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A Benchmarking Study of Peptide–Biomineral Interactions

机译：肽生物霉素相互作用的基准研究

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摘要

A long-standing goal in the field of biomineralization has been to achieve a molecular-level mechanistic understanding of how proteins participate in the nucleation and growth of inorganic crystals (both in vitro and in vivo ). Computational methods offer an approach to explore these interactions and propose mechanisms at the atomic scale; however, to have confidence in the predictions of a computational method, the method must first be validated against a benchmark experimental data set of protein–mineral interactions. Relatively little work has been done to test the ability of computation to reproduce experimental results on mineral systems with biologically relevant additives present. The goal of this work is to develop a standard and varied benchmark to test whether a computational method is able to match experimental results at the length and time scales of biomineral–peptide interactions. We compare the results of the RosettaSurface algorithm to an experimental benchmark of kinetic and thermodynamic measurements on peptide–biomineral interactions taken from atomic force microscopy. The RosettaSurface algorithm successfully identifies which mineral face and step edges will bind peptides the strongest; however, the algorithm struggles to predict the correct rank order of binding for multiple peptides to the same face or step edge.
机译：在生物碳化领域的一个长期目标已经实现了对蛋白质如何参与无机晶体的成核（体外和体内）的成核和生长的分子水平机械理解。计算方法提供了一种探索这些互动的方法，并在原子规模提出机制;然而，为了对计算方法的预测有信心，必须首先针对蛋白质 - 矿物相互作用的基准实验数据集进行验证该方法。已经做出了相对较少的工作来测试计算能力，以在存在的生物学相关添加剂的矿物系统上再现实验结果。这项工作的目标是开发一种标准和变化的基准测试，以测试计算方法是否能够在生物霉素 - 肽相互作用的长度和时间尺度匹配实验结果。我们将玫瑰病菌曲线的结果与原子力显微镜显微镜显微镜肽 - 生物敏术相互作用的动力学和热力学测量的实验基准进行比较。玫瑰花苜蓿算法成功地识别哪个矿物面和步进边缘将结合最强的肽;然而，该算法努力预测多肽与相同面或步进边缘结合的正确等级顺序。

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  • 来源
    《Crystal growth & design》 |2018年第2期|共10页
  • 作者

    Michael S. Pacella; Jeffrey J. Gray;

  • 作者单位

    Department of Biomedical Engineering Department of Chemical and Biomolecular Engineering and Program in Molecular Biophysics Johns Hopkins University 3400 North Charles Street Baltimore Maryland 21218 United States;

    Department of Biomedical Engineering Department of Chemical and Biomolecular Engineering and Program in Molecular Biophysics Johns Hopkins University 3400 North Charles Street Baltimore Maryland 21218 United States;

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  • 正文语种 eng
  • 中图分类 晶体学;
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