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
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
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DOI：
10.1016/j.jmr.2006.02.008
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发表时间：
2006-06-01
影响因子：
2.2
通讯作者：
Huber, Martina
中科院分区：
文献类型：
--
作者：
Borovykh, Igor V.;Ceola, Stefano;Huber, Martina
天然辅因子和自旋标记的顺磁状态之间的距离是在光合反应中心从细菌Rhodobacter sphaeroides R26测量的。使用双频脉冲电子顺磁共振方法[双电子-电子自旋共振（DEER）]。发现主受体的半醌阴离子态（Q（A））与H亚基中156位天然半胱氨酸的自旋标记之间的距离为3.05 nm，并用分子动力学（MD）模拟解释了该距离。包含整个RC蛋白的6 ns运行产生接近实验的距离分布。通过MD模拟发现的平均距离比通过DEER获得的距离小至少0.2nm。为了更好地代表在低温（60 K）下进行的实验，引入了一种模拟室温构象冻结的MD方法。两种MD方法产生相似的距离，但第二种方法具有更宽的距离分布的趋势。(c)2006年爱思唯尔公司All rights reserved.
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.