Temperature dependence of protein backbone motion from carbonyl 13C and amide 15N NMR relaxation

Chang, Shou-Lin; Tjandra, Nico

doi:10.1016/j.jmr.2005.01.008

Cited by 77 publications

(131 citation statements)

References 45 publications

(88 reference statements)

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“…In a recent combined computational and NMR study, the dynamics of ubiquitin were explored in more detail, showing that the binding selectivity for ubiquitin targets can be tuned by perturbing ubiquitin's pre-existing conformational equilibrium (Michielssens et al 2014). For most residues, the order parameters derived from the EROS ensemble are lower compared with those predicted by Lipari-Szabo analysis (Chang & Tjandra, 2005). Analysis of the supra-τ c regime thus reveals additional mobility, in good agreement with the structural heterogeneity observed in the EROS ensemble.…”

Section: Ubiquitinmentioning

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: Ubiquitinmentioning

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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“…The calculation is based on the experimentally determined H N -N order parameters obtained from relaxation measurements [166]. The nitrogen atoms were assumed to be located on a rigid backbone and the amide protons to sample a cone with Gaussian distributed weights (depending on the excursion from the average orientation) consistent with the [67].…”

Section: Impact Of Motionmentioning

confidence: 99%

The nuclear Overhauser effect from a quantitative perspective

Vögeli¹

2014

Progress in Nuclear Magnetic Resonance Spectroscopy

128

103

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“…[8,9] Interestingly, a periodic variation of the S 2 rdc value can be observed with a periodicity of two residues in the b strands of ubiquitin (amino acids 2-6, 12-16, 41-45, 66-71), while it is largely absent from the S 2 LS and exchange-rate data. Most prominently, the S 2 rdc values are larger for residues Gln 41, Leu 43, and Phe 45, and smaller for residues Arg 42 and Ile 44 in the b strand 41-45 (Figure 1).…”

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confidence: 99%

Side‐Chain Orientation and Hydrogen‐Bonding Imprint Supra‐τ_c Motion on the Protein Backbone of Ubiquitin

et al. 2005

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Knowledge about protein dynamics is crucial for the understanding of protein function.[1] NMR spectroscopy can characterize the amplitudes and rates of motions that are either faster than the rotational correlation time t c (sub-t c motion) with heteronuclear relaxation experiments or between approximately 50 ms and 10 ms (ms/ms motion) with relaxation dispersion. [2, 3] The extent of motions occurring in folded proteins on the time scale between the rotational correlation time t c and the ms/ms range (supra-t c motion) has been a matter of debate.[4] However, the functional relevance of such motions has recently been shown for the aggregation rate of natively unfolded proteins involved in neurodegenerative diseases.[5] Very recently, motions on this supra-t c time scale have been observed in a 0.2 ms molecular dynamics simulation of ubiquitin. [6] Residual dipolar couplings (rdcs) were recognized early on as an ideal tool to widen the time window of dynamics that can be characterized by NMR spectroscopy, since they are sensitive to motional averaging occurring over the sub-and supra-t c time scales (ps to ms).[4] We recently analyzed NH rdcs of ubiquitin measured in 31 different alignment conditions and derived the order parameters , 7] To differentiate between the sub-and supra-t c time scale, these order parameters were compared to Lipari-Szabo order parameters S 2 LS that are derived from conventional relaxation time measurements and that are only sensitive to the sub-t c time scale. [8,9] Interestingly, a periodic variation of the S 2 rdc value can be observed with a periodicity of two residues in the b strands of ubiquitin (amino acids 2-6, 12-16, 41-45, 66-71), while it is largely absent from the S 2 LS and exchange-rate data. Most prominently, the S 2 rdc values are larger for residues Gln 41, Leu 43, and Phe 45, and smaller for residues Arg 42 and Ile 44 in the b strand 41-45 (Figure 1). Correspondingly, the side chains of residues Gln 41, Leu 43, and Phe 45 point towards the hydrophobic core (core residues), whereas the side chains of Arg 42 and Ile 44 are exposed to solvent (exposed residues). Thus, the alternating pattern of the S 2 rdc values seems to correlate with the orientation of the side chains towards the solvent or away from it (Figure 2).The observation that solvent-exposed residues exhibit reduced S 2 rdc values relative to core residues holds not only for the b strands but also for the rest of the protein. The amino acids of ubiquitin (1d3z) are color coded in Figure 3 according to the S 2 rdc value of the backbone amide groups. Residues with less-mobile NH vectors (blue and green) have side chains predominantly pointing towards the hydrophobic core (Figure 3 a), while for those with more-mobile NH vectors (yellow, orange, and red), the side chains are solvent-exposed (Figure 3 b).To investigate this effect quantitatively, an order parameter for only the supra-t c time scale is derived:. For residues with supra-t c motions, we expect a value for S

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Temperature dependence of protein backbone motion from carbonyl 13C and amide 15N NMR relaxation

Cited by 77 publications

References 45 publications

Protein dynamics and function from solution state NMR spectroscopy

Protein dynamics and function from solution state NMR spectroscopy

The nuclear Overhauser effect from a quantitative perspective

Side‐Chain Orientation and Hydrogen‐Bonding Imprint Supra‐τ_c Motion on the Protein Backbone of Ubiquitin

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Temperature dependence of protein backbone motion from carbonyl 13C and amide 15N NMR relaxation

Cited by 77 publications

References 45 publications

Protein dynamics and function from solution state NMR spectroscopy

Protein dynamics and function from solution state NMR spectroscopy

The nuclear Overhauser effect from a quantitative perspective

Side‐Chain Orientation and Hydrogen‐Bonding Imprint Supra‐τc Motion on the Protein Backbone of Ubiquitin

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Product

Resources

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Side‐Chain Orientation and Hydrogen‐Bonding Imprint Supra‐τ_c Motion on the Protein Backbone of Ubiquitin