Feng Yuan, Huang Jing, Kim Seongheun, Shim Ji Hyun, MacKerell Alexander D, Ge Nien-Hui
Department of Chemistry, University of California at Irvine , Irvine, California 92697-2025, United States.
Department of Pharmaceutical Science, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201, United States.
J Phys Chem B. 2016 Jun 23;120(24):5325-39. doi: 10.1021/acs.jpcb.6b02608. Epub 2016 Jun 14.
We have studied the structure of (Ala)5, a model unfolded peptide, using a combination of 2D IR spectroscopy and molecular dynamics (MD) simulation. Two different isotopomers, each bis-labeled with (13)C═O and (13)C═(18)O, were strategically designed to shift individual site frequencies and uncouple neighboring amide-I' modes. 2D IR spectra taken under the double-crossed ⟨π/4, -π/4, Y, Z⟩ polarization show that the labeled four-oscillator systems can be approximated by three two-oscillator systems. By utilizing the different polarization dependence of diagonal and cross peaks, we extracted the coupling constants and angles between three pairs of amide-I' transition dipoles through spectral fitting. These parameters were related to the peptide backbone dihedral angles through DFT calculated maps. The derived dihedral angles are all located in the polyproline-II (ppII) region of the Ramachandran plot. These results were compared to the conformations sampled by Hamiltonian replica-exchange MD simulations with three different CHARMM force fields. The C36 force field predicted that ppII is the dominant conformation, consistent with the experimental findings, whereas C22/CMAP predicted similar population for α+, β, and ppII, and the polarizable Drude-2013 predicted dominating β structure. Spectral simulation based on MD representative conformations and structure ensembles demonstrated the need to include multiple 2D spectral features, especially the cross-peak intensity ratio and shape, in structure determination. Using 2D reference spectra defined by the C36 structure ensemble, the best spectral simulation is achieved with nearly 100% ppII population, although the agreement with the experimental cross-peak intensity ratio is still insufficient. The dependence of population determination on the choice of reference structures/spectra and the current limitations on theoretical modeling relating peptide structures to spectral parameters are discussed. Compared with the previous results on alanine based oligopeptides, the dihedral angles of our fitted structure, and the most populated ppII structure from the C36 simulation are in good agreement with those suggesting a major ppII population. Our results provide further support for the importance of ppII conformation in the ensemble of unfolded peptides.
我们使用二维红外光谱和分子动力学（MD）模拟相结合的方法，研究了模型解折叠肽（Ala）5的结构。精心设计了两种不同的同位素异构体，每种都用（13）C═O和（13）C═（18）O进行双标记，以移动各个位点的频率并解耦相邻的酰胺-I'模式。在双交叉⟨π/4, -π/4, Y, Z⟩偏振下获得的二维红外光谱表明，标记的四振子系统可以近似为三个双振子系统。通过利用对角峰和交叉峰不同的偏振依赖性，我们通过光谱拟合提取了三对酰胺-I'跃迁偶极矩之间的耦合常数和角度。这些参数通过密度泛函理论（DFT）计算的图谱与肽主链二面角相关。推导得到的二面角都位于拉马钱德兰图的多聚脯氨酸-II（ppII）区域。将这些结果与使用三种不同CHARMM力场的哈密顿量副本交换MD模拟采样的构象进行了比较。C36力场预测ppII是主要构象，这与实验结果一致，而C22/CMAP预测α+、β和ppII的丰度相似，可极化的Drude-2013预测主要为β结构。基于MD代表性构象和结构集合的光谱模拟表明，在结构确定中需要纳入多个二维光谱特征，特别是交叉峰强度比和形状。使用由C36结构集合定义的二维参考光谱，尽管与实验交叉峰强度比的一致性仍然不足，但在ppII丰度接近100%时实现了最佳光谱模拟。讨论了丰度确定对参考结构/光谱选择的依赖性以及当前将肽结构与光谱参数相关联的理论建模的局限性。与之前关于基于丙氨酸的寡肽的结果相比，我们拟合结构的二面角以及C36模拟中最丰富的ppII结构与那些表明主要为ppII丰度的结果高度一致。我们的结果进一步支持了ppII构象在解折叠肽集合中的重要性。
