Influence of rapid intramolecular motion on NMR cross-relaxation rates. A molecular dynamics study of antamanide in solution

Brueschweiler, Rafael; Roux, Benoît; Blackledge, Martin; Griesinger, Christian; Karplus, Martin; Ernst, R. R.

doi:10.1021/ja00033a002

Cited by 161 publications

(152 citation statements)

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“…Recently, new methods for the detection of internal motions by homonuclear NMR have been developed (18,(25)(26)(27). These exploit the fact that the NOESY and ROESY crosspeak intensities depend on both the internuclear distances and internal motion (28,29). Moreover, intraresidue and sequential NOESY H ␣ -H N cross-peak intensities are directly related to the dihedral angles and , respectively.…”

Section: Resultsmentioning

confidence: 99%

Concerted Motions of the Integrin-binding Loop and the C-terminal Tail of the Non-RGD Disintegrin Obtustatin

Monleón

Moreno-Murciano

Kovacs

et al. 2003

Journal of Biological Chemistry

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Obtustatin is a potent and selective inhibitor of the ␣ 1 ␤ 1 integrin in vitro and of angiogenesis in vivo. It possesses an integrin recognition loop that harbors, in a lateral position, the inhibitory 21 KTS 23 motif. We report an analysis of the dynamics of the backbone and sidechain atoms of obtustatin by homonuclear NMR methods. Angular mobility has been calculated for 90 assigned cross-peaks from 22 off-resonance rotating frame nuclear Overhauser effect spectroscopy spectra recorded at three magnetic fields. Our results suggest that the integrin binding loop and the C-terminal tail display concerted motions, which can be interpreted by hinge effects. Among the integrin-binding motif, threonine 22 and serine 23 exhibit the lowest and the highest sidechain flexibility, respectively. It is noteworthy that the side chain of threonine 22 is not solvent-exposed, although based on synthetic peptides it appears to be the most critical residue for the inhibitory activity of obtustatin on the binding of integrin ␣ 1 ␤ 1 to collagen IV. Instead, the side chain of threonine 22 is oriented toward the loop center and hydrogen-bonded to residues Thr 25 and Ser 26 . This network of interactions explains the restrained mobility of threonine 22 and suggests that its functional importance lies in maintaining the active conformation of the ␣ 1 ␤ 1 inhibitory loop.Disintegrins represent a group of cysteine-rich peptides released in Crotalidae and Viperidae snake venoms by proteolytic processing of PII metalloproteinases (1). Disintegrins are potent inhibitors of the binding of ␤ 1 and ␤ 3 integrins to their ligands. Biochemical (2,3) and structural studies (4 -7) have disclosed that the inhibitory activity of disintegrins is linked to a tripeptide motif, which mimics the recognition sequence of the integrin ligands. The tripeptide is maintained in the active conformation at the apex of a mobile loop by the appropriate pairing of cysteine residues (8, 9).Disintegrins are divided into five different groups (10). The first group includes short disintegrins composed of 49 -51 residues and four disulfide bonds. The second group is formed by medium sized disintegrins, which contain about 70 amino acids and six disulfide bonds. The third group includes long disintegrins composed of 84 residues cross-linked by seven disulfide bonds. The disintegrin domains of PIII snake venom metalloproteases contain about 100 amino acids with 16 cysteine residues involved in the formation of eight disulfide bonds. These constitute the fourth group of the disintegrin family. Unlike the short, medium, and long disintegrins, which are single-chain molecules, the fifth group is composed of homo-and heterodimers. Dimeric disintegrins contain subunits of about 67 residues with 10 cysteines involved in the formation of four intrachain disulfide bonds and two interchain cysteine linkages. Current biochemical and genetic data support the view that structural diversification among the disintegrin family occurred through disulfide bond engineering (10).The inte...

