NMR Order Parameters of Biomolecules: A New Analytical Representation and Application to the Gaussian Axial Fluctuation Model

Brueschweiler, Rafael; Wright, Peter E.

doi:10.1021/ja00097a084

Cited by 134 publications

(125 citation statements)

References 0 publications

Supporting

Mentioning

121

Contrasting

Unclassified

Order By: Relevance

“…1b, we provide a summary of the correlation analysis, where the crankshaft motion, a rotation of the peptide plane about the C a i À 1 -C a i axis that leads to the anti-correlation of c i À 1 and f i often observed in MD simulations, is shown in italics 24 . The crankshaft motion is equivalent to that put forward in the onedimensional Gaussian axial fluctuation model (1D-GAF) of the protein backbone and to the g motion of the related 3D-GAF motional model, the amplitudes of which have been extensively studied by NMR spectroscopy 20,21,[25][26][27] . The anti-correlation is due to the rigidity of the peptide plane, which couples the motion Figure 1 | b-sheet ensemble correlations observed within and between the strands.…”

Section: Resultsmentioning

confidence: 99%

Correlated motions are a fundamental property of β-sheets

et al. 2014

View full text Add to dashboard Cite

Correlated motions in proteins can mediate fundamental biochemical processes such as signal transduction and allostery. The mechanisms that underlie these processes remain largely unknown due mainly to limitations in their direct detection. Here, based on a detailed analysis of protein structures deposited in the protein data bank, as well as on state-of-the art molecular simulations, we provide general evidence for the transfer of structural information by correlated backbone motions, mediated by hydrogen bonds, across b-sheets. We also show that the observed local and long-range correlated motions are mediated by the collective motions of b-sheets and investigate their role in large-scale conformational changes. Correlated motions represent a fundamental property of b-sheets that contributes to protein function.

show abstract

Section: Resultsmentioning

confidence: 99%

Correlated motions are a fundamental property of β-sheets

et al. 2014

View full text Add to dashboard Cite

show abstract

“…We have recently demonstrated (33,34) the utility of applying a simple physical model of peptide reorientation [1D GAF (35)] to study conformational averaging by combining 1 D HN RDCs from more than one alignment medium. Although this approach has been shown to be relatively insensitive to structural noise (36), the model nevertheless assumes that motion about the C iϪ1 ␣ -C i ␣ axis connecting sequential amino acids is dominant and that reorientations about orthogonal axes are less ample and therefore cannot provide further insight into the presence of more complex reorientational modes.…”

Section: Determination Of Long Time-scale Dynamic Modes and Amplitudementioning

confidence: 99%

Identification of slow correlated motions in proteins using residual dipolar and hydrogen-bond scalar couplings

Bouvignies

Bernadó

Meier

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

224

311

View full text Add to dashboard Cite

Despite their importance for biological activity, slower molecular motions beyond the nanosecond range remain poorly understood. We have assembled an unprecedented set of experimental NMR data, comprising up to 27 residual dipolar couplings per amino acid, to define the nature and amplitude of backbone motion in protein G using the Gaussian axial fluctuation model in three dimensions. Slower motions occur in the loops, and in the ␤-sheet, and are absent in other regions of the molecule, including the ␣-helix. In the ␤-sheet an alternating pattern of dynamics along the peptide sequence is found to form a long-range network of slow motion in the form of a standing wave extending across the ␤-sheet, resulting in maximal conformational sampling at the interaction site. The alternating nodes along the sequence match the alternation of strongly hydrophobic side chains buried in the protein core. Confirmation of the motion is provided through extensive crossvalidation and by independent hydrogen-bond scalar coupling analysis that shows this motion to be correlated. These observations strongly suggest that dynamical information can be transmitted across hydrogen bonds and have important implications for understanding collective motions and long-range information transfer in proteins.protein dynamics ͉ slow motions ͉ correlated M olecular dynamics, manifest in backbone and side-chain mobilities, play a crucial role in protein stability and function (1-4). The accurate characterization and understanding of protein motions thus adds an additional dimension to the structural information derived from genomics projects (5, 6). Although local backbone fluctuations on the picosecond to nanosecond time scale have been the subject of detailed characterization using NMR (7, 8) and molecular dynamics simulations (2), slower motions, in the submicrosecond to second range, remain poorly understood. Relaxation dispersion has been used to successfully identify sites of conformational exchange between states experiencing different chemical shifts in peptides (9) and proteins (10), but specific geometric motional models are often difficult to extract from these data. Slow time scales are, however, of particular interest because functionally important biological processes, including enzyme catalysis (11), signal transduction (12), ligand binding, and allosteric regulation (13), as well as collective motions involving groups of atoms or whole amino acids (14), are expected to occur in this time range. Residual dipolar couplings (RDCs) report on averages over longer time scales (up to the millisecond range) and therefore encode key information for understanding slower protein motions over a very broad time scale (15,16). Recent studies have exploited the orientational averaging properties of RDCs to characterize the amplitude and direction of motions of NH vectors (17)(18)(19) or to study local variations in position and dynamics of the amide proton (20,21). Despite this activity, key questions remain concerning the nature and amplitude of ...

show abstract

“…To quantitatively model the base motions about the glycosidic bond, their standard deviation of rotation about was calculated using the Gaussian axial fluctuation model (Bruschweiler and Wright 1994), which is a variant of the wobbling in a cone model. As expected, a larger angle was explored by those bases with a smaller order parameter (Hall and Tang 1998).…”

Section: The Ire Loop Structure and Dynamicsmentioning

confidence: 99%

Dynamics of the IRE RNA hairpin loop probed by 2-aminopurine fluorescence and stochastic dynamics simulations

Hall¹,

Williams²

2003

RNA

View full text Add to dashboard Cite

The iron responsive element (IRE) RNA hairpin loop contains six phylogenetically conserved nucleotides, which constitute part of the sequence-specific binding site of the IRE-binding protein. The NMR structure of the loop has been solved, showing that 3 of the 6 nt are poorly constrained. Here, two purine nucleotides in the IRE loop are individually replaced with the fluorescent purine analog 2-aminopurine (2AP). Steady-state and time-resolved fluorescence methods are used to describe the structure and dynamics of 2AP in the IRE loop. The data indicate that 2AP at the position of the adenosine in the loop moves between stacked and unstacked positions, whereas 2AP at the adjacent guanosine is predominantly solvent exposed. Stochastic dynamics simulations are used to provide a physical description of how those nucleotides might move.

show abstract

NMR Order Parameters of Biomolecules: A New Analytical Representation and Application to the Gaussian Axial Fluctuation Model

Cited by 134 publications

References 0 publications

Correlated motions are a fundamental property of β-sheets

Correlated motions are a fundamental property of β-sheets

Identification of slow correlated motions in proteins using residual dipolar and hydrogen-bond scalar couplings

Dynamics of the IRE RNA hairpin loop probed by 2-aminopurine fluorescence and stochastic dynamics simulations

Contact Info

Product

Resources

About