+ 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

Parametrization, molecular dynamics simulation, and calculation of electron spin resonance spectra of a nitroxide spin label on a polyalanine alpha-helix



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



The nitroxide spin label 1-oxyl-2,2,5,5-tetramethylpyrroline-3-methyl-methanethiosulfonate (MTSSL), commonly used in site-directed spin labeling of proteins, is studied with molecular dynamics (MD) simulations. After developing force field parameters for the nitroxide moiety and the spin label linker, we simulate MTSSL attached to a polyalanine alpha-helix in explicit solvent to elucidate the factors affecting its conformational dynamics. Electron spin resonance spectra at 9 and 250 GHz are simulated in the time domain using the MD trajectories and including global rotational diffusion appropriate for the tumbling of T4 Lysozyme in solution. Analysis of the MD simulations reveals the presence of significant hydrophobic interactions of the spin label with the alanine side chains.

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

Accession: 054862262

Download citation: RISBibTeXText

PMID: 18412413

DOI: 10.1021/jp711375x


Related references

Simulating electron spin resonance spectra of nitroxide spin labels from molecular dynamics and stochastic trajectories. Journal of Chemical Physics 128(16): 165106, 2008

Pulsed electron-electron double resonance spectroscopy between a high-spin Mn(2+) ion and a nitroxide spin label. Physical Chemistry Chemical Physics 17(10): 6760-6766, 2015

Solution of the nitroxide spin-label spectral overlap problem using pulse electron spin resonance. Biophysical Journal 53(4): 525-531, 1988

Experimental molecular dynamics of an alanine-based helical peptide determined by spin label electron spin resonance. Biochemistry. 32(31): 8014-8021, 1993

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

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

Exploring the peptide 3(10)-helix<-->alpha-helix equilibrium with double label electron spin resonance. Biopolymers 37(6): 421, 1995

Exploring the peptide 3(10)-helix reversible alpha-helix equilibrium with double label electron spin resonance. Biopolymers 37(4): 243-250, 1995

Simulation of electron paramagnetic resonance spectra of spin-labeled molecules from replica-exchange molecular dynamics. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics 88(4): 042701, 2014

Molecular dynamics simulation of dipalmitoylphosphatidylcholine modified with a MTSL nitroxide spin label in a lipid membrane. Biochimica et Biophysica Acta 1828(11): 2770-2777, 2013

Factors that determine the EPR spectra of nitroxide side-chains in spin labeled proteins and analysis by molecular dynamics simulation. Biophysical Journal 66(2 PART 2): A40, 1994

Liposome immunoassay using a spin label, TEMPO choline ammonium-2,2,6,6-tetramethylpiperidine-1-oxyl A new strategy for detecting this spin label using an ion-selective electrode in place of electron spin resonance. Analytical Letters 31(1): 55-66, 1998

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

Spin-label electron spin resonance studies on the dynamics of the different phases of N-biotinylphosphatidylethanolamines. Biochemistry 33(38): 11656-11663, 1994

Kinetic Model for Determination of Reaction and Polarization Dynamics from Chemically Induced Electron Spin Polarized Electron Spin Resonance Spectra. Journal of Physical Chemistry A 107(43): 9045-9050, 2003