Institut für Informatik, Fachbereich 08, Staudingerweg 9, 55099 Mainz, Germany.
BMC Bioinformatics. 2010 Aug 11;11:424. doi: 10.1186/1471-2105-11-424.
Protein conformation and protein/protein interaction can be elucidated by solution-phase Hydrogen/Deuterium exchange (sHDX) coupled to high-resolution mass analysis of the digested protein or protein complex. In sHDX experiments mutant proteins are compared to wild-type proteins or a ligand is added to the protein and compared to the wild-type protein (or mutant). The number of deuteriums incorporated into the polypeptides generated from the protease digest of the protein is related to the solvent accessibility of amide protons within the original protein construct.
In this work, sHDX data was collected on a 14.5 T FT-ICR MS. An algorithm was developed based on combinatorial optimization that predicts deuterium exchange with high spatial resolution based on the sHDX data of overlapping proteolytic fragments. Often the algorithm assigns deuterium exchange with single residue resolution.
With our new method it is possible to automatically determine deuterium exchange with higher spatial resolution than the level of digested fragments.
通过溶液相氢/氘交换（sHDX）与经消化的蛋白质或蛋白质复合物的高分辨率质量分析相结合，可以阐明蛋白质构象和蛋白质/蛋白质相互作用。在 sHDX 实验中，将突变蛋白与野生型蛋白进行比较，或者将配体添加到蛋白中并与野生型蛋白（或突变体）进行比较。从蛋白酶消化蛋白质生成的多肽中掺入的氘的数量与原始蛋白质结构中酰胺质子的溶剂可及性有关。
在这项工作中，在 14.5 T FT-ICR MS 上收集了 sHDX 数据。基于组合优化开发了一种算法，该算法基于重叠的蛋白水解片段的 sHDX 数据，以高空间分辨率预测氘交换。该算法通常可以分配具有单个残基分辨率的氘交换。
使用我们的新方法，可以自动确定具有比消化片段更高空间分辨率的氘交换。