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Section: Resultsmentioning

confidence: 99%

Concerted Motions of the Integrin-binding Loop and the C-terminal Tail of the Non-RGD Disintegrin Obtustatin

Monleón

Moreno-Murciano

Kovacs

et al. 2003

Journal of Biological Chemistry

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“…(3). 74 Note that the time dependence in g(s) arises from both angular and radial degrees of freedom, r IS and X IS (as can be appreciated from the analyses in the previous sections, these degrees of freedom are coupled and cannot be easily separated). The MD-based correlation functions g(s) were subsequently used to evaluate the spectral density and predict the PRE rates.…”

Section: Model 5: MD Simulations Of the Pre Effectmentioning

confidence: 99%

Paramagnetic relaxation enhancements in unfolded proteins: Theory and application to drkN SH3 domain

et al. 2009

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Site-directed spin labeling in combination with paramagnetic relaxation enhancement (PRE) measurements is one of the most promising techniques for studying unfolded proteins. Since the pioneering work of Gillespie and Shortle (J Mol Biol 1997;268:158), PRE data from unfolded proteins have been interpreted using the theory that was originally developed for rotational spin relaxation. At the same time, it can be readily recognized that the relative motion of the paramagnetic tag attached to the peptide chain and the reporter spin such as 1 H N is best described as a translation. With this notion in mind, we developed a number of models for the PRE effect in unfolded proteins: (i) mutual diffusion of the two tethered spheres, (ii) mutual diffusion of the two tethered spheres subject to a harmonic potential, (iii) mutual diffusion of the two tethered spheres subject to a simulated mean-force potential (Smoluchowski equation); (iv) explicit-atom molecular dynamics simulation. The new models were used to predict the dependences of the PRE rates on the 1 H N residue number and static magnetic field strength; the results are appreciably different from the Gillespie-Shortle model. At the same time, the Gillespie-Shortle approach is expected to be generally adequate if the goal is to reconstruct the distance distributions between 1 H N spins and the paramagnetic center (provided that the characteristic correlation time is known with a reasonable accuracy). The theory has been tested by measuring the PRE rates in three spin-labeled mutants of the drkN SH3 domain in 2M guanidinium chloride. Two modifications introduced into the measurement scheme-using a reference compound to calibrate the signals from the two samples (oxidized and reduced) and using peak volumes instead of intensities to determine the PRE rates-lead to a substantial improvement in the quality of data. The PRE data from the denatured drkN SH3 are mostly consistent with the model of moderately expanded random-coil protein, although part of the data point toward a more compact structure (local hydrophobic cluster). At the same time, the radius of gyration reported by Choy et al. (J Mol Biol 2002;316:101) suggests that the protein is highly expanded. This seemingly contradictory evidence can be reconciled if one assumes that denatured drkN SH3 forms a conformational ensemble that is dominated by extended conformations, yet also contains compact (collapsed) species. Such behavior is apparently more complex than predicted by the model of a random-coil protein in good solvent/poor solvent.Additional Supporting Information may be found in the online version of this article.Abbreviations: drkN SH3, N-terminal SH3 domain of the Drosophila adapter protein drk; EDTA, ethylenediaminetetraacetic acid; ESR, electron spin resonance; FRET, fluorescence resonance energy transfer; MTSL, methanethiosulfonate spin label; NOE, nuclear Overhauser effect; NAG, N-acetyl-glycine.

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“…16,[26][27][28] This approach requires both a proper description of internal motions as well as an accurate modeling of overall tumbling. A related approach directly compares spectral density components J(ω), 16 whereby the extraction of spectral densities from the experiment requires additional experiments or makes additional assumptions.…”

Section: Introductionmentioning

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.

245

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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Influence of rapid intramolecular motion on NMR cross-relaxation rates. A molecular dynamics study of antamanide in solution

Cited by 161 publications

References 0 publications

Concerted Motions of the Integrin-binding Loop and the C-terminal Tail of the Non-RGD Disintegrin Obtustatin

Concerted Motions of the Integrin-binding Loop and the C-terminal Tail of the Non-RGD Disintegrin Obtustatin

Paramagnetic relaxation enhancements in unfolded proteins: Theory and application to drkN SH3 domain

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

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