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开发一个系统的和可扩展的力量场,以化物 (STEPs)

Bradley S Harris¹, Karteek K Bejagam¹, Marcel D Baer¹

¹Physical Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States.

The journal of physical chemistry. B

|July 18, 2023

概括

研究人员开发了一个新的计算力场,用于类 (N替代甘氨酸),提高了预测这些仿生聚合物结构的准确性,用于先进的材料设计.

科学领域:

生物模拟聚合物生物模拟聚合物
计算化学计算化学
材料科学材料科学材料科学

背景情况:

化物比聚化物提供了更高的稳定性,但对计算结构预测提出了挑战.
现有的蛋白质计算模型并不直接适用于peptoids.
开发类特异力场的分散努力阻碍了进步.

研究的目的:

开发和验证一个全面的peptoid特定的力场.
为了提高基于peptoid的材料的计算建模的准确性.
为了方便peptoid序列的 de novo设计和结构预测.

主要方法:

使用GAFF2作为基础开发了一种特定于peptoid的力场,并对70个侧链进行了参数化.
使用DFT优化对Ramachandran类图表验证了力场.
将力场产生的潜力和自由能量表面与DFT结果进行比较.
评估了螺旋残留的实验 cis/trans 均衡值的重现.

主要成果:

创建了一个经过验证的peptoid特定力场,具有70个参数化的侧链.
该力场准确地复制了潜在和自由能量表面.
对所有残留物估计了平衡 cis/trans 分布,确定了对特定状态的倾向.

结论:

开发的力场显著推进了对类动物的计算结构预测.
这项工作为更强大的基于peptoid的材料设计提供了基础.
精确的力场对于实现类聚合物的潜力至关重要.

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