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首页> 外文期刊>The Journal of Chemical Physics >Folding simulations of gramicidin A into the β-helix conformations:Simulated annealing molecular dynamics study
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Folding simulations of gramicidin A into the β-helix conformations:Simulated annealing molecular dynamics study

机译：将短杆菌肽A折叠成β-螺旋构象的模拟：退火分子动力学研究

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摘要

Gramicidin A is a linear hydrophobic 15-residue peptide which consists of alternating D- and L-amino acids and forms a unique tertiary structure, called the β~(6.3)-helix, to act as a cation-selective ion channel in the natural conditions. In order to investigate the intrinsic ability of the gramicidin A monomer to form secondary structures, we performed the folding simulation of gramicidin A using a simulated annealing molecular dynamics (MD) method in vacuum mimicking the low-dielectric, homogeneous membrane environment. The initial conformation was a fully extended one. From the 200 different MD runs, we obtained a right-handed β~(4.4)-helix as the lowest-potential-energy structure, and left-handed β~(4.4)-helix, right-handed and left-handed β~(6.3)-helix as local-minimum energy states. These results are in accord with those of the experiments of gramicidin A in homogeneous organic solvent. Our simulations showed a slight right-hand sense in the lower-energy conformations and a quite β-sheet-forming tendency throughout almost the entire sequence. In order to examine the stability of the obtained right-handed β~(6.3)-helix and β~(4.4)-helix structures in more realistic membrane environment, we have also performed all-atom MD simulations in explicit water, ion, and lipid molecules, starting from these β-helix structures. The results suggested that β~(6.3)-helix is more stable than β~(4.4)-helix in the inhomogeneous, explicit membrane environment, where the pore water and the hydrogen bonds between Trp side-chains and lipid-head groups have a role to further stabilize the ~(6.3)-helix conformation.
机译：Gramicidin A是一种线性的15个残基的疏水性肽，由D和L氨基酸交替组成，形成一个独特的三级结构，称为β〜（6.3）-螺旋，可在自然界中充当阳离子选择性离子通道条件。为了研究短杆菌肽A单体形成二级结构的内在能力，我们在真空模拟低介电质均匀膜环境中，使用模拟退火分子动力学（MD）方法对短杆菌肽A进行了折叠模拟。最初的构象是完全延伸的构象。从200个不同的MD行程中，我们获得了右旋β〜（4.4）-螺旋作为最低势能结构，左旋β〜（4.4）-螺旋，右旋和左旋β〜 （6.3）-螺旋是局部最小能量状态。这些结果与在均质有机溶剂中的大蒜素A的实验结果一致。我们的模拟结果显示，低能构象略有右手感，几乎在整个序列中都有相当大的β-折叠形成趋势。为了检验在更真实的膜环境中获得的右旋β〜（6.3）-螺旋和β〜（4.4）-螺旋结构的稳定性，我们还对水，离子和水进行了全原子MD模拟。从这些β螺旋结构开始的脂质分子。结果表明，在非均质的，明显的膜环境中，β〜（6.3）-螺旋比β〜（4.4）-螺旋更稳定，在膜环境中，Trp侧链与脂质头基团之间的孔隙水和氢键具有进一步稳定〜（6.3）-螺旋构象的作用。

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