J Phys Chem B. 2019 Mar 14;123(10):2325-2334. doi: 10.1021/acs.jpcb.9b01117. Epub 2019 Feb 28.
The tetrapyrrole chromophore biliverdin IXα (BV) in the bacteriophytochrome from Deinococcus radiodurans (DrBphP) is usually assumed to be fully protonated, but this assumption has not been systematically validated by experiments or extensive computations. Here, we use force field molecular dynamics simulations and quantum mechanics/molecular mechanics calculations with density functional theory and XMCQDPT2 methods to investigate the effect of the five most probable protonation forms of BV on structural stability, binding pocket interactions, and absorption spectra in the two photochromic states of DrBphP. While agreement with X-ray structural data and measured UV/vis spectra suggest that in both states the protonated form of the chromophore dominates, we also find that a minor population with a deprotonated D-ring could contribute to the red-shifted tail in the absorption spectra.
细菌视紫红质（Bacteriophytochrome）来源于耐辐射球菌（Deinococcus radiodurans）的四吡咯发色团胆绿素 IXα（BV）通常被假定为完全质子化，但这一假设尚未通过实验或广泛的计算得到系统验证。在这里，我们使用力场分子动力学模拟和量子力学/分子力学计算，结合密度泛函理论和 XMCQDPT2 方法，研究了 BV 的五种最可能的质子化形式对 DrBphP 两种光致变色状态的结构稳定性、结合口袋相互作用和吸收光谱的影响。虽然与 X 射线结构数据和测量的紫外/可见光谱的一致性表明，在两种状态下，发色团的质子化形式占主导地位，但我们也发现，D-环去质子化的较小部分可能会导致吸收光谱的红移尾巴。
