Distance restraints from crosslinking mass spectrometry: Mining a molecular dynamics simulation database to evaluate lysine-lysine distances
Distance restraints from crosslinking mass spectrometry: Mining a molecular dynamics simulation database to evaluate lysine-lysine distances
复制标题
DOI：
10.1002/pro.2458
复制
发表时间：
2014-06-01
期刊：
影响因子：
8
通讯作者：
Adkins, Joshua N.
中科院分区：
文献类型：
--
作者：
Merkley, Eric D.;Rysavy, Steven;Adkins, Joshua N.
综合结构生物学试图通过将计算结构建模与实验方法的数据相结合来模拟用经典结构方法(由于大小、动力学或异质性)具有挑战性或难以处理的蛋白质复合体的结构。一种这样的实验方法是化学交联质谱(XL-MS)，在这种方法中，蛋白质络合物被交联，并使用液-质联用来精确定位结构接近的特定氨基酸残基。常用的赖氨酸反应性N-羟基琥珀酰亚胺酯试剂琥珀酸二丁二酰亚胺(DSS)和双(磺基琥珀酰亚胺)琥珀酸双酯(BS3)在完全伸展时具有11.4埃长的连接臂，使得交联赖氨酸残基的C(蛋白质主链的α碳)原子之间的距离可达24埃。然而，XL-MS对已知结构的蛋白质的研究经常报告超过这一距离的交联键。通常，约3埃的公差被添加到理论上的最大值以说明该观察结果，而所选值的合理性有限。我们使用动态组学数据库，一个代表不同蛋白质折叠的高质量分子动力学模拟数据库，来研究实验起始结构和模拟系综中赖氨酸-赖氨酸距离之间的关系。我们的结论是，对于DSS/BS3，C原子之间的距离限制为26-30埃是合适的。这一分析为在将XL-MS结果与结构或建模进行比较时增加交联剂长度公差的广泛实践提供了理论基础。我们还讨论了XL-MS结果与MD模拟和已知结构的比较，以此作为测试和验证实验XL-MS方法的手段。
Integrative structural biology attempts to model the structures of protein complexes that are challenging or intractable by classical structural methods (due to size, dynamics, or heterogeneity) by combining computational structural modeling with data from experimental methods. One such experimental method is chemical crosslinking mass spectrometry (XL-MS), in which protein complexes are crosslinked and characterized using liquid chromatography-mass spectrometry to pinpoint specific amino acid residues in close structural proximity. The commonly used lysine-reactive N-hydroxysuccinimide ester reagents disuccinimidylsuberate (DSS) and bis(sulfosuccinimidyl)suberate (BS3) have a linker arm that is 11.4 angstrom long when fully extended, allowing C (alpha carbon of protein backbone) atoms of crosslinked lysine residues to be up to approximate to 24 angstrom apart. However, XL-MS studies on proteins of known structure frequently report crosslinks that exceed this distance. Typically, a tolerance of approximate to 3 angstrom is added to the theoretical maximum to account for this observation, with limited justification for the chosen value. We used the Dynameomics database, a repository of high-quality molecular dynamics simulations of 807 proteins representative of diverse protein folds, to investigate the relationship between lysine-lysine distances in experimental starting structures and in simulation ensembles. We conclude that for DSS/BS3, a distance constraint of 26-30 angstrom between C atoms is appropriate. This analysis provides a theoretical basis for the widespread practice of adding a tolerance to the crosslinker length when comparing XL-MS results to structures or in modeling. We also discuss the comparison of XL-MS results to MD simulations and known structures as a means to test and validate experimental XL-MS methods.