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Title: Accurate small and wide angle x-ray scattering profiles from atomic models of proteins and nucleic acids

A new method is introduced to compute X-ray solution scattering profiles from atomic models of macromolecules. The three-dimensional version of the Reference Interaction Site Model (RISM) from liquid-state statistical mechanics is employed to compute the solvent distribution around the solute, including both water and ions. X-ray scattering profiles are computed from this distribution together with the solute geometry. We describe an efficient procedure for performing this calculation employing a Lebedev grid for the angular averaging. The intensity profiles (which involve no adjustable parameters) match experiment and molecular dynamics simulations up to wide angle for two proteins (lysozyme and myoglobin) in water, as well as the small-angle profiles for a dozen biomolecules taken from the BioIsis.net database. The RISM model is especially well-suited for studies of nucleic acids in salt solution. Use of fiber-diffraction models for the structure of duplex DNA in solution yields close agreement with the observed scattering profiles in both the small and wide angle scattering (SAXS and WAXS) regimes. In addition, computed profiles of anomalous SAXS signals (for Rb{sup +} and Sr{sup 2+}) emphasize the ionic contribution to scattering and are in reasonable agreement with experiment. In cases where an absolute calibration of the experimental data atmore » q = 0 is available, one can extract a count of the excess number of waters and ions; computed values depend on the closure that is assumed in the solution of the Ornstein–Zernike equations, with results from the Kovalenko–Hirata closure being closest to experiment for the cases studied here.« less
Authors:
 [1] ; ; ;  [2] ;  [1] ;  [3]
  1. BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway, New Jersey 08854 (United States)
  2. School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853 (United States)
  3. (United States)
Publication Date:
OSTI Identifier:
22314267
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of Chemical Physics; Journal Volume: 141; Journal Issue: 22; Other Information: (c) 2014 AIP Publishing LLC; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY; ATOMIC MODELS; CALIBRATION; LIQUIDS; LYSOZYME; MOLECULAR DYNAMICS METHOD; MYOGLOBIN; SMALL ANGLE SCATTERING; SOLUTIONS; WATER; X RADIATION; X-RAY DIFFRACTION