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Validation of protein structural models using THz spectroscopy: a promising approach to solve three-dimensional structures

机译：使用太赫兹光谱法验证蛋白质结构模型：一种解决三维结构的有前途的方法

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摘要

Terahertz (THz) spectroscopy is a promising technique for the study of protein structure and internal flexibility. Here, we used THz spectroscopy and molecular modeling for bovine serum albumin (BSA) structure investigation. BSA molecule was built using homol-ogy modeling methods and 30 different more relaxed models were obtained by molecular dynamics simulations of the hydrated protein. As the experimental and simulated THz spectra are linear, we compared them by comparing the slopes of the lines that fit them. Six BSA structures had slope values in the range given by the slope of the experimental spectrum ±0.2 and a total of sixteen BSA structures had slope values in the 0.6 interval near the experimental slope value. BSA average structures were calculated over the six and the sixteen identified BSA molecules. Based on the similarity with the crystal structure of BSA, we validated the average structure calculated over the sixteen BSA conformations. The comparison with the crystal structure showed that the structure validated using THz spectroscopy is a coarse model of BSA, as its root-mean-square deviation relative to the crystal structure is 1.9 A. The regions from our model that present the highest deviation from the crystal structure are exterior loops. The results presented here show that using THz spectroscopy and molecular modeling is a promising approach to determine the structure of proteins.
机译：太赫兹（THz）光谱技术是研究蛋白质结构和内部柔韧性的有前途的技术。在这里，我们使用THz光谱和分子建模进行牛血清白蛋白（BSA）结构研究。使用同源建模方法构建BSA分子，并通过水合蛋白的分子动力学模拟获得30个不同的更宽松的模型。由于实验和模拟的太赫兹光谱是线性的，因此我们通过比较适合它们的直线的斜率来比较它们。 6个BSA结构的斜率值在实验光谱的斜率±0.2的范围内，总共16个BSA结构的斜率值在实验斜率值附近的0.6区间内。计算了六个和十六个已识别的BSA分子的BSA平均结构。基于与BSA晶体结构的相似性，我们验证了16种BSA构象的平均结构。与晶体结构的比较表明，使用THz光谱法验证的结构是BSA的粗略模型，因为其相对于晶体结构的均方根偏差为1.9A。晶体结构是外部回路。此处显示的结果表明，使用太赫兹光谱和分子建模是确定蛋白质结构的一种有前途的方法。

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  • 来源
    《Optical and quantum electronics》 |2014年第4期|505-514|共10页
  • 作者

    Maria Mernea; Octavian Calborean; Oana Grigore; Traian Dascalu; Dan Florin Mihailescu;

  • 作者单位

    Faculty of Biology, University of Bucharest, Splaiul Independentei, No 91-95, 050095 Bucharest, Romania;

    Faculty of Biology, University of Bucharest, Splaiul Independentei, No 91-95, 050095 Bucharest, Romania;

    Laboratory of Solid-State Quantum Electronics, National Institute for Laser, Plasma and Radiation Physics, PO Box MG-36 , 077125 Magurele, Romania;

    Laboratory of Solid-State Quantum Electronics, National Institute for Laser, Plasma and Radiation Physics, PO Box MG-36 , 077125 Magurele, Romania;

    Faculty of Biology, University of Bucharest, Splaiul Independentei, No 91-95, 050095 Bucharest, Romania;

  • 收录信息 美国《科学引文索引》(SCI);美国《工程索引》(EI);
  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类
  • 关键词

    THz spectroscopy; Proteins; Molecular modeling; Structural models validation; Three-dimensional structure;

    机译：太赫兹光谱蛋白质;分子建模;结构模型验证;三维结构;

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