Dimer domain swapping versus monomer folding in apo-myoglobin studied by molecular simulations
Dimer domain swapping versus monomer folding in apo-myoglobin studied by molecular simulations
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DOI：
10.1039/c4cp05203j
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发表时间：
2015-01-01
影响因子：
3.3
通讯作者：
Takada, Shoji
中科院分区：
文献类型：
--
作者：
Ono, Koji;Ito, Mashiho;Takada, Shoji
最近的实验表明，在某些条件下，肌红蛋白可以形成结构域交换二聚体。在这里，我们使用一个粗粒度的对称Go模型，对两个载脂蛋白肌红蛋白分子在高密度下进行了一系列的折叠模拟，解决了结构域交换二聚体与折叠到两个单体结构的形成竞争。除了在x射线晶体学中发现的畴交换二聚体外，我们还发现了一些其他形式的畴交换。随着蛋白质密度的增加，结构域交换的概率增加。折叠途径分析表明，单体折叠和结构域交换的分离发生在相对较早的阶段，一条链的螺旋AB和另一条链的螺旋GH之间的链间接触往往导致结构域交换二聚体。这类似于先前提出的细胞色素c的结构域交换机制。
Recent experiments showed that myoglobin can form a domain-swapped dimer under certain conditions. Here, using a coarse-grained symmetrized Go model, we performed a series of folding simulations of two apo-myoglobin molecules restrained at a high density, addressing competition of formation of a domain-swapped dimer with folding to two monomer structures. In addition to the domain-swapped dimer found in X-ray crystallography, we also found some other forms of domain swapping. With the protein density, the probability of domain-swapping increased. Folding pathway analysis clarified that separation between monomer folding and domain-swapping arose at a relatively early stage, where inter-chain contacts between helices AB of one chain and helices GH of another chain tend to result in the domain swapped dimer. This resembles the mechanism of domain swapping suggested previously for cytochrome c.