Electrostatic interactions in macromolecules: theory and applications.

CONTENTS PERSPECTIVE AND OVERVIEW 301 DIELECTRIC THEORY . . . . . . . . . . . ... . . . . . ........ . . . . . . . 303 The Poisson Equation . . . . . . . . . . . . . . . . . ... . . . . . . ... . . . ... . 303 Electronic Polarizability 304 Permanent Dipoles . . . ..... . . . ...... . . . . . . .... . . . . ... . ... ..... 307 Mobile Ions . . . . . . . . . . . . . . . . . ... . . . . . ... ... . . . . . ... . . . . . . . . . . . . . . . . . . . . . ... . . . . ... . ....... 309 METHODS 3 1 0 The Protein Dipole Langevin Dipole Method. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 1 2 Analytical Solutions t o the Poisson-Boltzmann Equation 3 1 2 Numerical Solutions to the Poisson-Boltzmann Equation 3 13 The Finite Diff erence Poisson-Boltzmann Method ......... . . . . . . . ..... . . . . . . ... . . ... 3 14 APPLICATIONS ..... 317 Electrical Potentials around Macromolecules. . . . . . . . . . . . . . . . . . . . .. ..... . . . . .. . ... . .. . . . . . . . . ..... . ...... 317 Solvation Energies . . ....... . . . . . . . . . . . . . . . . . . . . . . . . . 319 Catalysis ... ... . . . ... . . ... . ... . . . ....... . . . . . . . . . . . . .... ... ....... ..... . . ... . . . . . . 321 Acid-Base Equilibria. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 322 Redox Potentials . . ... . . . . .... . . . . . . ..... . . . . ... . . ........ ...... 324 Forces in DynamiCS Simulations . . . . . . . .... . . . . . . . . . . . . . . . . . ... ..... . . . . . . . . . . . . . . . . . . . . . ..... ... 326 Electrostatic Energies and Stability: Folding, Denaturation, and Binding . ........ . . . ..... 327 SUMMARY AND PROSPECTS ....... ......... . . . . . ....... . . . . . . . . . . . . . . . . . . . . 329