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A challenge for peptide coarse graining: Transferability of fragment-based models

机译：肽粗粒化面临的挑战：基于片段的模型的可移植性

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摘要

Peptides are highly promising building blocks for design and development of novel materials with potential application areas ranging from drug design to biotechnology. The necessity to understand the structural and thermodynamic properties of these complex materials has led to a dramatic increase in the development of computational techniques geared specifically towards peptide-based systems. Both all-atom (AA) and coarse-grained (CG) simulations of such materials have become extremely important, where the latter is an indispensable tool for reaching the time and length scales relevant to the experiments. Here, we review different approaches and discuss the challenges in the development of CG models for peptides. In particular, we concentrate on the transferability of fragment-based CG models. We analyze the transferability of a solvent-free CG model developed to model hydrophobic phenylalanine dipeptides (FF) in water. Here, we employ the same CG strategy-with non-bonded potentials based on peptide fragments-to two other hydrophobic dipeptides, valine-phenylalanine (VF) and isoleucine-phenylalanine (IF). In line with the previously developed model, the dipeptides are described by seven beads and the potentials developed for FF (bonded and non-bonded) are directly applied to describe the phenylalanine and backbone atoms, while new potentials are developed to account for the valine and isoleucine sidechains. By comparing AA and CG intra and intermolecular samplings, we show the ability of the CG model to reproduce the conformational behavior and thermodynamic association properties of the corresponding atomistic systems.
机译：肽是用于新型材料设计和开发的高度有前途的基石，其潜在应用领域从药物设计到生物技术。了解这些复杂材料的结构和热力学性质的必要性，导致专门针对基于肽的系统的计算技术的发展急剧增加。这种材料的全原子（AA）和粗粒（CG）模拟都变得非常重要，后者是达到与实验相关的时间和长度尺度必不可少的工具。在这里，我们回顾了不同的方法，并讨论了肽CG模型开发中的挑战。特别是，我们专注于基于片段的CG模型的可传递性。我们分析了无溶剂的CG模型的可转移性，该模型是为在水中建模疏水性苯丙氨酸二肽（FF）而设计的。在这里，我们采用相同的CG策略-基于肽片段的非键合电位-与另外两个疏水二肽，缬氨酸-苯丙氨酸（VF）和异亮氨酸-苯丙氨酸（IF）。与先前开发的模型一致，二肽由七个珠子描述，为FF（键合和非键合）开发的电势直接应用于描述苯丙氨酸和骨架原子，而开发了新的电势以解释缬氨酸和异亮氨酸侧链。通过比较AA和CG的分子内和分子间采样，我们证明了CG模型能够重现相应原子系统的构象行为和热力学缔合特性。

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