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At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately 105 times per second. These two chair conformers are in equilibrium. The rapid ring flipping results in the interconversion of the axial proton to an equatorial proton and an equatorial to the axial proton. Such interconversions are too rapid and cannot be detected on the NMR timescale. Hence, the NMR spectrometer cannot distinguish between the...
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Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
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In an organic molecule, free rotation about the carbon-carbon single bond results in energetically different conformers of the molecule. Due to this rotation, called the internal rotation, ethane has two major conformations — staggered and eclipsed.
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Adolf von Baeyer attempted to explain the instabilities of small and large cycloalkane rings using the concept of angle strain — the strain caused by the deviation of bond angles from the ideal 109.5° tetrahedral value for sp3  hybridized carbons. However, while cyclopropane and cyclobutane are strained, as expected from their highly compressed bond angles, cyclopentane is more strained than predicted, and cyclohexane is virtually strain-free. Hence, Baeyer’s theory that...
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AFsample2预测了多重构造,并与AlphaFold2进行组合.

Yogesh Kalakoti1, Björn Wallner2

  • 1Division of Bioinformatics, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden.

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概括
此摘要是机器生成的。

AFsample2通过产生多样化的结构状态来增强蛋白质结构预测,帮助药物开发和理解生物过程. 这种方法提高了多个蛋白质状态的准确性,并揭示了潜在的中间形状.

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科学领域:

  • 结构生物学是结构生物学.
  • 计算生物学是一种计算生物学.
  • 生物物理学的生物物理.

背景情况:

  • 了解蛋白质动力学和结构灵活性对于生物过程和疾病机制至关重要.
  • 准确预测蛋白质结构对于药物开发至关重要.
  • 像AlphaFold2 (AF2) 这样的现有方法在捕获多种不同的形状状态方面存在局限性.

研究的目的:

  • 介绍AFsample2,一种新的方法来增强AlphaFold2的结构预测.
  • 为了改善替代和中间蛋白质状态的预测.
  • 增加AF2.2生成的蛋白质模型中的结构多样性.

主要方法:

  • AFsample2使用随机多重序列对齐 (MSA) 列掩盖来减少共同进化的信号.
  • 这种掩盖使AF2.2的结构预测变得多样化.
  • 该方法在OC23数据集和膜蛋白载体上进行了评估.

主要成果:

  • AFsample2成功预测了各种蛋白质的替代状态,改善了模型质量.
  • 在实验终点状态中观察到显著的TM得分改善 (高达50%).
  • 与标准AF2相比,中间形状多样性增加了70%,一些预测状态与已知的同类相匹配.

结论:

  • AFsample2有效地产生高质量,多样化的形状组合,包括潜在的中间状态.
  • 该方法为具有多个功能状态的蛋白质提供了有价值的结构见解.
  • AFsample2有助于理解蛋白质动态和构成状态之间的潜在途径,这与药物发现有关.