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The ribosome's energy landscape: Recent insights from computation

机译:核糖体的能量格局:计算的最新见解

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摘要

The ever-increasing capacity of computing resources has extended ribosome calculations from the study of small-scale fluctuations to large-scale barriercrossing processes. As the field of computational/theoretical biophysics shifts focus to large-scale conformational transitions, there is a growing need for a systematic framework to interpret and analyze ribosome dynamics. To this end, energy landscape principles, largely developed for the study of biomolecular folding, have proven to be invaluable. These tools not only provide a foundation for describing simulations but can be used to reconcile experimental results, as well. In this review, I will discuss recent efforts to employ computational methods to reveal the characteristics of the ribosome's landscape and how these studies can help guide a new generation of experiments that more closely probe the underlying energetics. As a result of these investigations, general principles about ribosome function are beginning to emerge, including that: (1) smallscale fluctuations are the result of structure, rather than detailed energetics, (2) molecular flexibility leads to entropically favored rearrangements, and (3) tRNA dynamics may be accurately described as diffusive movement across an energy landscape.
机译:计算资源的不断增长将核糖体的计算从小规模波动的研究扩展到了大规模的障碍穿越过程。随着计算/理论生物物理学领域的注意力转移到大规模构象转变,对解释和分析核糖体动力学的系统框架的需求日益增长。为此,事实证明,主要用于研究生物分子折叠的能量分布原理是无价的。这些工具不仅为描述仿真提供了基础,而且还可以用于调和实验结果。在这篇综述中,我将讨论最近采用计算方法揭示核糖体景观特征的努力,以及这些研究如何帮助指导新一代实验,从而更紧密地探究潜在的能量学。这些研究的结果是,关于核糖体功能的一般原理开始出现,包括:(1)小范围的波动是结构的结果,而不是详细的能量学,(2)分子的柔性导致了熵有利的重排,以及(3) )tRNA动力学可以准确地描述为在能量分布中的扩散运动。

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