Electrostatics of nanosystems: Application to microtubules and the ribosome

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

N. A. Baker; D. Sept; S. Joseph; M. J. Holst; J. A. McCammon


Scholarcy highlights

  • 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
  • Using APBS on 343 processors of the National Partnership for Advanced Computational Infrastructure Blue Horizon, linearized PBE was solved to give the electrostatic potential of the small ribosomal subunit at 0.41-Å resolution
  • We have described the combination of standard finite difference focusing techniques and the Bank-Holst algorithm into a parallel focusing method to facilitate the solution of the Poisson-Boltzmann equation for nanoscale systems
  • Unlike previous multiprocessor algorithms for solving the PBE, this method has excellent parallel complexity that permits the solution of these problems on massively parallel computational platforms
  • Solution of the LPBE for the 1.2 million-atom microtubule system provided electrostatic potential data, which revealed interesting features near drug binding sites and provided possible insight into stability differences at the ϩ and Ϫ ends of the microtubule. Such detailed electrostatic information will be central to future studies that examine the possible collective effects involved in the formation of structural defects and the stabilizing effects of taxol binding to the interior of microtubules
  • The ability to determine the contribution of electrostatics to the forces and energies of nanoscale systems should extend the scale of implicit solvent dynamics methods to much larger macromolecular complexes
  • This technique relies on the efficient solution of the Poisson-Boltzmann equation combined with parallel focusing techniques to solve these large problems in a variety of distributed computational environments

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