Assessment of inconsistencies in the solvent-accessible surfaces of proteins between crystal structures and solution structures observed by LC-MS
Assessment of inconsistencies in the solvent-accessible surfaces of proteins between crystal structures and solution structures observed by LC-MS
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DOI：
10.1016/j.bbrc.2022.11.094
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发表时间：
2022-12-08
影响因子：
3.1
通讯作者：
Kodera，Yoshio
中科院分区：
文献类型：
--
作者：
Matsui，Takashi;Kojitani，Eiji;Kodera，Yoshio
结构蛋白质组学技术可用于鉴定蛋白质的结合位点。使用羟基自由基、氘或低分子量化学品人工标记具有和不具有结合的结合配偶体的靶蛋白的表面，并确定具有和不具有结合配偶体的标记强度的差异。然后在蛋白质数据库（PDB）结构上制备标记强度图，以识别结合表面。然而，使用这种结构蛋白质组学方法确定的表面可及位点经常与基于PDB结构计算的位点不一致，推测测量确定化学可及性而不是溶剂可及性。在这项研究中，人血清白蛋白的溶剂可及的表面进行了分析，使用共价蛋白质标记与不同浓度的CH 2 O，然后比较来自27 PDB结构的表面。结果表明，从PDB结构计算的溶剂可及表面积值的不一致性不是由液相色谱-质谱联用共价蛋白质绘画的有限能力引起的，而是由于缺乏PDB数据代表溶液中的结构。
Structural proteomics techniques are useful for identifying the binding sites of proteins. The surface of a target protein with and without a bound binding partner is artificially labeled using a hydroxy radical, deuterium, or a low-molecular-weight chemical, and the difference in the label strength with and without the bound partner is determined. Label strength maps are then prepared on the Protein Data Bank (PDB) structure to identify the binding surface. However, the surface-accessible sites determined using such structural proteomics methods are frequently inconsistent with those calculated based on PDB structures, speculating that the measurement determines chemical accessibility rather than solvent accessibility. In this study, the solvent-accessible surface of human serum albumin was analyzed using covalent protein labeling with varying concentrations of CH2O and then compared to surfaces derived from 27 PDB structures. The results indicated that inconsistencies in solvent-accessible surface area values calculated from PDB structures are not caused by the limited capabilities of liquid chromatography–mass spectrometry coupled with covalent protein painting but instead are due to the lack of PDB data representing the structures in solution.