Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing

Biophys J. 1999 Jun;76(6):2879-86. doi: 10.1016/S0006-3495(99)77443-6.

Abstract

A method is proposed to restore ab initio low resolution shape and internal structure of chaotically oriented particles (e.g., biological macromolecules in solution) from isotropic scattering. A multiphase model of a particle built from densely packed dummy atoms is characterized by a configuration vector assigning the atom to a specific phase or to the solvent. Simulated annealing is employed to find a configuration that fits the data while minimizing the interfacial area. Application of the method is illustrated by the restoration of a ribosome-like model structure and more realistically by the determination of the shape of several proteins from experimental x-ray scattering data.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biophysical Phenomena
  • Biophysics
  • Computer Simulation
  • Macromolecular Substances*
  • Models, Molecular
  • Protein Conformation
  • Proteins / chemistry
  • Scattering, Radiation
  • Solutions
  • X-Rays

Substances

  • Macromolecular Substances
  • Proteins
  • Solutions