Molecular dynamics simulation of Pf1 coat protein.
Molecular dynamics simulation of Pf1 coat protein.
复制标题
Pf1外壳蛋白的分子动力学模拟。
DOI：
10.1016/s0006-3495(93)81426-7
复制
发表时间：
1993
影响因子：
3.4
通讯作者：
Opella,SJ
中科院分区：
文献类型：
--
作者：
Tobias,DJ;Klein,ML;Opella,SJ
Pf 1外壳蛋白的分子动力学模拟的结果进行了描述和比较实验NMR数据的膜结合和结构形式的这种病毒外壳蛋白。根据一个简单的协议进行的46个残基的外壳蛋白和相关的模型序列的分子动力学模拟。模拟开始与多肽在一个完全统一的α螺旋构象在介电连续体（ε = 2）和运动的各个残基的后续作为时间的函数，通过监测酰胺NH键矢量的角波动。Pf 1外壳蛋白的模拟能够鉴定在蛋白质的膜结合形式的实验NMR研究中发现的相同的移动的和结构化的片段（Shon，K. J.，Y.金湖，澳-地A. Colnago和S. J·奥佩拉1991.科学（Wash）DC）。252：1303-1305）。值得注意的是，除了移动的氨基和羧基末端区域外，还发现了一个移动的内环，该内环连接蛋白质中的刚性疏水螺旋和两亲螺旋。NMR实验表明，该移动的环存在于病毒和膜结合形式的蛋白质中，并且它在病毒组装中起作用（Nambudripad，R.，W.斯塔克，S。J. Opella和L.马科夫斯基1991.科学（Wash）DC）252：1305-1308）。几个丙氨酸为基础的46个残基的多肽与Pf 1外壳蛋白序列中存在的一些带电残基的模拟结果表明，天冬氨酸14和天冬氨酸18侧链和肽骨架之间的相互作用是负责形成的移动的环。（250字处删节）
The results of molecular dynamics simulations of Pf1 coat protein are described and compared to experimental NMR data on both the membrane bound and structural forms of this viral coat protein. Molecular dynamics simulations of the 46 residue coat protein and related model sequences were performed according to a simple protocol. The simulations were initiated with the polypeptides in a completely uniform alpha helical conformation in a dielectric continuum (epsilon = 2) and the motions of individual residues were followed as a function of time by monitoring the angular fluctuations of amide NH bond vectors. The simulations of Pf1 coat protein were able to identify the same mobile and structured segments found in experimental NMR studies of the membrane bound form of the protein (Shon, K.-J., Y. Kim, L. A. Colnago, and S. J. Opella. 1991. Science (Wash. DC). 252:1303–1305). Significantly, in addition to mobile amino and carboxyl terminal regions, a mobile internal loop was found that connects the rigid hydrophobic and amphipathic helices in the protein. NMR experiments show that this mobile loop is present in both the viral and membrane bound forms of the protein and that it plays a role in viral assembly (Nambudripad, R., W. Stark, S. J. Opella, and L. Makowski. 1991. Science (Wash. DC) 252:1305–1308). The results of simulations of several alanine based 46 residue polypeptides with some of the charged residues present in the Pf1 coat protein sequence suggest that interactions between the Asp 14 and Asp 18 sidechains and the peptide backbone are responsible for the formation of the mobile loop.(ABSTRACT TRUNCATED AT 250 WORDS)