular, were estimated as 2.47 x 10(7) and 1.49 x 10(7) s-1, respectively. By estimating the angle between the amide bond vectors and the major axis of the rotational diffusion tensor from the family of structures determined by NMR spectroscopy [see accompanying paper, Hardman et al. (1995) Biochemistry 34, 16596-16607], we were able to show that the ellipsoid spectral density equation can reproduce the major features of the 15N T1 and T2 profiles of the three helices in the HMG1 A-domain. The backbone dynamics of the A-domain were then compared with those of the B-domain and the HMG box from HMG-D. This comparison strongly supported the differences observed in the orientation of helix I in the three structures, where the B-domain appears to be more similar to HMG-D than it is to the A-domain. These differences may turn out to be related to subtle differences in the DNA-binding properties of the A- and B-domains of HMG1.

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“…The determined η values are given in Table . Owing to the symmetry, the molecules of 1 reorient in isotropic solutions as symmetrical tops. , The values of the appropriate rotational diffusion parameters: D ∥ = 3.0(3) × 10 9 s –1 and D ⊥ = 8.6(8) × 10 9 s –1 have been calculated using the measured T 1 and η data for protonated carbons, the DFT optimized molecular geometry, and the computer program described elsewhere . During the analysis of the relaxation data the theoretically calculated equilibrium C–H bond lengths have been multiplied by a factor of 1.03 to compensate for the effect of molecular vibrations. − The determined rotational diffusion coefficients and molecular geometry allowed us to calculate the contributions to the overall relaxation of C-9 carbon coming from the dipolar interactions , with protons, T 1,DD ( 13 C···H) = 165 s, from the dipolar interactions with bromine isotopes, T 1,DD ( 13 C– 79 Br) = 271 s and T 1,DD ( 13 C– 81 Br) = 234 s, and from the contribution from the relaxation mechanism caused by the magnetic shielding anisotropy, ,, T 1,SA ( 13 C-9) = 408 s. The last contribution has been estimated using the theoretically calculated Δσ( 13 C-9) = 39.2 ppm value.…”

Section: Resultsmentioning

confidence: 99%

Scalar Relaxation of the Second Kind. A Potential Source of Information on the Dynamics of Molecular Movements. 4. Molecules with Collinear C–H and C–Br Bonds

et al. 2014

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Continuing studies based on measurements of the nuclear spin relaxation rates running via the SC2 mechanism (scalar relaxation of the second kind), we present in this work the results obtained for three molecules: 9-bromotriptycene, 1,3,5-tribromobenzene, and 1-(2-bromoethynyl)-4-ethynylbenzene in which C-Br bond and one of C-H bonds are collinear. Separation of saturation-recovery or inversion-recovery curves of (13)C NMR signals of bromine-bonded carbons in the investigated compounds on two components has provided the longitudinal SC2 relaxation rates of these carbons in (79)Br- and (81)Br-containing isotopomers. These data have enabled experimental determination of the bromine-carbon spin-spin coupling constants and relaxation rates of quadrupole bromine nuclei, hardly accessible by direct measurements. At the same time the rotational diffusion parameters describing the reorientation of the C-Br vectors have been determined for the investigated molecules on the basis of the dipolar relaxation of protonated carbons. These diffusion parameters are crucial for interpretation of the bromine relaxation rates. The values of the indirect (1)J((13)C,(79)Br) coupling constants, magnetic shielding of carbon nuclei and quadrupole coupling constants of bromines, determined for the investigated compounds, have been compared with the results of the theoretical calculations which take into account relativistic effects. The origin of some divergences between the results obtained by different methods has been discussed.

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Orientation of the rotational diffusion principal axis system determined by nuclear relaxation data

Cited by 24 publications

References 95 publications

Larmor frequency selective model free analysis of protein NMR relaxation

Larmor frequency selective model free analysis of protein NMR relaxation

Backbone Dynamics of the A-Domain of HMG1 As Studied by 15N NMR Spectroscopy

Scalar Relaxation of the Second Kind. A Potential Source of Information on the Dynamics of Molecular Movements. 4. Molecules with Collinear C–H and C–Br Bonds

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