A novel projection approximation algorithm for the fast and accurate computation of molecular collision cross sections (II). Model parameterization and definition of empirical shape factors for proteins
A novel projection approximation algorithm for the fast and accurate computation of molecular collision cross sections (II). Model parameterization and definition of empirical shape factors for proteins
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DOI：
10.1016/j.ijms.2012.08.027
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发表时间：
2013-07-01
影响因子：
1.8
通讯作者：
Bowers, Michael T.
中科院分区：
文献类型：
--
作者：
Bleiholder, Christian;Contreras, Stephanie;Bowers, Michael T.
根据在约80 ~ 550 K温度范围内的实验碰撞截面，导出了与投影叠加近似（PSA）方法结合计算碰撞截面的元素H、C、N、Na和K的参数。基于从蛋白质数据库下载的一组396种蛋白质结构，讨论了PSA方法对重量高达约300 kDa的蛋白质的应用。一般的方法允许确定的横截面基本上相同的精度的轨迹方法，但在几个数量级的计算成本。此外，我们定义了一个经验的形状因子（rho）的波浪线的蛋白质，近似的计算密集的部分的PSA计算，并可用于估计的PSA截面的基础上的经典投影近似。这种经验方法再现碰撞截面的精度约为10%。(c)2012爱思唯尔有限公司版权所有。
Parameters for the elements H, C, N, Na, and K for use in conjunction with the projected superposition approximation (PSA) method to compute collision cross sections are derived based on experimental collision cross sections in the temperature range from approximately 80 to 550 K. The application of the PSA method to proteins of up to approximately 300 kDa in weight is discussed based on a set of 396 protein structures downloaded from the protein data bank. The general method allows determination of cross sections with essentially the same accuracy as the trajectory method but at several orders of magnitude less computational cost. In addition, we define an empirical shape factor (rho) over tilde for proteins that approximates the computationally intensive part of the PSA calculation and can be used to estimate the PSA cross section based on the classical projection approximation. This empirical method reproduces collision cross sections with an accuracy of approximately 10%. (c) 2012 Elsevier B.V. All rights reserved.