Vreede Jocelyne, Crielaard Wim, Hellingwerf Klaas J, Bolhuis Peter G
Swammerdam Institute for Life Sciences, and van 't Hoff Institute of Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands.
Biophys J. 2005 May;88(5):3525-35. doi: 10.1529/biophysj.104.055103. Epub 2005 Feb 18.
As a bacterial blue light sensor the photoactive yellow protein (PYP) undergoes conformational changes upon signal transduction. The absorption of a photon triggers a series of events that are initially localized around the protein chromophore, extends to encompass the whole protein within microseconds, and leads to the formation of the transient pB signaling state. We study the formation of this signaling state pB by molecular simulation and predict its solution structure. Conventional straightforward molecular dynamics is not able to address this formation process due to the long (microsecond) timescales involved, which are (partially) caused by the presence of free energy barriers between the metastable states. To overcome these barriers, we employed the parallel tempering (or replica exchange) method, thus enabling us to predict qualitatively the formation of the PYP signaling state pB. In contrast to the receptor state pG of PYP, the characteristics of this predicted pB structure include a wide open chromophore-binding pocket, with the chromophore and Glu(46) fully solvent-exposed. In addition, loss of alpha-helical structure occurs, caused by the opening motion of the chromophore-binding pocket and the disruptive interaction of the negatively charged Glu(46) with the backbone atoms in the hydrophobic core of the N-terminal cap. Recent NMR experiments agree very well with these predictions.
作为一种细菌蓝光传感器，光敏黄色蛋白（PYP）在信号转导时会发生构象变化。光子的吸收引发了一系列事件，这些事件最初局限于蛋白质发色团周围，在微秒内扩展到整个蛋白质，并导致瞬态pB信号状态的形成。我们通过分子模拟研究这种信号状态pB的形成，并预测其溶液结构。由于涉及较长的（微秒）时间尺度，传统的直接分子动力学无法解决这个形成过程，这（部分）是由亚稳态之间存在自由能垒导致的。为了克服这些障碍，我们采用了并行回火（或副本交换）方法，从而使我们能够定性地预测PYP信号状态pB的形成。与PYP的受体状态pG相比，这种预测的pB结构的特征包括一个宽开放的发色团结合口袋，发色团和Glu(46)完全暴露于溶剂中。此外，由于发色团结合口袋的开放运动以及带负电荷的Glu(46)与N端帽疏水核心中的主链原子的破坏性相互作用，导致α-螺旋结构丧失。最近的核磁共振实验与这些预测非常吻合。
