+ Site Statistics
References:
54,258,434
Abstracts:
29,560,870
PMIDs:
28,072,757
+ Search Articles
+ Subscribe to Site Feeds
Most Shared
PDF Full Text
+ PDF Full Text
Request PDF Full Text
+ Follow Us
Follow on Facebook
Follow on Twitter
Follow on LinkedIn
+ Translate
+ Recently Requested

Simulating electron spin resonance spectra of nitroxide spin labels from molecular dynamics and stochastic trajectories



Simulating electron spin resonance spectra of nitroxide spin labels from molecular dynamics and stochastic trajectories



Journal of Chemical Physics 128(16): 165106



Simulating electron spin resonance spectra of nitroxide spin labels from motional models is necessary for the quantitative analysis of experimental spectra. We present a framework for modeling the spin label dynamics by using trajectories such as those from molecular dynamics (MD) simulations combined with stochastic treatment of the global protein tumbling. This is achieved in the time domain after two efficient numerical integrators are developed: One for the quantal dynamics of the spins and the other for the classical rotational diffusion. For the quantal dynamics, we propagate the relevant part of the spin density matrix in Hilbert space. For the diffusional tumbling, we work with quaternions, which enables the treatment of anisotropic diffusion in a potential expanded as a sum of spherical harmonics. Time-averaging arguments are invoked to bridge the gap between the smaller time step of the MD trajectories and the larger time steps appropriate for the rotational diffusion and/or quantal spin dynamics.

(PDF emailed within 0-6 h: $19.90)

Accession: 055783492

Download citation: RISBibTeXText

PMID: 18447510

DOI: 10.1063/1.2908075


Related references

Simulating electron spin resonance spectra of macromolecules labeled with two dipolar-coupled nitroxide spin labels from trajectories. Physical Chemistry Chemical Physics 13(28): 12785-12797, 2012

Parametrization, molecular dynamics simulation, and calculation of electron spin resonance spectra of a nitroxide spin label on a polyalanine alpha-helix. Journal of Physical Chemistry. B 112(18): 5755-5767, 2008

Use of the integral of saturation transfer electron paramagnetic resonance spectra to determine molecular rotational correlation times. Slowly tumbling spin labels in the presence of rapidly tumbling spin labels. Journal of Magnetic Resonance 44(1): 109-116, 1969

Using Markov models to simulate electron spin resonance spectra from molecular dynamics trajectories. Journal of Physical Chemistry. B 112(35): 11014-11027, 2008

Using nitroxide spin labels. How to obtain T1e from continuous wave electron paramagnetic resonance spectra at all rotational rates. Biophysical Journal 64(3): 594-604, 1993

Molecular dynamics in liquids: Spin-lattice relaxation of nitroxide spin labels. Science (Washington D C) 263(5146): 490-493, 1994

Multifrequency electron spin resonance spectra of a spin-labeled protein calculated from molecular dynamics simulations. Journal of the American Chemical Society 131(7): 2597-2605, 2009

The internal dynamics of mini c TAR DNA probed by electron paramagnetic resonance of nitroxide spin-labels at the lower stem, the loop, and the bulge. Biochemistry 51(43): 8530-8541, 2013

Reappraisal of the electron spin resonance spectra of maleimide and iodoacetamide spin labels in erythrocyte ghosts. Archives of Biochemistry and Biophysics 190(2): 611-616, 1978

X- and Q-Band Electron Spin Echo Study of Stochastic Molecular Librations of Spin Labels in Lipid Bilayers. Applied Magnetic Resonance 44(1-2): 133-142, 2013

Electron paramagnetic resonance spectra simulation directly from molecular dynamics trajectories of a liquid crystal with a doped paramagnetic spin probe. Physical Review Letters 102(1): 013005, 2009

Simulation of nitroxide electron paramagnetic resonance spectra from brownian trajectories and molecular dynamics simulations. Biophysical Journal 94(10): 3798-3809, 2008

Backbone dynamics of alamethicin bound to lipid membranes: spin-echo electron paramagnetic resonance of TOAC-spin labels. Biophysical Journal 94(7): 2698-2705, 2007

Magnetic resonance imaging of biological specimens by electron paramagnetic resonance of nitroxide spin labels. Science 227(4686): 517-519, 1985

The effect of divalent metal binding on the electron spin resonance spectra of spin-labeled actin. Evidence for spin-spin interactions involving manganese. II. Archives of Biochemistry and Biophysics 150(2): 792-796, 1972