Simulation studies of amide IIR absorption and two-dimensional IR spectra of β hairpins in liquid water
Simulation studies of amide IIR absorption and two-dimensional IR spectra of β hairpins in liquid water
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DOI：
10.1021/jp050450j
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发表时间：
2005-06-16
影响因子：
3.3
通讯作者：
Cho, M
中科院分区：
文献类型：
--
作者：
Hahn, S;Ham, S;Cho, M
采用半经验量子化学计算和分子动力学模拟相结合的方法，对模型发夹在水溶液中的红外吸收光谱和二维红外光子回波光谱进行了理论研究和模拟。通过对溶液中发夹的瞬时简正模分析，得到了发夹的态密度和单激子态的逆参与率。对于线性和非线性响应函数，采用时间相关函数理论考虑了运动和交换的窄化过程。然后，数值模拟的红外吸收和2D光谱发现，很大程度上是由两条链上多肽上的酰胺I简正模离域决定的。讨论了特定位置的同位素标记对红外光谱和二维红外光谱的影响。对理想的(A(17))β发夹的模拟结果与来自免疫球蛋白G结合蛋白的现实的16个残基(GB 1)发夹的模拟结果直接进行了比较。结果表明，理想的(A(17))β发夹和GB1β发夹的红外光谱和二维光谱特征是相同的。GB 1β发夹的模拟红外光谱与实验结果吻合较好，说明该计算方法在定量上是可靠的
Amide I IR absorption and two-dimensional (2D) IR photon echo spectra of a model hairpin in aqueous solution are theoretically studied and simulated by combining semiempirical quantum chemistry calculations and molecular dynamics simulation methods. The instantaneous normal-mode analysis of the hairpin in solution is performed to obtain the density of states and the inverse participation ratios of the one-exciton states. The motional and exchange narrowing processes are taken into account by employing the time-correlation function theory for the linear and nonlinear response functions. Numerically simulated IR absorption and 2D spectra are then found to be determined largely by the amide I normal modes delocalized on the peptides in the two strands. The site-specific isotope-labeling effects on the IR and 2D IR spectra are discussed. The simulation results for the ideal (A(17)) beta hairpin are directly compared with those of the realistic 16-residue (GB 1) hairpin from an immunoglobulin G-binding protein. It was found that the characteristic features in IR and 2D spectra of both the ideal (A(17)) beta hairpin and the GB1 beta hairpin are the same. The Simulated IR spectrum of the GB 1 beta hairpin is found to be in good agreement with experiment, which demonstrates that the present computational method is quantitatively reliable.