Fast internal main-chain dynamics of human ubiquitin

Schneider, Diane M.; Dellwo, Martin J.; Wand, A. Joshua

doi:10.1021/bi00129a013

Cited by 194 publications

(179 citation statements)

References 31 publications

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“…Indeed, it was shown quite early that the uncertainty of the breadth of the chemical shift tensor at amide N-H can dwarf the uncertainty introduced by the imprecision of the measurement itself. 81 In some cases, the simple model-free treatment fails and an extended form that incorporates time scale separation for internal motion faster than overall tumbling is often employed. 82, 83 Statistical tests have been introduced to distinguish between various limiting cases of the simple and extended model-free spectral densities in various limits.…”

Section: Quantitative Analysismentioning

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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Section: Quantitative Analysismentioning

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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“…Indeed, a premise of the derivation presented, that the angular excursions of the vibrator are small, precludes the use of this treatment in the analysis of the highly dynamic unfolded state. It should noted, however, that recursive approaches such as those used to interpret the solvent exposed and highly dynamic C-terminus of ubiquitin may be generally applicable to the unfolded state (Schneider et al, 1992).…”

Section: Subsequent Curves Correspond To Calculations Using Values Ofmentioning

confidence: 99%

Insights into the local residual entropy of proteins provided by NMR relaxation

Li¹,

Raychaudhuri²,

Wand³

1996

Protein Science

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A simple model is used to illustrate the relationship between the dynamics measured by NMR relaxation methods and the local residual entropy of proteins. The expected local dynamic behavior of well-packed extended amino acid side chains are described by employing a one-dimensional vibrator that encapsulates both the spatial and temporal character of the motion. This model is then related to entropy and to the generalized order parameter of the popular "model-free" treatment often used in the analysis of NMR relaxation data. Simulations indicate that order parameters observed for the methyl symmetry axes in, for example, human ubiquitin correspond to significant local entropies. These observations have obvious significance for the issue of the physical basis of protein structure, dynamics, and stability.Keywords: protein dynamics; protein stability; protein entropy; NMR relaxationThe physical basis of protein structure, dynamics, and stability has been a subject of intense study and debate for several decades. While the taxonomy of protein structure appears to be well understood, a similar depth of understanding of the existence and character of the dynamics of proteins remains to be developed (for a review, see Frauenfelder et al., 1991). These issues are fundamental to a complete understanding of the origins, temporal behavior, and marginal stability of protein structure. For example, empirical evidence indicates that entropic effects dominate the free energy changes that accompany folding of a solvated "random coil" polypeptide usually to a dominant structure of lower free energy. The observed net increase in system entropy upon folding has been attributed to the dominance of a large increase in solvent entropy upon side-chain dehydration over a putatively smaller decrease in side-chain entropy upon packing in the folded globular state. have extremely high packing densities, which in turn, suggests that proteins are rigid with residual motion being extremely restricted and local. Accordingly, in discussions of protein stability and related issues, it is commonly assumed that the residual entropy of proteins is negligible. Nevertheless, over the past two decades there has been an accumulation of experimental (vide infra) and computational evidence (e.g., Karplus et al., 1987) that suggests quite a different view-that proteins are quite dynamic on time scales relevant to the question of residual entropy (for a recent review, see Doig and Sternberg, 1995). The magnitude of the residual entropy of proteins is of critical importance to an understanding of protein structure, stability, and ultimately function. In principle, nuclear magnetic resonance spectroscopy can be employed to estimate the local dynamics throughout a protein. Though comprehensive studies of the backbone dynamics of proteins based on analysis of I5N relaxation have appeared, it is only recently that general techniques have emerged to probe the fast dynamics of amino acid side chains. Earlier approaches employing 13C relaxation in selec...

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“…Our values at 27°C, t c = 7.1(20.3) ns for 19 mM BPTI at pD 4.7 and t c = 7.8(20.3) ns for 14 mM ubiquitin at pD 4.6, may be compared with the values (scaled to our temperature and solvent viscosity assuming t c A h/T ): t c = 3.1(20.8) ns for 5 mM BPTI at pH 4.6 (Szyperski et al, 1993) and t c = 4.3 ns for 2 mM ubiquitin at pH 5.0 (Schneider et al, 1992), both obtained from 15 N relaxation, and t c = 5.5 ns for 25 mM BPTI at pD 4.5, obtained from 13 C relaxation Data were obtained from files 5PTI and 1UBQ in the Protein Data Bank. † Angle between the principal axes of the 17 O electric field gradient and protein rotational diffusion tensors, the latter being parallel to the line connecting the C a atom of Gly36 with the C b atom of Tyr23 in BPTI.…”

Section: Surface Watermentioning

confidence: 99%

Protein Hydration Dynamics in Aqueous Solution: A Comparison of Bovine Pancreatic Trypsin Inhibitor and Ubiquitin by Oxygen-17 Spin Relaxation Dispersion

Денисов

Halle

1995

Journal of Molecular Biology

162

177

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Water oxygen-17 spin relaxation was used to study hydration and dynamics Condensed Matter Magnetic Resonance Group, Chemical of the globular proteins bovine pancreatic trypsin inhibitor (BPTI) and ubiquitin in aqueous solution. The frequency dispersion of the longitudinal Center, Lund University P. O. Box 124, S-22100 Lund and transverse relaxation rates was measured over the Larmor frequency Sweden range 2.6 to 49 MHz in the pD range 2 to 11 at 27°C. While the protein-induced relaxation enhancement was similar for the two proteins at high frequencies, it was an order of magnitude smaller for ubiquitin than for BPTI at low frequencies. This difference was ascribed to the abscence, in ubiquitin, of highly ordered internal water molecules, which are known to be present in BPTI and in most other globular proteins. These observations demonstrate that the water relaxation dispersion in protein solutions is essentially due to a few structural water molecules buried within the protein matrix, but exchanging rapidly with the external water. The relaxation data indicate that the internal water molecules of BPTI exchange with bulk water on the time-scale 10 −8 to 10 −6 second thus lowering the recently reported upper bound on the residence time of these internal water molecules by four orders of magnitude, and implying that local unfolding occurs on the submicrosecond time-scale. The water molecules residing at the surface of the two proteins were found to be highly mobile, with an average rotational correlation time of approximately 20 picoseconds. For both proteins, the oxygen-17 relaxation depended only very weakly on pD, showing that ionic residues do not perturb hydration water dynamics more than other surface residues. We believe that the present results resolve the long-standing controversy regarding the mechanism behind the spin relaxation dispersion of water nuclei in protein solutions, thus establishing oxygen-17 relaxation as a powerful tool for studies of structurally and functionally important water molecules in proteins and other biomolecules.

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Fast internal main-chain dynamics of human ubiquitin

Cited by 194 publications

References 31 publications

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

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

Insights into the local residual entropy of proteins provided by NMR relaxation

Protein Hydration Dynamics in Aqueous Solution: A Comparison of Bovine Pancreatic Trypsin Inhibitor and Ubiquitin by Oxygen-17 Spin Relaxation Dispersion

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