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首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >Energetics of short hydrogen bonds in photoactive yellow protein
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Energetics of short hydrogen bonds in photoactive yellow protein

机译：光敏黄色蛋白中短氢键的能量学

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摘要

Recent neutron diffraction studies of photoactive yellow protein (PYP) proposed that the H bond between protonated Glu46 and the chromophore [ionized p-coumaric acid (pCA)] was a low-barrier H bond (LBHB). Using the atomic coordinates of the high-resolution crystal structure, we analyzed the energetics of the short H bond by two independent methods: electrostatic pK_a calculations and a quantum mechanical/molecular mechanical (QM/MM) approach. (Ⅰ) In the QM/MM optimized geometry, we reproduced the two short H-bond distances of the crystal structure: Tyr42-pCA (2.50 A) and Glu46-pCA (2.57 A). However, the H atoms obviously belonged to the Tyr or Glu moieties, and were not near the midpoint of the donor and acceptor atoms, (Ⅱ) The potential-energy curves of the two H bonds resembled those of standard asymmetric double-well potentials, which differ from those of LBHB. (Ⅲ) The calculated pK_a values for Glu46 and pCA were 8.6 and 5.4, respectively. The pK_a difference was unlikely to satisfy the prerequisite for LBHB. (Ⅳ) The LBHB in PYP was originally proposed to stabilize the ionized pCA because deprotonated Arg52 cannot stabilize it. However, the calculated pK_a of Arg52 and QM/MM optimized geometry suggested that Arg52 was protonated on the protein surface. The short H bond between Glu46 and ionized pCA in the PYP ground state could be simply explained by electrostatic stabilization without invoking LBHB.
机译：最近对光敏黄色蛋白（PYP）的中子衍射研究表明，质子化Glu46和发色团之间的H键[电离的对香豆酸（pCA）]是低势垒的H键（LBHB）。使用高分辨率晶体结构的原子坐标，我们通过两种独立的方法分析了短氢键的能量：静电pK_a计算和量子力学/分子力学（QM / MM）方法。 （Ⅰ）在QM / MM优化的几何结构中，我们复制了晶体结构的两个短H键距离：Tyr42-pCA（2.50 A）和Glu46-pCA（2.57 A）。然而，H原子显然属于Tyr或Glu部分，并且不位于供体和受体原子的中点附近。（Ⅱ）两个H键的势能曲线类似于标准的不对称双阱势能，与LBHB不同。 （Ⅲ）Glu46和pCA的pK_a值分别为8.6和5.4。 pK_a差异不可能满足LBHB的先决条件。 （Ⅳ）最初提出在PYP中使用LBHB来稳定离子化的pCA，因为去质子化的Arg52无法使其稳定。但是，计算得出的Arg52的pK_a和QM / MM优化的几何结构表明Arg52在蛋白质表面质子化。在PYP基态下，Glu46与离子化pCA之间的短H键可以通过静电稳定简单地解释，而无需调用LBHB。

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  • 作者

    Keisuke Saito; Hiroshi Ishikita;

  • 作者单位

    Career-Path Promotion Unit for Young Life Scientists, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan;

    Career-Path Promotion Unit for Young Life Scientists, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan,Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan;

  • 收录信息 美国《科学引文索引》(SCI);美国《生物学医学文摘》(MEDLINE);美国《化学文摘》(CA);
  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类
  • 关键词

    low-barrier hydrogen bond; NMR; proton transfer; photoreceptor;

    机译：低势垒氢键NMR;质子转移感光体;

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