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首页> 外文期刊>The European physical journal, E. Soft matter >Thermodynamic stability of polypeptides folding within modeled ribosomal exit tunnel: A density functional study
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Thermodynamic stability of polypeptides folding within modeled ribosomal exit tunnel: A density functional study

机译：在模拟核糖体出口通道内折叠的多肽的热力学稳定性：密度泛函研究

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The mechanism of polypeptide folding, especially for the formation of tertiary structures, within the ribosomal exit tunnel, remains one of the most important unsolved problems in biophysical chemistry and molecular biology. In this work, we use a density functional theory (DFT) to explore the polypeptide folding within a modified nanopore, which mimics the confined environment of ribosomal exit tunnel. Results indicate that too long polypeptides (N > 100 cannot fold into a helix state within the nanopore, and the helix polypeptides favor folding into a negative coiled coil rather than a positive one, because the negative coiled coil has a lower grand potential than the positive one, and the polypeptide folding into the negative coiled coil therefore needs less driving force than the positive one. To fold into the positive coiled coil, the helix polypeptides must have a small minor radius or a short chain length, which provides helpful insights into the design of nanodevices for manipulating the positive coiled coil. In the presence of attractive interaction, helices need more driving force to fold into coiled coil. Importantly, we have also proposed a scaling relation to understand the folding behavior. The scaling relation gives a good estimate for the computational results, and provides a reasonable explanation for the folding behavior. In summary, it is expected that the proposed DFT approach and the scaling relation provide alternative means for the investigation of polypeptide folding in confined environment, and these impressive results could give useful insights into nascent polypeptide folding.
机译：多肽折叠的机制，特别是在核糖体出口隧道内形成三级结构的机制，仍然是生物物理化学和分子生物学中最重要的未解决问题之一。在这项工作中，我们使用密度泛函理论（DFT）探索修饰纳米孔内的多肽折叠，该孔模拟了核糖体出口隧道的封闭环境。结果表明，太长的多肽（N> 100不能折叠成纳米孔内的螺旋状，并且螺旋状多肽更倾向于折叠成负性卷曲螺旋而不是正性卷曲螺旋，因为负性卷曲螺旋的整体电位低于正性螺旋卷曲因此，折叠成负卷曲螺旋的多肽所需的驱动力要比正卷曲螺旋所需的驱动力小。要折叠成正卷曲螺旋，螺旋多肽必须具有较小的小半径或较短的链长，这有助于深入了解操纵正性线圈的纳米器件的设计在存在吸引相互作用的情况下，螺旋需要更多的驱动力才能折叠成线圈，重要的是，我们还提出了一个比例关系来理解折叠行为，该比例关系给出了很好的估计对于计算结果，并为折叠行为提供了合理的解释。 DFT方法和比例关系为在受限环境中研究多肽折叠提供了另一种方法，这些令人印象深刻的结果可以为新生的多肽折叠提供有用的见识。

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