Structural changes in the cytoplasmic domain of phospholamban by phosphorylation at Ser16: a molecular dynamics study.
Structural changes in the cytoplasmic domain of phospholamban by phosphorylation at Ser16: a molecular dynamics study.
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DOI：
10.1021/bi061071z
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发表时间：
2006-09
期刊：
影响因子：
2.9
通讯作者：
Y. Sugita;N. Miyashita;T. Yoda;M. Ikeguchi;C. Toyoshima
中科院分区：
文献类型：
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作者：
Y. Sugita;N. Miyashita;T. Yoda;M. Ikeguchi;C. Toyoshima
磷蛋白是一种52残基整体膜蛋白，可调节心肌肌浆网钙泵的活性。当磷酸蛋白被camp依赖性蛋白激酶磷酸化其Ser16位点时，其抑制作用被解除。为了计算探索磷酸化形式的所有可能构象，从而了解磷酸化的结构效应，复制交换分子动力学（REMD）应用于包括Ser16的细胞质结构域。模拟结果表明：(1)在没有磷酸化的情况下，从Lys3到Ser16的区域具有所有的α -螺旋构象；（ii）当被磷酸化时，α -螺旋在c端部分（从Ser10到Ala15）部分解开，导致较少的延伸构象；（iii） Ser16上的磷酸盐与Arg9、Arg13和/或Arg14形成盐桥；（iv）含有Arg13和Arg14的盐桥使α -螺旋扭曲，导致c端部分解绕。然后，我们将传统的全原子分子动力学模拟应用于磷脂双分子层中的全长磷蛋白。结果与REMD模拟的结果一致，表明磷蛋白的跨膜部分和脂质双分子层本身对细胞质域构象变化的影响很小。涉及Ser16磷酸的盐桥引起的扭曲很容易解释磷酸化减轻磷蛋白的抑制作用，因为它们将大大减少所有螺旋构象的数量，这些构象可能是与钙泵结合所必需的。这也是从激酶中释放磷酸化磷蛋白的机制。
Phospholamban is a 52-residue integral membrane protein that regulates the activity of the sarcoplasmic reticulum calcium pump in cardiac muscle. Its inhibitory action is relieved when phospholamban is phosphorylated at Ser16 by cAMP-dependent protein kinase. To computationally explore all possible conformations of the phosphorylated form, and thereby to understand the structural effects of phosphorylation, replica-exchange molecular dynamics (REMD) was applied to the cytoplasmic domain that includes Ser16. The simulations showed that (i) without phosphorylation, the region from Lys3 to Ser16 takes all alpha-helical conformations; (ii) when phosphorylated, the alpha-helix is partially unwound in the C-terminal part (from Ser10 to Ala15) resulting in less extended conformations; (iii) the phosphate at Ser16 forms salt bridges with Arg9, Arg13, and/or Arg14; and (iv) the salt bridges with Arg13 and Arg14 distort the alpha-helix and induce unwinding of the C-terminal part. We then applied conventional all-atom molecular dynamics simulations to the full-length phospholamban in the phospholipid bilayer. The results were consistent with those obtained with REMD simulations, suggesting that the transmembrane part of phospholamban and the lipid bilayer itself have only minor effects on the conformational changes in the cytoplasmic domain. The distortions caused by the salt bridges involving the phosphate at Ser16 readily explain the relief of the inhibitory effect of phospholamban by phosphorylation, as they will substantially reduce the population of all helical conformations, which are presumably required for the binding to the calcium pump. This will also be the mechanism for releasing the phosphorylated phospholamban from kinase.