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首页> 外文期刊>Journal of Molecular Biology >Essential dynamics of reversible peptide folding: memory-free conformational dynamics governed by internal hydrogen bonds.
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Essential dynamics of reversible peptide folding: memory-free conformational dynamics governed by internal hydrogen bonds.

机译：可逆肽折叠的基本动力学：由内部氢键控制的无记忆构象动力学。

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摘要

A principal component analysis has been applied on equilibrium simulations of a beta-heptapeptide that shows reversible folding in a methanol solution. The analysis shows that the configurational space contains only three dense sub-states. These states of relatively low free energy correspond to the "native" left-handed helix, a partly helical intermediate, and a hairpin-like structure. The collection of unfolded conformations form a relatively diffuse cloud with little substructure. Internal hydrogen-bonding energies were found to correlate well with the degree of folding. The native helical structure folds from the N terminus; the transition from the major folding intermediate to the native helical structure involves the formation of the two most C-terminal backbone hydrogen bonds. A four-state Markov model was found to describe transition frequencies between the conformational states within error limits, indicating that memory-effects are negligible beyond the nanosecond time-scale. The dominant native state fluctuations were found to be very similar to unfolding motions, suggesting that unfolding pathways can be inferred from fluctuations in the native state. The low-dimensional essential subspace, describing 69% of the collective atomic fluctuations, was found to converge at time-scales of the order of one nanosecond at all temperatures investigated, whereas folding/unfolding takes place at significantly longer time-scales, even above the melting temperature.
机译：主成分分析已应用于显示在甲醇溶液中可逆折叠的β-七肽平衡模拟中。分析表明，配置空间仅包含三个密集子状态。自由能相对较低的这些状态对应于“天然”左手螺旋，部分螺旋的中间体和发夹状结构。展开的构象的集合形成了具有较少子结构的相对分散的云。发现内部氢键能与折叠程度很好地相关。天然的螺旋结构从N末端折叠。从主要折叠中间体到天然螺旋结构的转变涉及两个最C端主链氢键的形成。发现四态马尔可夫模型描述了误差极限内构象状态之间的跃迁频率，表明在纳秒级的时间范围内，记忆效应可忽略不计。发现主要的原始状态波动与展开运动非常相似，这表明可以从原始状态的波动推断出展开途径。发现低维基本子空间（描述了总原子波动的69％）在所有研究温度下都以大约1纳秒的时间尺度收敛，而折叠/展开发生在更长的时间尺度上，甚至更高。熔化温度。

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