Free-energy cost for translocon-assisted insertion of membrane proteins
Free-energy cost for translocon-assisted insertion of membrane proteins
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DOI：
10.1073/pnas.1012758108
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发表时间：
2011-03-01
影响因子：
11.1
通讯作者：
Schulten, Klaus
中科院分区：
文献类型：
--
作者：
Gumbart, James;Chipot, Christophe;Schulten, Klaus
新生膜蛋白通常通过蛋白质传导通道（Sec 易位子）以顺序方式插入膜中。尽管已经提出了通道和膜环境之间的热力学分配，但该过程如何发生仍不清楚。然而，基于实验和模拟的各种氨基酸插入自由能的尺度存在差异，前者似乎比后者处于更窄的范围内。例如，根据分子动力学模拟，精氨酸的膜插入需要 14-17 kcal/mol，但根据实验只需 2-3 kcal/mol。我们建议通过假设两阶段插入过程来解决这一分歧，其中第一步，插入易位子，由蛋白质合成提供能量，因此自由能成本实际上为零；第二步，插入膜中，调用易位子作为完全水合位置和完全插入位置之间的中介。使用自由能扰动计算，已经确定了背景多亮氨酸螺旋携带的精氨酸和亮氨酸氨基酸从易位子到膜的有效转移自由能。事实上，与从水中直接插入相比，精氨酸的插入损失以及从易位子到膜的亮氨酸的插入增益被发现显着减少，导致与基于实验的规模中观察到的相同的压缩。
Nascent membrane proteins typically insert in a sequential fashion into the membrane via a protein-conducting channel, the Sec translocon. How this process occurs is still unclear, although a thermodynamic partitioning between the channel and the membrane environment has been proposed. Experiment-and simulation-based scales for the insertion free energy of various amino acids are, however, at variance, the former appearing to lie in a narrower range than the latter. Membrane insertion of arginine, for instance, requires 14-17 kcal/mol according to molecular dynamics simulations, but only 2-3 kcal/mol according to experiment. We suggest that this disagreement is resolved by assuming a two-stage insertion process wherein the first step, the insertion into the translocon, is energized by protein synthesis and, therefore, has an effectively zero free-energy cost; the second step, the insertion into the membrane, invokes the translocon as an intermediary between the fully hydrated and the fully inserted locations. Using free-energy perturbation calculations, the effective transfer free energies from the translocon to the membrane have been determined for both arginine and leucine amino acids carried by a background polyleucine helix. Indeed, the insertion penalty for arginine as well as the insertion gain for leucine from the translocon to the membrane is found to be significantly reduced compared to direct insertion from water, resulting in the same compression as observed in the experiment-based scale.