Distance between a native cofactor and a spin label in the reaction centre of Rhodobacter sphaeroides by a two-frequency pulsed electron paramagnetic resonance method and molecular dynamics simulations

Journal of Magnetic Resonance
Igor V BorovykhMartina Huber

Abstract

The distance between the paramagnetic state of a native cofactor and a spin label is measured in the photosynthetic reaction centre from the bacterium Rhodobacter sphaeroides R26. A two-frequency pulsed electron paramagnetic resonance method [double-electron-electron spin resonance (DEER)] is used. A distance of 3.05 nm between the semiquinone anion state of the primary acceptor (Q(A)) and the spin label at the native cysteine at position 156 in the H-subunit is found. Molecular-dynamics (MD) simulations are performed to interpret the distance. A 6 ns run comprising the entire RC protein yields a distance distribution that is close to the experimental one. The average distance found by the MD simulation is smaller than the distance obtained by DEER by at least 0.2 nm. To better represent the experiments performed at low temperature (60K), a MD method to mimic the freezing-in of the room-temperature conformations is introduced. Both MD methods yield similar distances, but the second method has a trend towards a wider distance distribution.

References

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Citations

Sep 4, 2009·Photosynthesis Research·Johann P Klare, Heinz-Jürgen Steinhoff
Oct 29, 2013·Progress in Nuclear Magnetic Resonance Spectroscopy·Klaus MöbiusAnton Savitsky
Jun 15, 2007·Quarterly Reviews of Biophysics·Olav Schiemann, Thomas F Prisner
Nov 6, 2009·Journal of the American Chemical Society·Michael A SwansonSandra S Eaton
Mar 13, 2012·The Journal of Physical Chemistry. B·Jessica L SarverSunil Saxena
Apr 22, 2009·Photosynthesis Research·Maurice van Gastel
Dec 26, 2006·Journal of Magnetic Resonance·Ye PolyhachG Jeschke
Jan 27, 2011·Biochemical Society Transactions·Gunnar W Reginsson, Olav Schiemann
Nov 16, 2010·Journal of Structural Biology·Kelli KazmierHassane S McHaourab
Feb 21, 2013·Angewandte Chemie·Philipp E SpindlerThomas F Prisner
Apr 14, 2007·Physical Chemistry Chemical Physics : PCCP·Gunnar Jeschke, Yevhen Polyhach
Jul 30, 2009·Physical Chemistry Chemical Physics : PCCP·Sabine BöhmeHeinz-Jürgen Steinhoff
Apr 20, 2010·The Journal of Physical Chemistry. B·Zhongyu YangSunil Saxena

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