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Biophys J. Nov 1993; 65(5): 1810–1816.
PMCID: PMC1225916

Brownian dynamics simulations of probe and self-diffusion in concentrated protein and DNA solutions.


We have developed a Brownian dynamics algorithm for simulating probe and self-diffusion in concentrated solutions of DNA and protein. In these simulations, proteins are represented as spheres with radii given by their hydrodynamic radii, while DNA is modeled as a wormlike chain of hydrodynamically equivalent spherical frictional elements. The molecular interaction potentials employed by the program allow for intramolecular stretching and bending motions of the DNA chains, short-range Lennard-Jones interactions, and long-range electrostatic interactions. To test the program, we have carried out simulations of bovine serum albumin (BSA) probe diffusion and DNA self-diffusion in solutions of short-chain DNA as a function of both DNA concentration and solution ionic strength. In addition, we report on simulations of BSA self-diffusion as a function of BSA concentration and ionic strength. Based on a comparison to available experimental data, we find that our simulations accurately predict these transport properties under conditions of physiological salt concentration and predict the stronger concentration dependence observed at lower salt concentrations. These results are discussed in light of the nature of the intermolecular interactions in such systems and the approximations and limitations of the simulation algorithm.

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Selected References

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  • Muramatsu N, Minton AP. Tracer diffusion of globular proteins in concentrated protein solutions. Proc Natl Acad Sci U S A. 1988 May;85(9):2984–2988. [PMC free article] [PubMed]
  • Squire PG, Moser P, O'Konski CT. The hydrodynamic properties of bovine serum albumin monomer and dimer. Biochemistry. 1968 Dec;7(12):4261–4272. [PubMed]
  • Stigter D. Interactions of highly charged colloidal cylinders with applications to double-stranded. Biopolymers. 1977 Jul;16(7):1435–1448. [PubMed]
  • Zimmerman SB, Minton AP. Macromolecular crowding: biochemical, biophysical, and physiological consequences. Annu Rev Biophys Biomol Struct. 1993;22:27–65. [PubMed]

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