Wang Panyue, Dhananjayan Nithin, Hagras Muhammad A, Stuchebrukhov Alexei A
Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, CA 95616, United States of America.
Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, CA 95616, United States of America.
Biochim Biophys Acta Bioenerg. 2021 Jan 1;1862(1):148326. doi: 10.1016/j.bbabio.2020.148326. Epub 2020 Oct 9.
The structure of the entire respiratory complex I is now known at reasonably high resolution for many species - bacteria, yeast, and several mammals, including human. The structure reveals an almost 30 angstrom tunnel-like chamber for ubiquinone binding in the core part of the enzyme, at the joint between the membrane and hydrophilic arms of the enzyme. Here we characterize the geometric bottleneck forming the entrance of the quinone reaction chamber. Computer simulations of quinone/quinol passage through the bottleneck suggest that in all structures available, from bacterial to human, this bottleneck is too narrow for the quinone or quinol to pass and that a conformational change is required to open the channel. Moreover, the bottleneck is too narrow even for isoprenoid tail free passage. The closed structure can be an artifact of the crystallization packing forces, low temperature, or other unnatural conditions occurring in the structural data acquisition procedure that affect this flexible part of the enzyme. Two of the helices forming the bottleneck are in direct contact with the subunit (ND3) that was recently demonstrated to be involved in conformational changes during the redox proton pumping cycle, which indicates flexibility of that part of the enzyme. We conclude that the published structures are all locked in the unfunctional states and do not represent correctly the functional enzyme; we discuss possible ways to open the structure in the context of possible mechanisms of the enzyme.
现在，对于许多物种——细菌、酵母以及包括人类在内的几种哺乳动物，整个呼吸复合体I的结构已在相当高的分辨率下被知晓。该结构揭示了在酶的核心部分、膜与亲水臂的连接处，存在一个近30埃的隧道状腔室用于泛醌结合。在此，我们对形成醌反应腔室入口的几何瓶颈进行了表征。通过瓶颈的醌/醌醇的计算机模拟表明，在所有可得结构中，从细菌到人类，这个瓶颈对于醌或醌醇来说都太窄而无法通过，并且需要构象变化来打开通道。此外，这个瓶颈甚至对于类异戊二烯尾巴的自由通过来说也太窄。这种封闭结构可能是结晶堆积力、低温或结构数据采集过程中出现的其他非自然条件造成的假象，这些条件影响了酶的这个灵活部分。形成瓶颈的两条螺旋与亚基（ND3）直接接触，最近已证明该亚基在氧化还原质子泵浦循环中参与构象变化，这表明酶的该部分具有灵活性。我们得出结论，已发表的结构都锁定在无功能状态，不能正确代表有功能的酶；我们在酶的可能机制的背景下讨论打开该结构的可能方法。
