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

Autor(en): Borovykh, Igor V.
Ceola, Stefano
Gajula, Prasad
Gast, Peter
Steinhoff, Heinz-J rgen
Huber, Martina
Stichwörter: BINDING; Biochemical Research Methods; Biochemistry & Molecular Biology; CONSTRAINTS; distance determination; DISTRIBUTIONS; double-electron-electron resonance; ENDOR; EPR SPECTROSCOPY; INDUCED STRUCTURAL-CHANGES; molecular-dynamics simulations; NITROXIDE SIDE-CHAINS; PACKAGE; PHOTOSYNTHETIC REACTION CENTERS; Physics; Physics, Atomic, Molecular & Chemical; QUINONE; reaction centre Rhodobacter sphaeroides; Spectroscopy; spin-label EPR
Erscheinungsdatum: 2006
Volumen: 180
Ausgabe: 2
Startseite: 178
Seitenende: 185
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 (60 K), 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. (c) 2006 Elsevier Inc. All rights reserved.
ISSN: 10907807
DOI: 10.1016/j.jmr.2006.02.008

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