A Protocol for the Interpretation of Side-Chain Dynamics Based on NMR Relaxation:  Application to Phenylalanines in Antamanide

Bremi, Tobias; Brüschweiler, and R.; Ernst, R. R.

doi:10.1021/ja9636505

Cited by 85 publications

(109 citation statements)

References 41 publications

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“…In Fig. 9, we observe that a tentative fit of the simulated G(t) for iPP and sPP based on the three parameters DLM functional form ͑using a unique set of parameters 2 and a for both tacticities͒ appears to be as good as the more flexible fit with the four parameters SEHH model function ͑15͒. Table IV gathers values of DLM parameters for both iPP and sPP oligomers.…”

Section: ͑14͒mentioning

confidence: 89%

“…In some favorable cases, like in the dynamics of a flexible short chain attached to a quasirigid large molecule, it has been possible to follow the above mentioned ideal program in the interpretation of the NMR data. 2 For the local dynamics of linear polymers in the liquid phase, one knows no analytical expression of G(t) which would have been derived rigorously for a dynamical model combining the elementary types of motions. One major difficulty lies in the incorporation in the dynamical model of correlations between successive conformational jumps or between a conformational jump and subsequent dihedral angle cooperative damped counterrotations in the neighborhood of the jumping one.…”

Section: Introductionmentioning

confidence: 99%

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Local dynamics of isotactic and syndiotactic polypropylene in solution

Destrée

Lauprêtre

Lyulin

et al. 2000

The Journal of Chemical Physics

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The local dynamics of polypropylene ͑PP͒ in solution is studied by 13 C NMR relaxation and by molecular dynamics ͑MD͒ simulation via the orientational autocorrelation function ͑OACF͒ of C-H bonds. The interpretation protocol of this function proposed by Dejean de la Bâtie, Lauprêtre and Monnerie ͑DLM͒ ͓R. Dejean de la Bâtie, F. Lauprêtre, and L. Monnerie, Macromolecules 21, 2045͑1988͔͒ is applied and tested on new NMR measurements of the various microstructures of polypropylene. This interpretation scheme of the OACF is supported by a detailed study employing simulated PP trajectories in an atomistic heat bath. MD simulations indicate that, quite generally, the correlation time for segmental motions, 1 , extracted from the DLM motional model is closely linked with the mean time between conformational jumps. Both experiments and simulations suggest a slightly higher mobility of meso sequences by comparison with racemic sequences. Our analysis of the microscopic aspects of the segmental dynamics and its manifestation in motional models allows us to trace the microscopic origin of the larger mobility of meso sequences.

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Section: ͑14͒mentioning

confidence: 89%

Section: Introductionmentioning

confidence: 99%

Local dynamics of isotactic and syndiotactic polypropylene in solution

Destrée

Lauprêtre

Lyulin

et al. 2000

The Journal of Chemical Physics

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“…The S 2 axis order parameters for Ile d1 methyls were calculated from Cg1-Cd1 bond vectors extracted from four of these windows using the trjtool software (Xue et al, 2014;Bremi et al, 1997). The average ±standard deviation of these order parameters over the four windows is reported for each Ile d1 methyl.…”

Section: Force Fields and MD Simulationsmentioning

confidence: 99%

Ligand Modulation of Sidechain Dynamics in a Wild-Type Human GPCR

Clark

Dikiy

Chapman

et al. 2018

Biophysical Journal

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GPCRs regulate all aspects of human physiology, and biophysical studies have deepened our understanding of GPCR conformational regulation by different ligands. Yet there is no experimental evidence for how sidechain dynamics control allosteric transitions between GPCR conformations. To address this deficit, we generated samples of a wild-type GPCR (A 2A R) that are deuterated apart from 1 H/ 13 C NMR probes at isoleucine d1 methyl groups, which facilitated 1 H/ 13 C methyl TROSY NMR measurements with opposing ligands. Our data indicate that low [Na + ] is required to allow large agonist-induced structural changes in A 2A R, and that patterns of sidechain dynamics substantially differ between agonist (NECA) and inverse agonist (ZM241385) bound receptors, with the inverse agonist suppressing fast ps-ns timescale motions at the G protein binding site. Our approach to GPCR NMR creates a framework for exploring how different regions of a receptor respond to different ligands or signaling proteins through modulation of fast ps-ns sidechain dynamics.

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“…16,[26][27][28] This approach requires both a proper description of internal motions as well as an accurate modeling of overall tumbling. A related approach directly compares spectral density components J(ω), 16 whereby the extraction of spectral densities from the experiment requires additional experiments or makes additional assumptions.…”

Section: Introductionmentioning

confidence: 99%

Validation of Molecular Dynamics Simulations of Biomolecules Using NMR Spin Relaxation as Benchmarks: Application to the AMBER99SB Force Field

Showalter

Brüschweiler

2007

J. Chem. Theory Comput.

258

277

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Biological function of biomolecules is accompanied by a wide range of motional behavior. Accurate modeling of dynamics by molecular dynamics (MD) computer simulations is therefore a useful approach toward the understanding of biomolecular function. NMR spin relaxation measurements provide rigorous benchmarks for assessing important aspects of MD simulations, such as the amount and time scales of conformational space sampling, which are intimately related to the underlying molecular mechanics force field. Until recently, most simulations produced trajectories that exhibited too much dynamics particularly in flexible loop regions. Recent modifications made to the backbone and ψ torsion angle potentials of the AMBER and CHARMM force fields indicate that these changes produce more realistic molecular dynamics behavior. To assess the consequences of these changes, we performed a series of 5-20 ns molecular dynamics trajectories of human ubiquitin using the AMBER99 and AMBER99SB force fields for different conditions and water models and compare the results with NMR experimental backbone N-H S 2 order parameters. A quantitative analysis of the trajectories shows significantly improved agreement with experimental NMR data for the AMBER99SB force field as compared to AMBER99. Because NMR spin relaxation data (T 1 , T 2 , NOE) reflect the combined effects of spatial and temporal fluctuations of bond vectors, it is found that comparison of experimental and back-calculated NMR spin-relaxation data provides a more objective way of assessing the quality of the trajectory than order parameters alone. Analysis of a key mobile -hairpin in ubiquitin demonstrates that the dynamics of mobile sites are not only reduced by the modified force field, but the extent of motional correlations between amino acids is also markedly diminished.

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A Protocol for the Interpretation of Side-Chain Dynamics Based on NMR Relaxation: Application to Phenylalanines in Antamanide

Cited by 85 publications

References 41 publications

Local dynamics of isotactic and syndiotactic polypropylene in solution

Local dynamics of isotactic and syndiotactic polypropylene in solution

Ligand Modulation of Sidechain Dynamics in a Wild-Type Human GPCR

Validation of Molecular Dynamics Simulations of Biomolecules Using NMR Spin Relaxation as Benchmarks: Application to the AMBER99SB Force Field

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