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Role ofBackbone Dipole Interactions in the Formationof Secondary and Supersecondary Structures of Proteins

机译：的角色地层中的骨干偶极相互作用蛋白质的二级和超二级结构

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摘要

We present a generic solvated coarse-grained protein model that can be used to characterize the driving forces behind protein folding. Each amino acid is coarse-grained with two beads, a backbone, and a side chain. Although the backbone beads are modeled as polar entities, side chains are hydrophobic, polar, or charged, thus allowing the exploration of how sequence patterning determines a protein fold. The change in orientation of the atoms of the coarse-grained unit is captured by the addition of two oppositely charged dummy particles inside the backbone coarse-grained bead. These two dummy charges represent a dipole that can fluctuate, thus introducing structural polarization into the coarse-grained model. Realistic α/β content is achieved de novo without any biases in the force field toward a particular secondary structure. The dipoles created by the dummy particles interact with each other and drive the protein models to fold into unique structures depending on the amino acid patterning and presence of capping residues. We have also characterizedthe role of dipole–dipole and dipole–charge interactionsin shaping the secondary and supersecondary structure of proteins.Formation of helix bundles and β-strands are also discussed.
机译：我们提出了一种通用的溶剂化粗粒蛋白质模型，可用于表征蛋白质折叠背后的驱动力。每个氨基酸都带有两个小珠，一个主链和一个侧链。尽管将主链珠建模为极性实体，但侧链是疏水的，极性的或带电荷的，因此可以探索序列模式如何确定蛋白质折叠。粗粒单元原子取向的变化是通过在骨架粗粒珠粒内添加两个带相反电荷的虚拟粒子来捕获的。这两个虚拟电荷代表可以波动的偶极子，从而将结构极化引入到粗粒度模型中。从头获得了实际的α/β含量，而力场中没有偏向特定二级结构的情况。虚拟粒子产生的偶极子相互影响，并根据氨基酸图谱和加帽残基的存在，驱动蛋白质模型折叠成独特的结构。我们还表征了偶极-偶极和偶极-电荷相互作用的作用在塑造蛋白质的二级和超二级结构方面。还讨论了螺旋束和β链的形成。

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