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首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >Calculated vibrational properties of pigments in protein binding sites
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Calculated vibrational properties of pigments in protein binding sites

机译：色素在蛋白质结合位点的振动特性计算

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FTIR difference spectroscopy is widely used to probe molecular bonding interactions of protein-bound electron transfer cofactors. The technique is particularly attractive because it provides information on both neutral and radical cofactor states. Such dual information is not easily obtainable using other techniques. Although FTIR difference spectroscopy has been used to study cofactors in biological protein complexes, in nearly all cases interpretation of the spectra has been purely qualitative. Virtually no computational work has been undertaken in an attempt to model the spectra. To address this problem we have developed the use of ONIOM (our own N-layered integrated molecular Orbital + Molecular mechanics package) (quantum mechanicakmolecular mechanics) methods to calculate FTIR difference spectra associated with protein-bound cofactors. As a specific example showing the utility of the approach we have calculated isotope edited FTIR difference spectra associated with unlabeled and labeled ubiquinones in the Q_A binding site in Rhodobacter sphaeroides photosynthetic reaction centers. The calculated spectra are in remarkable agreement with experiment. Such agreement cannot be obtained by considering ubiquinone molecules in the gas phase or in solution. A calculation including the protein environment is required. The ONIOM calculated spectra agree well with experiment but indicate a very different interpretation of the experimental data compared to that proposed previously. In particular the calculations do not predict that one of the carbonyl groups of Q_A is very strongly hydrogen bonded. We show that a computational-based interpretation of FTIR difference spectra associated with protein-bound cofactors is now possible. This approach will be applicable to FTIR studies of many cofactor-containing proteins.
机译：FTIR差异光谱学被广泛用于探测结合蛋白质的电子转移辅助因子的分子键相互作用。该技术特别吸引人，因为它提供了中性和自由基辅因子状态的信息。使用其他技术不容易获得这种双重信息。尽管已使用FTIR差异光谱法研究生物蛋白质复合物中的辅因子，但几乎在所有情况下，对光谱的解释都是纯定性的。几乎没有进行任何计算工作来对光谱建模。为了解决这个问题，我们开发了使用ONIOM（我们自己的N层集成分子轨道+分子力学软件包）（量子力学-分子力学）方法来计算与蛋白质结合的辅因子相关的FTIR差异光谱的方法。作为显示该方法实用性的一个特定示例，我们已经计算了与球形红细菌光合反应中心Q_A结合位点中未标记和标记的泛醌相关的同位素编辑的FTIR差异光谱。计算的光谱与实验明显吻合。通过考虑气相或溶液中的泛醌分子无法获得这种一致性。需要进行包括蛋白质环境在内的计算。 ONIOM计算得出的光谱与实验吻合得很好，但与先前提出的结果相比，表明实验数据的解释有很大不同。特别地，该计算不能预测Q_A的羰基之一非常牢固地氢键合。我们表明与蛋白质结合的辅因子相关的FTIR差异光谱的基于计算的解释现在是可能的。该方法将适用于许多含有辅因子的蛋白质的FTIR研究。

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