Sinnecker Sebastian, Flores Marco, Lubitz Wolfgang
Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470, Mülheim an der Ruhr, Germany.
Phys Chem Chem Phys. 2006 Dec 28;8(48):5659-70. doi: 10.1039/b612568a. Epub 2006 Nov 24.
The effect of hydrogen bonding to the primary quinone (Q(A) and Q()(-)(A)) in bacterial reaction centers was studied using density functional theory (DFT) calculations. The charge neutral state Q(A) was investigated by optimizing the hydrogen atom positions of model systems extracted from 15 different X-ray structures. From this analysis, mean values of the H-bond lengths and directions were derived. It was found that the N(delta)-H of His M219 forms a shorter H-bond to Q(A) than the N-H of Ala M260. The H-bond of His M219 is linear and more twisted out of the quinone plane. The radical anion Q()(-)(A) in the protein environment was investigated by using a mixed quantum mechanics/molecular mechanics (QM/MM) approach. Two geometry optimizations with a different number of flexible atoms were performed. H-bond lengths were obtained and spectroscopic parameters calculated, i.e. the hyperfine and nuclear quadrupole couplings of magnetic nuclei coupled to the radical. Good agreement was found with the results provided by EPR/ENDOR spectroscopy. This implies that the calculated lengths and directions of the H-bonds to Q(*)(-)(A) are reliable values. From a comparison of the neutral and reduced state of Q(A) it was concluded that the H-bond distances are shortened by approximately 0.17 Angstroms (His M219) and approximately 0.13 Angstroms (Ala M260) upon single reduction of the quinone. It is shown that the point-dipole approximation can not be used for an estimation of H-bond lengths from measured hyperfine couplings in a system with out-of-plane H-bonding. In contrast, the evaluation of the nuclear quadrupole couplings of (2)H nuclei substituted in the hydrogen bonds yields H-bond lengths close to the values that were deduced from DFT geometry optimizations. The significance of hydrogen bonding to the quinone cofactors in biological systems is discussed.
利用密度泛函理论（DFT）计算研究了氢键对细菌反应中心初级醌（Q(A)和Q()(-)(A)）的影响。通过优化从15种不同X射线结构中提取的模型系统的氢原子位置，研究了电荷中性态Q(A)。通过该分析，得出了氢键长度和方向的平均值。结果发现，His M219的N(δ)-H与Q(A)形成的氢键比Ala M260的N-H形成的氢键短。His M219的氢键是线性的，且更多地扭曲出醌平面。采用量子力学/分子力学混合方法（QM/MM）研究了蛋白质环境中的自由基阴离子Q()(-)(A)。进行了两种具有不同数量柔性原子的几何优化。获得了氢键长度并计算了光谱参数，即与自由基耦合的磁性核的超精细和核四极耦合。发现与电子顺磁共振/电子核双共振光谱（EPR/ENDOR）提供的结果吻合良好。这意味着计算得到的与Q(*)(-)(A)的氢键长度和方向是可靠的值。通过比较Q(A)的中性态和还原态得出，醌单还原后，氢键距离缩短了约0.17埃（His M219）和约0.13埃（Ala M260）。结果表明，在具有面外氢键的系统中，点偶极近似不能用于从测量的超精细耦合估计氢键长度。相反，对氢键中取代的(2)H核的核四极耦合进行评估，得到的氢键长度接近从DFT几何优化推导的值。讨论了氢键对生物系统中醌辅因子的重要性。
