Characterization of the Dynamics of Biomacromolecules Using Rotating-Frame Spin Relaxation NMR Spectroscopy

Palmer, Arthur G.; Massi, Francesca

doi:10.1021/cr0404287

Cited by 322 publications

(384 citation statements)

References 81 publications

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“…4.3 R 1ρ rotating frame relaxation R 1ρ relaxation experiments measure NMR spin relaxation in the rotating frame (Palmer & Massi, 2006) and can be used to monitor transverse relaxation rate constants on a μs-to-ms time scale. They are closely related to the CPMG experiments described in Section 4.2 , but R 1ρ experiments enable the observation of protein dynamics on a time scale that is around one order of magnitude faster time than is possible with CPMG-based experiments because they permit the use of higher refocusing frequencies and do not exceed the duty cycle of the CPMG pulse train.…”

Section: Properties/structures Of Minor Statesmentioning

confidence: 99%

Protein dynamics and function from solution state NMR spectroscopy

Kovermann

Rogne

Wolf‐Watz

2016

Quart. Rev. Biophys.

148

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: Properties/structures Of Minor Statesmentioning

confidence: 99%

Protein dynamics and function from solution state NMR spectroscopy

Kovermann

Rogne

Wolf‐Watz

2016

Quart. Rev. Biophys.

148

122

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“…Transforming the random Hamiltonian into the interaction frame (9) and substituting this expression into the equation for Γ ik (see Equation 6b) gives: (10) After some rearrangement, the integral in Equation 10 can be identified as the spectral density function : (11) Spectral density and correlation functions will be discussed in more detail in Section 4 of this review. For now, it suffices to say that the spectral density functions represent the frequency spectra of molecular motions.…”

Section: Formal Relationship Between Fast Dynamics and Relaxationmentioning

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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“…For an axial magnetic frame, Q, one has the explicit expression: (9) with only the diagonal terms, j K (ω), with K = 0, 1, 2, and the non-diagonal terms, j KK' (ω), with KK' = (0, 2) , (−1,1) and, (−2, 2) contributing.…”

Section: The Slowly Relaxing Local Structure (Srls) Modelmentioning

confidence: 99%

An Improved Picture of Methyl Dynamics in Proteins from Slowly Relaxing Local Structure Analysis of ²H Spin Relaxation

et al. 2007

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Protein dynamics is intimately related to biological function. Core dynamics is usually studied with 2 H spin relaxation of the 13 CDH 2 group, analyzed traditionally with the model-free (MF) approach. We showed recently that MF is oversimplified in several respects. This includes the assumption that the local motion of the dynamic probe and the global motion of the protein are decoupled, the local geometry is simple, and the local ordering has axial symmetry. Because of these simplifications MF has yielded a puzzling picture where the methyl rotation axis is moving rapidly with amplitudes ranging from nearly complete disorder to nearly complete order in tightly packed protein cores. Our conclusions emerged from applying to methyl dynamics in proteins the slowly relaxing local structure (SRLS) approach of Polimeno and Freed (J. Phys. Chem. 1995, 99, 1099), which can be considered the generalization of MF, with all the simplifications mentioned above removed. The SRLS picture derived here for the B1 immunoglobulin binding domain of peptostreptococcal protein L, studied over the temperature range of 15 − 45 °C, is fundamentally different from the MF picture. Thus, methyl dynamics is characterized structurally by rhombic local potentials with varying symmetries, and dynamically by tenfold slower rates of local motion. On average potential rhombicity decreases, mode-coupling increases and the rate of local motion increases with increasing temperature. The average activation energy for local motion is 2.0 ± 0.2 kcal/mol. Mode-coupling affects the analysis even at 15 o C. The accuracy of the results is improved by including in the experimental data set relaxation rates associated with rank 2 coherences. Keywords slowly relaxing local structure; methyl dynamics in proteins; NMR spin relaxation in proteins

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Characterization of the Dynamics of Biomacromolecules Using Rotating-Frame Spin Relaxation NMR Spectroscopy

Cited by 322 publications

References 81 publications

Protein dynamics and function from solution state NMR spectroscopy

Protein dynamics and function from solution state NMR spectroscopy

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

An Improved Picture of Methyl Dynamics in Proteins from Slowly Relaxing Local Structure Analysis of ²H Spin Relaxation

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Characterization of the Dynamics of Biomacromolecules Using Rotating-Frame Spin Relaxation NMR Spectroscopy

Cited by 322 publications

References 81 publications

Protein dynamics and function from solution state NMR spectroscopy

Protein dynamics and function from solution state NMR spectroscopy

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

An Improved Picture of Methyl Dynamics in Proteins from Slowly Relaxing Local Structure Analysis of 2H Spin Relaxation

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An Improved Picture of Methyl Dynamics in Proteins from Slowly Relaxing Local Structure Analysis of ²H Spin Relaxation