The dynamics of subunit rotation in a eukaryotic ribosome.
The dynamics of subunit rotation in a eukaryotic ribosome.
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真核核糖体中亚基旋转的动力学。
DOI：
10.3390/biophysica1020016
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发表时间：
2021-06
期刊：
影响因子：
--
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中科院分区：
文献类型：
--
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核糖体的蛋白质合成是通过一系列复杂的大规模构象重排来协调的。结构研究可以提供关于长寿命状态的信息，然而生物动力学受干预的自由能势垒控制。虽然在描述细菌核糖体的能量景观方面取得了进展，但对真核系统中大规模重排的能量学知之甚少。为了解决这个问题，我们构建了一个全原子模型与简化的能量和亚基旋转酵母核糖体进行模拟。在这些模拟中，小亚基（SSU; ~ 1 MDa）经历自发和可逆旋转（~8°）。通过在平衡条件下模拟这种重排，这些计算提供了对真核核糖体中控制动力学的分子因素的初步了解。通过这一点，我们能够确定特定的亚基间的相互作用，有一个显着的影响限速自由能垒。我们还表明，由于分子的灵活性的变化，旋转和未旋转状态之间的热力学平衡是温度依赖性的。这种效果可以解释在旋转和未旋转状态内的差分分子的灵活性。总之，这些计算提供了一个基础，在此基础上，该领域可以开始剖析这些复杂分子机器的能量学。
Protein synthesis by the ribosome is coordinated by an intricate series of large-scale conformational rearrangements. Structural studies can provide information about long-lived states, however biological kinetics are controlled by the intervening free-energy barriers. While there has been progress describing the energy landscapes of bacterial ribosomes, very little is known about the energetics of large-scale rearrangements in eukaryotic systems. To address this topic, we constructed an all-atom model with simplified energetics and performed simulations of subunit rotation in the yeast ribosome. In these simulations, the small subunit (SSU; ~1MDa) undergoes spontaneous and reversible rotations (~8°). By enabling the simulation of this rearrangement under equilibrium conditions, these calculations provide initial insights into the molecular factors that control dynamics in eukaryotic ribosomes. Through this, we are able to identify specific inter-subunit interactions that have a pronounced influence on the rate-limiting free-energy barrier. We also show that, as a result of changes in molecular flexibility, the thermodynamic balance between the rotated and unrotated states is temperature-dependent. This effect may be interpreted in terms of differential molecular flexibility within the rotated and unrotated states. Together, these calculations provide a foundation, upon which the field may begin to dissect the energetics of these complex molecular machines.
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DOI：
10.1073/pnas.0408098102
发表时间：
2005-05-10
影响因子：
11.1
作者：
Best, RB;Hummer, G
通讯作者：
Hummer, G
影响因子：
14.9
作者：
Bock LV;Blau C;Vaiana AC;Grubmüller H
通讯作者：
Grubmüller H
影响因子：
3
作者：
Duan, Y;Wu, C;Kollman, P
通讯作者：
Kollman, P
影响因子：
16.6
作者：
Frank J;Gonzalez RL Jr
通讯作者：
Gonzalez RL Jr
DOI：
10.1126/science.1202692
发表时间：
2011-05-20
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Dunkle JA;Wang L;Feldman MB;Pulk A;Chen VB;Kapral GJ;Noeske J;Richardson JS;Blanchard SC;Cate JH
通讯作者：
Cate JH