The Dynamical Theory of Nuclear Induction

Wangsness, Ronald K.; Bloch, F.

doi:10.1103/physrev.89.728

Cited by 801 publications

(516 citation statements)

References 1 publication

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“…This was followed by the development of the model-free approach for quantifying protein motion, which was presented by Lipari & Szabo (1982a) and is important in the study of dynamics by NMR. The Lipari and Szabo theory applies in the Redfield limit of the Bloch-Wangsness-Redfield theory (Redfield, 1957(Redfield, , 1965Wangsness & Bloch, 1953). A subsequent fundamental contribution was made by Kay et al (1989) with the development of inverse detected heteronuclear pulse sequences for determining the longitudinal and transversal relaxation rates (R 1 and R 2 , respectively) as well as the heteronuclear nuclear Overhauser effect (hNOE).…”

Section: Development Of Nmr Spectroscopy For Quantification Of Proteimentioning

confidence: 99%

Protein dynamics and function from solution state NMR spectroscopy

Kovermann

Rogne

Wolf‐Watz

2016

Quart. Rev. Biophys.

143

122

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Abstract. It is well-established that dynamics are central to protein function; their importance is implicitly acknowledged in the principles of the Monod, Wyman and Changeux model of binding cooperativity, which was originally proposed in 1965. Nowadays the concept of protein dynamics is formulated in terms of the energy landscape theory, which can be used to understand protein folding and conformational changes in proteins. Because protein dynamics are so important, a key to understanding protein function at the molecular level is to design experiments that allow their quantitative analysis. Nuclear magnetic resonance (NMR) spectroscopy is uniquely suited for this purpose because major advances in theory, hardware, and experimental methods have made it possible to characterize protein dynamics at an unprecedented level of detail. Unique features of NMR include the ability to quantify dynamics (i) under equilibrium conditions without external perturbations, (ii) using many probes simultaneously, and (iii) over large time intervals. Here we review NMR techniques for quantifying protein dynamics on fast (ps-ns), slow (μs-ms), and very slow (s-min) time scales. These techniques are discussed with reference to some major discoveries in protein science that have been made possible by NMR spectroscopy.

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Section: Development Of Nmr Spectroscopy For Quantification Of Proteimentioning

confidence: 99%

Protein dynamics and function from solution state NMR spectroscopy

Kovermann

Rogne

Wolf‐Watz

2016

Quart. Rev. Biophys.

143

122

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“…Bloch-Wangsness-Redfield spin relaxation theory [44][45][46][47] expresses spin-relaxation rates induced by reorientational motion in terms of the spectral density functions:…”

Section: Correlations Functions and Ordermentioning

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.

252

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 series of papers were devoted to the derivation and generalization of the Bloch equations (Wangsness and Bloch, 1953;Bloch, 1957;Redfield, 1957). Below we will illustrate the derivation from the model (8) in several limits of the qubit's dynamics.…”

Section: Bloch Equationsmentioning

confidence: 99%

Dissipative effects in Josephson qubits

2004

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Abstract. Josephson-junction systems have been studied as potential realizations of quantum bits. For their operation as qubits it is crucial to maintain quantum phase coherence for long times. Frequently relaxation and dephasing effects are described in the frame of the Bloch equations. Recent experiments demonstrate the importance of 1/f noise, or operate at points where the linear coupling to noise sources is suppressed. This requires generalizations and extensions of known methods and results. In this tutorial we present the Hamiltonian for Josephson qubits in a dissipative environment and review the derivation of the Bloch equations as well as systematic generalizations. We discuss 1/f noise, nonlinear coupling to the noise source, and effects of strong pulses on the dissipative dynamics. The examples illustrate the renormalization of qubit parameters by the high-frequency noise spectrum as well as non-exponential decay governed by low-frequency modes.

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The Dynamical Theory of Nuclear Induction

Cited by 801 publications

References 1 publication

Protein dynamics and function from solution state NMR spectroscopy

Protein dynamics and function from solution state NMR spectroscopy

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

Dissipative effects in Josephson qubits

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