Abstract：
Light-dependent protochlorophyllide oxidoreductase (LPOR) is a chlorophyll synthetase that catalyzes the reduction of protochlorophyllide (Pchlide) to chlorophyllide (Chlide) with indispensable roles in regulating photosynthesis processes. A recent study confirmed that thylakoid lipids (TL) were able to allosterically enhance modulator-induced LPOR activation. However, the allosteric modulation mechanism of LPOR by these compounds remains unclear. Herein, we integrated multiple computational approaches to explore the potential cavities in the Arabidopsis thaliana LPOR and an allosteric site around the helix-G region where high affinity for phosphatidyl glycerol (PG) was identified. Adopting accelerated molecular dynamics simulation for different LPOR states, we rigorously analyzed binary LPOR/PG and ternary LPOR/NADPH/PG complexes in terms of their dynamics, energetics, and attainable allosteric regulation. Our findings clarify the experimental observation of increased NADPH binding affinity for LPOR with PGs. Moreover, the simulations indicated that allosteric regulators targeting LPOR favor a mechanism involving lid opening upon binding to an allosteric hinge pocket mechanism. This understanding paves the way for designing novel LPOR activators and expanding the applications of LPOR.
摘要：
光依赖性原叶绿素氧化还原酶（LPOR）是一种叶绿素合成酶，可催化原叶绿素（Pchlide）还原为叶绿素（Chlide），在调节光合作用过程中具有不可或缺的作用。最近的一项研究证实，类囊体脂质（TL）能够以变构方式增强调节剂诱导的LPOR激活。然而,这些化合物对LPOR的变构调节机制尚不清楚。在这里，我们整合了多种计算方法来探索拟南芥LPOR中的潜在空腔和螺旋G区域周围的变构位点，该位点对磷脂酰甘油（PG）具有高亲和力。对不同的LPOR状态采用加速分子动力学模拟，我们严格分析了二元LPOR/PG和三元LPOR/NADPH/PG复合物的动力学，能量学,和可实现的变构调节。我们的发现阐明了NADPH与PG对LPOR的结合亲和力增加的实验观察。此外，模拟表明，以LPOR为目标的变构调节剂倾向于在结合到变构铰链口袋机制时涉及盖子打开的机制。这种理解为设计新型LPOR活化剂和扩展LPOR的应用铺平了道路。
