Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands.
Biochemistry. 2010 Jan 26;49(3):478-86. doi: 10.1021/bi9016236.
Protein nuclear magnetic resonance (NMR) secondary chemical shifts are widely used to predict the secondary structure, and in solid-state NMR, they are often the only unambiguous structural parameters available. However, the employed prediction methods are empirical in nature, relying on the assumption that secondary shifts are only affected by shielding effects of neighboring atoms. We analyzed the secondary shifts of a photosynthetic membrane protein with a high density of chromophores and very tight packing, the light-harvesting 2 (LH2) complex of Rhodopseudomonas acidophila. A relation was found between secondary shift anomalies and protein-protein or pigment-protein tertiary and quaternary contacts. For several residues, including the bacteriochlorophyll-coordinating histidines (alphaH31 and betaH30) and the phenylalanine alphaF41 that has strongly twisted C(b)-C(a)-C and C(a)-C-N conformations in the LH2 crystal structure, the perturbing effects on the backbone chemical shifts were tested by density functional theory (DFT) calculations. We propose that higher-order interactions in the tightly packed complex can induce localized perturbations of the backbone conformation and electronic structure, related to functional pigment-protein or protein-protein interactions.
蛋白质核磁共振（NMR）二级化学位移广泛用于预测二级结构，在固态 NMR 中，它们通常是唯一可用的明确结构参数。然而，所采用的预测方法本质上是经验性的，依赖于这样的假设，即二级位移仅受相邻原子屏蔽效应的影响。我们分析了具有高密度发色团和非常紧密堆积的光合膜蛋白，即嗜酸红假单胞菌的光捕获 2（LH2）复合物的二级位移异常。发现二级位移异常与蛋白质-蛋白质或色素-蛋白质三级和四级接触之间存在关系。对于几个残基，包括与细菌叶绿素配位的组氨酸（αH31 和 βH30）和在 LH2 晶体结构中具有强烈扭曲的 C(b)-C(a)-C 和 C(a)-C-N 构象的苯丙氨酸αF41，通过密度泛函理论（DFT）计算测试了对骨架化学位移的干扰效应。我们提出，在紧密堆积的复合物中的高阶相互作用可以诱导骨架构象和电子结构的局部扰动，与功能色素-蛋白质或蛋白质-蛋白质相互作用有关。
