Backbone Dynamics of trp Repressor Studied by 15N NMR Relaxation

Zheng, Zhiwen; Czaplicki, Jerzy; Jardetzky, Oleg

doi:10.1021/bi00015a035

Cited by 73 publications

(141 citation statements)

References 47 publications

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“…As pointed out by Kay et al (1989), if the amplitude of internal motions is small (SE> 0.7; Xe << Xc; see also Zheng et al, 1995) the RN(Nz)/RN(Nx.y) ratio can be used to determine an initial estimate of Zc. The experimentally determined relaxation ratio has a mean value of 0.83 + 0.06 at 27 ~ and 0.65 + 0.05 at 5 ~ The average ~c over all backbone nitrogens determined from the RN(Nz)/RN(Nx,y) relaxation ratio is 1.2+0.4 ns at 27 ~ and 2.4+0.3 ns at 5 ~ The ~c at 27 ~ is reduced to 1.1 +0.2 ns by excluding residues 17, 19, and 20, for which the xc values fall outside one standard deviation of the mean for all residues.…”

Section: Molecular Rotational Correlation Timesmentioning

confidence: 99%

Backbone dynamics of an alamethicin in methanol and aqueous detergent solution determined by heteronuclear 1H?15N NMR spectroscopy

1996

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The (15)N relaxation rates of the α-aminoisobutyric acid (Aib)-rich peptide alamethicin dissolved in methanol at 27°C and 5°C, and dissolved in aqueous sodium dodecylsulfate (SDS) at 27°C, were measured using inverse-detected one-and two-dimensional (1)H-(15)N NMR spectroscopy. Measurements of (15)N longitudinal (R(N)(N(z))) and transverse (R(N)(N(x,y))) relaxation rates and the {(1)H} (15)N nuclear Overhauser enhancement (NOE) at 11.7 Tesla were used to calculate (quasi-) spectral density values at 0, 50, and 450 MHz for the peptide in methanol and in SDS. Spectral density mapping at 0, 50, 450, 500, and 550 MHz was done using additional measurements of the (1)H-(15)N lingitudinal two-spin order, R(NH)(2H (infZ) (supN) N(Z)), two-spin antiphase coherence, R(NH)(2H (infN) (supZ) N(x,y)), and the proton longitudinal relaxation rate, R(H)(H (infN) (supZ) ), for the peptide dissolved in methanol only. The spectral density of motions was also modeled using the three-parameter Lipari-Szabo function. The overall rotational correlation times were determined to be 1.1, 2.5, and 5.7 ns for alamethicin in methanol at 27°C and 5°C, and in SDS at 27°C, respectively. From the rotational correlation time determined in SDS the number of detergent molecules associated with the peptide was estimated to be about 40. The average order parameter was about 0.7 and the internal correlation times were about 70 ps for the majority of backbone amide (15)N sites of alamethicin in methanol and in SDS. The relaxation data, spectral densities, and order parameters suggest that the peptide N-H vectors of alamethicin are not as highly constrained as the 'core' regions of folded globular proteins. However, the peptide backbone is clearly not as mobile as the most unconstrained regions of folded proteins, such as those found in the 'frayed' C-and N-termini of some proteins, or in randomcoil peptides. The data also suggest significant mobility at both ends of the peptide dissolved in methanol. In SDS the mobility in the middle and at the ends of the peptide is reduced. The implications of the results with respect to the sterically hindered Aib residues and the biological activities of the peptide are discussed.

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Section: Molecular Rotational Correlation Timesmentioning

confidence: 99%

Backbone dynamics of an alamethicin in methanol and aqueous detergent solution determined by heteronuclear 1H?15N NMR spectroscopy

1996

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“…Two approaches are usually employed, one based on the calculation of local diffusion coefficients D i , 72,73 and the other based on the direct fitting of the R 2 /R 1 ratios. 74,75 In the local D i approach, individual values of "local" tumbling times τ ci are obtained for each 15 N-1 H pair by fitting either the isotropic Lipari-Szabo function that also includes the part responsible for local motions, 72 or the R 2 /R 1 ratios. 73 For fast, small-amplitude internal motions R 2 /R 1 ratios to a good approximation depend only on the spectral densities for the global motion calculated as a Fourier transform of Equation 48.…”

Section: Rotational Diffusionmentioning

confidence: 99%

Characterization of the Fast Dynamics of Protein Amino Acid Side Chains Using NMR Relaxation in Solution

Igumenova¹,

Frederick²,

Wang³

2006

ChemInform

142

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“…Overall rotational motion of the protein is characterized by one or more rotational correlation times, depending on the symmetry of the rotational diffusion tensor. [10][11][12] In contrast, the spectral density mapping approach directly determines values of the power spectral density function at the eigenfrequencies of the spin system but does not directly separate internal and overall dynamical properties of the molecule.…”

Section: Introductionmentioning

confidence: 99%

Accuracy and precision of NMR relaxation experiments and MD simulations for characterizing protein dynamics

et al. 1997

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Model-free parameters obtained from nuclear magnetic resonance (NMR) relaxation experiments and molecular dynamics (MD) simulations commonly are used to describe the intramolecular dynamical properties of proteins. To assess the relative accuracy and precision of experimental and simulated model-free parameters, three independent data sets derived from backbone 15N NMR relaxation experiments and two independent data sets derived from MD simulations of Escherichia-coli ribonuclease HI are compared. The widths of the distributions of the differences between the order parameters for pairs of NMR data sets are congruent with the uncertainties derived from statistical analyses of individual data sets; thus, current protocols for analyzing NMR data encapsulate random uncertainties appropriately. Large differences in order parameters for certain residues are attributed to systematic differences between samples for intralaboratory comparisons and unknown, possibly magnetic field-dependent, experimental effects for interlaboratory comparisons. The widths of distributions of the differences between the order parameters for two NMR sets are similar to widths of distributions for an NMR and an MD set or for two MD sets. The linear correlations between the order parameters for an MD set and an NMR set are within the range of correlations observed between pairs of NMR sets. These comparisons suggest that the NMR and MD generalized order parameters for the backbone amide N-H bond vectors are of comparable accuracy for residues exhibiting motions on a fast time scale (< 100 ps). Large discrepancies between NMR and MD order parameters for certain residues are attributed to the occurrence of "rare" motional events over the simulation trajectories, the disruption of an element of secondary structure in one of the simulations, and lack of consensus among the experimental data sets. Consequently, (easily detectable) severe distortions of local protein structure and infrequent motional events in MD simulations appear to be the most serious artifacts affecting the accuracy and precision, respectively, of MD order parameters relative to NMR values. In addition, MD order parameters for motions on a fast (< 100 ps) timescale are more precisely determined than their NMR counterparts, thereby permitting more detailed dynamic characterization of biologically important residues by MD simulation than is sometimes possible by experimental methods. Proteins 28:481-493, 1997.

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Backbone Dynamics of trp Repressor Studied by 15N NMR Relaxation

Cited by 73 publications

References 47 publications

Backbone dynamics of an alamethicin in methanol and aqueous detergent solution determined by heteronuclear 1H?15N NMR spectroscopy

Backbone dynamics of an alamethicin in methanol and aqueous detergent solution determined by heteronuclear 1H?15N NMR spectroscopy

Characterization of the Fast Dynamics of Protein Amino Acid Side Chains Using NMR Relaxation in Solution

Accuracy and precision of NMR relaxation experiments and MD simulations for characterizing protein dynamics

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