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首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >Testing protein-folding simulations by experiment: B domain of protein A
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Testing protein-folding simulations by experiment: B domain of protein A

机译：通过实验测试蛋白质折叠模拟：蛋白质A的B结构域

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摘要

We have assessed the published predictions of the pathway of folding of the B domain of protein A, the pathway most studied by computer simulation. We analyzed the transition state for folding of the three-helix bundle protein, by using experimental 4) values on some 70 suitable mutants. Surprisingly, the third helix, which has the most stable a-helical structure as a peptide fragment, is poorly formed in the transition state, especially at its C terminus. The protein folds around a nearly fully formed central helix, which is stabilized by extensive hydrophobic side chain interactions. The turn connecting the poorly structured first helix to the central helix is unstructured, but the turn connecting the central helix to the third is in the process of being formed as the N-terminal region of the third helix begins to coalesce. The transition state is inconsistent with a classical framework mechanism and is closer to nucleation-condensation. None of the published atomistic simulations are fully consistent with the experimental picture although many capture important features. There is a continuing need for combining simulation with experiment to describe folding pathways, and of continued testing to improve predictive methods.
机译：我们评估了已发表的蛋白质A B结构域折叠途径的预测，这是计算机模拟研究最多的途径。通过在约70个合适的突变体上使用实验4）值，我们分析了三螺旋束蛋白折叠的过渡状态。出乎意料的是，具有最稳定的α-螺旋结构作为肽片段的第三螺旋在过渡态，特别是在其C末端，形成得很差。蛋白质在几乎完全形成的中心螺旋周围折叠，该中心螺旋通过广泛的疏水性侧链相互作用而稳定。将结构不良的第一个螺旋连接到中心螺旋的转弯是非结构化的，但是当第三个螺旋的N端区域开始合并时，正在形成将中心螺旋连接到第三个螺旋的转弯。过渡态与经典的骨架机制不一致，并且更接近成核-凝聚。尽管许多捕捉到的重要特征，但已发表的原子模拟都没有与实验图片完全一致。持续需要将模拟与实验相结合以描述折叠路径，并需要持续进行测试以改善预测方法。

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