Yamato T, Niimura N, Go N
Graduate School of Science, Nagoya University, Japan.
Proteins. 1998 Aug 15;32(3):268-75. doi: 10.1002/(sici)1097-0134(19980815)32:3<268::aid-prot2>3.0.co;2-e.
Molecular dynamics simulations were carried out to study what happens in a photoreceptor protein, photoactive yellow protein (PYP), immediately after the vertical transition of the chromophore from the ground to the excited state. A photon absorption simulation was performed to investigate the movement of amino acid residues upon photoexcitation. To calculate the excited state of the chromophore, SCF-CI calculation was carried out with INDO/S Hamiltonian. We observed that some amino acid residues have strong interactions with the chromophore. Most of these amino acid residues are conserved in PYPs from three different species of bacteria. This observation indicates the biological importance of these residues.
进行了分子动力学模拟，以研究光受体蛋白——光活性黄色蛋白（PYP）中，发色团从基态垂直跃迁到激发态后立即发生的情况。进行了光子吸收模拟，以研究光激发时氨基酸残基的运动。为了计算发色团的激发态，使用INDO/S哈密顿量进行了自洽场组态相互作用（SCF-CI）计算。我们观察到一些氨基酸残基与发色团有强烈的相互作用。这些氨基酸残基中的大多数在来自三种不同细菌的PYP中是保守的。这一观察结果表明了这些残基的生物学重要性。
