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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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 550K. The application of the PSA method to proteins of up to approximately 300kDa 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 ρ˜ 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%.