Chemistry / Biophysics
Electrostatics of nanosystems: Application to microtubules and the ribosome
Nathan A. Baker*,,, David Sept§, Simpson Joseph*, Michael J. Holst¶, and J. Andrew McCammon*,,
Departments of * Chemistry and Biochemistry, ¶ Mathematics, and Pharmacology, and Howard Hughes Medical Institute, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093; and § Department of Biomedical Engineering, Washington University, One Brookings Drive, St. Louis, MO 63130-4899
Communicated by Peter G. Wolynes, University of California at San Diego, La Jolla, CA, July 5, 2001 (received for review May 8, 2001)
Evaluation of the electrostatic properties of biomolecules has become a standard practice in molecular biophysics. Foremost among the models used to elucidate the electrostatic potential is the Poisson-Boltzmann equation; however, existing methods for solving this equation have limited the scope of accurate electrostatic calculations to relatively small biomolecular systems. Here we present the application of numerical methods to enable the trivially parallel solution of the Poisson-Boltzmann equation for supramolecular structures that are orders of magnitude larger in size. As a demonstration of this methodology, electrostatic potentials have been calculated for large microtubule and ribosome structures. The results point to the likely role of electrostatics in a variety of activities of these structures.