Xin Yao, Mitchell Henrietta, Cameron Heather, Allison Stuart A
Department of Chemistry, Georgia State University, Atlanta, Georgia 30302-4098, USA.
J Phys Chem B. 2006 Jan 19;110(2):1038-45. doi: 10.1021/jp0544235.
A bead model to determine the electrophoretic mobilities and translational diffusion constants of weakly charged peptides is developed that is based on a approximate structural model of peptides and is also grounded in electrohydrodynamic theory. A peptide made up of X amino acids is modeled as N=2X beads with 2 beads representing each amino acid in the chain. For the two beads representing a particular amino acid in a peptide, the radius of one bead is set to one-half the nearest neighbor Calpha-Calpha distance, and the radius of the other bead is chosen on the basis of the diffusion constant of the free amino acid. Peptide conformations, which are defined by a set of psi-phi dihedral angles, are randomly generated by using the transformation matrix approach of Flory (Flory, P. Statistical Mechanics of Chain Molecules; John Wiley: New York, 1969) and rejecting conformations which result in bead overlap. The mobility and diffusion constants are computed for each conformation and at least 100 independent conformations are examined for each peptide. In general, the mobility is found to depend only weakly on peptide conformation. Model and experimental mobilities are compared by examining the data of Janini and co-workers (Janini, G.; et al. J. Chromatogr. 1999, 848, 417-433). A total of 58 peptides consisting of from 2 to 39 amino acids are considered. The average relative error between experimental and model mobilities is found to be 1.0% and the rms relative error 7.7%. In specific cases, the discrepancy can be substantial and possible reasons for this are discussed. It should be emphasized that the input parameters of the peptide model are totally independent of experimental mobilities. It is hoped that the peptide model developed here will be useful in the prediction of peptide mobility as well as in using peptide mobilities to extract information about peptide structure, conformation, and charge. Finally, we show how simultaneous measurements of translational diffusion and mobility can be used to estimate peptide charge.
开发了一种珠子模型，用于确定弱电荷肽的电泳迁移率和平动扩散常数。该模型基于肽的近似结构模型，并以电流体动力学理论为基础。由X个氨基酸组成的肽被建模为N = 2X个珠子，链中的每个氨基酸由2个珠子表示。对于肽中代表特定氨基酸的两个珠子，一个珠子的半径设置为最近邻Cα - Cα距离的一半，另一个珠子的半径根据游离氨基酸的扩散常数来选择。肽的构象由一组ψ - φ二面角定义，通过使用弗洛里（Flory, P. Statistical Mechanics of Chain Molecules; John Wiley: New York, 1969）的变换矩阵方法随机生成，并舍弃导致珠子重叠的构象。计算每个构象的迁移率和扩散常数，并且对每个肽至少检查100个独立构象。一般来说，发现迁移率仅微弱地依赖于肽的构象。通过检查贾尼尼及其同事（Janini, G.; et al. J. Chromatogr. 1999, 848, 417 - 433）的数据来比较模型迁移率和实验迁移率。总共考虑了58个由2至39个氨基酸组成的肽。发现实验迁移率和模型迁移率之间的平均相对误差为1.0%，均方根相对误差为7.7%。在特定情况下，差异可能很大，并讨论了其可能的原因。应该强调的是，肽模型的输入参数完全独立于实验迁移率。希望这里开发的肽模型将有助于预测肽的迁移率，以及利用肽的迁移率来提取有关肽的结构、构象和电荷的信息。最后，我们展示了如何通过同时测量平动扩散和迁移率来估计肽的电荷。
