Department of Medicine and Biomedical Sciences Graduate Program, University of California, 9500 Gilman Drive, mc 0656, La Jolla, San Diego, CA 92093, USA.
J Am Soc Mass Spectrom. 2012 Jan;23(1):43-56. doi: 10.1007/s13361-011-0267-9. Epub 2011 Oct 20.
Peptide amide hydrogen/deuterium exchange mass spectrometry (DXMS) data are often used to qualitatively support models for protein structure. We have developed and validated a method (DXCOREX) by which exchange data can be used to quantitatively assess the accuracy of three-dimensional (3-D) models of protein structure. The method utilizes the COREX algorithm to predict a protein's amide hydrogen exchange rates by reference to a hypothesized structure, and these values are used to generate a virtual data set (deuteron incorporation per peptide) that can be quantitatively compared with the deuteration level of the peptide probes measured by hydrogen exchange experimentation. The accuracy of DXCOREX was established in studies performed with 13 proteins for which both high-resolution structures and experimental data were available. The DXCOREX-calculated and experimental data for each protein was highly correlated. We then employed correlation analysis of DXCOREX-calculated versus DXMS experimental data to assess the accuracy of a recently proposed structural model for the catalytic domain of a Ca(2+)-independent phospholipase A(2). The model's calculated exchange behavior was highly correlated with the experimental exchange results available for the protein, supporting the accuracy of the proposed model. This method of analysis will substantially increase the precision with which experimental hydrogen exchange data can help decipher challenging questions regarding protein structure and dynamics.
肽酰胺氢/氘交换质谱（DXMS）数据通常用于定性支持蛋白质结构模型。我们开发并验证了一种方法（DXCOREX），可以利用交换数据定量评估蛋白质结构三维（3-D）模型的准确性。该方法利用 COREX 算法通过参考假设结构来预测蛋白质的酰胺氢交换率，并且这些值用于生成虚拟数据集（每个肽的氘掺入量），可以与通过氢交换实验测量的肽探针的氘化水平进行定量比较。在对 13 种具有高分辨率结构和实验数据的蛋白质进行的研究中，确立了 DXCOREX 的准确性。每个蛋白质的 DXCOREX 计算数据和实验数据高度相关。然后，我们利用 DXCOREX 计算值与 DXMS 实验数据的相关分析来评估最近提出的钙（Ca2+）非依赖性磷脂酶 A2（PLA2）催化结构域结构模型的准确性。该模型的计算交换行为与该蛋白质的实验交换结果高度相关，支持了所提出模型的准确性。这种分析方法将大大提高实验氢交换数据在解决有关蛋白质结构和动力学的挑战性问题方面的精度。
