Computer simulations of mass transport for nonidentical interacting molecules

Abstract

We have developed a system for simulating the mass transport properties of interacting nonidentical macromolecules where the association is of the form A + B ⇄ C, C + B ⇄ D. Our simulation programs operate in a minicomputer (PDP 1104) with 16K of core and provide results identical to methods previously usable only with large computers. We use a rectangular approximation for the centrifuge cell which greatly simplifies calculation, although it introduces a few percent error into any attempt at quantitative fitting of actual data. The program as written is directly applicable to gel chromatography, simply by substitution of flow for centrifugal field and dispersion for diffusion. Simulations of centrifuge results have been compared with experimental results for two systems which have been proposed to fit the association pattern described—nitrogenase components and an antigen-antibody interaction. In both cases the results of our simulations suggest that the accepted interpretation of the experimental results may need to be modified. For the antigen-antibody interaction, the presence of multivalent higher order complexes apparently is required to explain the centrifuge results. For nitrogenase, one cannot readily distinguish the case of association to form both 1:1 and 1:2 molar complexes from that of formation of only the 1:1 complex on the basis of the published data. Criteria for making such a discrimination are discussed.