Journal ArticleDOI
Fractional protein dynamics seen by nuclear magnetic resonance spectroscopy: Relating molecular dynamics simulation and experiment
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It is shown that the model describes well the restricted rotational motion of N-H vectors in the amide groups of lysozyme obtained from molecular dynamics simulation and that reliable predictions of experimental relaxation rates can be obtained on that basis.Abstract:
We propose a fractional Brownian dynamics model for time correlation functions characterizing the internal dynamics of proteins probed by NMR relaxation spectroscopy. The time correlation functions are represented by a broad distribution of exponential functions which are characterized by two parameters. We show that the model describes well the restricted rotational motion of N-H vectors in the amide groups of lysozyme obtained from molecular dynamics simulation and that reliable predictions of experimental relaxation rates can be obtained on that basis.read more
Citations
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Distribution of Pico- and Nanosecond Motions in Disordered Proteins from Nuclear Spin Relaxation.
Shahid Nawaz Khan,Shahid Nawaz Khan,Shahid Nawaz Khan,Cyril Charlier,Cyril Charlier,Cyril Charlier,Rafal Augustyniak,Rafal Augustyniak,Rafal Augustyniak,Nicola Salvi,Victoire Déjean,Victoire Déjean,Victoire Déjean,Geoffrey Bodenhausen,Olivier Lequin,Olivier Lequin,Olivier Lequin,Philippe Pelupessy,Philippe Pelupessy,Philippe Pelupessy,Fabien Ferrage,Fabien Ferrage,Fabien Ferrage +22 more
TL;DR: A graphical representation is introduced that offers a convenient platform for a qualitative discussion of dynamics and shows that IMPACT often provides better quantitative agreement with experimental data than conventional model-free or extended model- free analyses with two or three correlation times.
Journal ArticleDOI
Generalized Kubo relations and conditions for anomalous diffusion: Physical insights from a mathematical theorem
TL;DR: The paper describes an approach to anomalous diffusion within the framework of the generalized Langevin equation using a Tauberian theorem for Laplace transforms due to Hardy, Littlewood, and Karamata and generalized Kubo relations for the relevant transport coefficients are derived from the asymptotic form of the mean square displacement.
Journal ArticleDOI
nMoldyn - Interfacing spectroscopic experiments, molecular dynamics simulations and models for time correlation functions
Vania Calandrini,E. Pellegrini,Paolo Calligari,Konrad Hinsen,Gerald R. Kneller,Gerald R. Kneller +5 more
TL;DR: A synoptic view of the range of applications of the latest version of nMoldyn is presented, which includes new modules for a simulation-based interpretation of data from nuclear magnetic resonance spectroscopy, far infraredSpectroscopy and for protein secondary structure analysis.
Journal ArticleDOI
Time-Resolved Protein Side-Chain Motions Unraveled by High-Resolution Relaxometry and Molecular Dynamics Simulations
Samuel F. Cousin,Pavel Kadeřávek,Nicolas Bolik-Coulon,Yina Gu,Cyril Charlier,Ludovic Carlier,Lei Bruschweiler-Li,Thorsten Marquardsen,Jean-Max Tyburn,Rafael Brüschweiler,Fabien Ferrage +10 more
TL;DR: A new NMR method based on high-resolution relaxometry and high-field relaxation is presented to determine quantitatively both motional amplitudes and time scales of methyl-bearing side chains in the picosecond-to-nanosecond range and unambiguously identify slow motions in the low nanosecondrange.
Journal ArticleDOI
Power-law and logarithmic relaxations of hydrated proteins: A molecular dynamics simulations study
TL;DR: Investigation of trajectories of consecutive nitrogen atoms along the protein backbone reveals that correlated forward-backward jumps, which exhibit a substantial degree of cooperativity, are a key feature of the anomalous dynamics.
References
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Journal ArticleDOI
Handbook of Mathematical Functions
Journal ArticleDOI
Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems
TL;DR: An N⋅log(N) method for evaluating electrostatic energies and forces of large periodic systems is presented based on interpolation of the reciprocal space Ewald sums and evaluation of the resulting convolutions using fast Fourier transforms.
Journal ArticleDOI
Scalable molecular dynamics with NAMD
James C. Phillips,Rosemary Braun,Wei Wang,James C. Gumbart,Emad Tajkhorshid,Elizabeth Villa,Christophe Chipot,Robert D. Skeel,Laxmikant V. Kale,Klaus Schulten +9 more
TL;DR: NAMD as discussed by the authors is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems that scales to hundreds of processors on high-end parallel platforms, as well as tens of processors in low-cost commodity clusters, and also runs on individual desktop and laptop computers.
Journal ArticleDOI
The missing term in effective pair potentials
TL;DR: On the other hand, in this paper, a superparamagnetically collapsed Mossbauer spectrum is obtained for carbon with fewer active sites, and these particles sinter and carburize in a manner more similar to that of Fe particles supported on graphite.
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