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Vibrational simulation of the biological systems---normal modes analysis and stochastic vibrational self-consistent field calculation.

机译：生物系统的振动模拟---正常模式分析和随机振动自洽场计算。

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摘要

The present research focuses on the vibrational simulation of the biological systems, including the harmonic-level normal modes analysis and the anharmonic-level vibrational self-consistent field (VSCF) calculation. Normal modes analysis was performed on a large biomolecule---ricin-A-chain (RTA)---in both apo- (no substrate) and holo- (adenosine monophosphate (AMP)-bound) state. It revealed that the shearing motion was shared by both apo- and holo-RTAs, whereas the breathing motion, as well as the upward hinge and the a-G bending characteristic motions, was dampened by substrate binding. We hypothesize that the breathing, a-G bending and upward hinging motions play an important role in substrate binding as these motions facilitate the entry of the substrate and provide space for the substrate realignment that is necessary for the depurination. The VSCF calculations, which were typically restricted to small systems, were performed in the present research on a moderate biomolecule---the VA-class dipeptide nanotubes; to the best of our knowledge, this is the first time condensed-phase VSCF calculation of biomolecules that has been preformed. By comparing the calculated Terahertz (THz) spectra against the experimental spectra, we found that in general the VSCF level calculations deomonstrated significant improvement over the harmonic calculations, which was mostly reflected in the overall blueshifts of the VSCF frequencies from the harmonic values. These blueshifts were accounted for the coupling between two similar sidechain-squeezing modes and the subsequent stiffening of the effective potential. Finally, we developed a stochastic-VSCF methodology to enable the anharmonic and coupling-incorporated vibrational simulation for large biomolecules. This method evaluates the inter-mode couplings and performs the vibrational calculations in a stochastic fashion. During this stochastic process, the insignificantly mode pairs are rapidly found and removed from the system without exhaustively exploring the entire PES, and therefore the computational expense is remarkably saved. A validation test was performed for the stochastic-VSCF method on the VA-class dipeptide nanotubes. It was fond that this method remarkably saved the computational expense while yielding the THz spectra very close to the exhaustive VSCF calculations. The stochastic-VSCF calculation was finally performed on a large biomolecule---bacteriorhodopsin.
机译：本研究的重点是生物系统的振动模拟，包括谐波水平正态分析和非谐波水平振动自洽场（VSCF）计算。正常模式分析是在apo-（无底物）和hlo-（单磷酸腺苷（AMP）结合状态）的大生物分子---蓖麻蛋白-A链（RTA）-上进行的。结果表明，剪切运动由脱辅基和全氟辛烷磺酸共同承担，而呼吸运动，向上铰链和α-G弯曲特征性运动则被底物结合所抑制。我们假设呼吸，α-G弯曲和向上铰接运动在底物粘合中起重要作用，因为这些运动有利于底物进入并为净化所需的底物重新排列提供空间。 VSCF计算通常限于小型系统，是在本研究中对中等生物分子-VA级二肽纳米管进行的；据我们所知，这是首次对生物分子进行浓缩相VSCF计算。通过将计算出的太赫兹（THz）光谱与实验光谱进行比较，我们发现VSCF电平计算总体上显示出与谐波计算相比有显着改善，这主要反映在VSCF频率相对于谐波值的总体蓝移中。这些蓝移解释了两个相似的侧链挤压模式之间的耦合以及随后有效电位的增强。最后，我们开发了一种随机VSCF方法，以实现对大生物分子进行非谐和耦合耦合的振动模拟。此方法评估模式间耦合并以随机方式执行振动计算。在此随机过程中，可以迅速找到无关紧要的模式对并将其从系统中删除，而无需详尽地研究整个PES，因此可以显着节省计算费用。对VA级二肽纳米管的随机VSCF方法进行了验证测试。人们喜欢这种方法可以显着节省计算费用，同时产生的THz频谱非常接近详尽的VSCF计算。最终，对大型生物分子细菌视紫红质进行了随机VSCF计算。

著录项

  • 作者

    Zhang, Hailiang.;

  • 作者单位

    University of Maryland, Baltimore County.;

  • 授予单位 University of Maryland, Baltimore County.;
  • 学科 Chemistry Physical.
  • 学位 Ph.D.
  • 年度 2009
  • 页码 239 p.
  • 总页数 239
  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类
  • 关键词

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