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Modeling the hydration layer around proteins: applications to small- and wide-angle x-ray scattering.

ABSTRACT: Small-/wide-angle x-ray scattering (SWAXS) experiments can aid in determining the structures of proteins and protein complexes, but success requires accurate computational treatment of solvation. We compare two methods by which to calculate SWAXS patterns. The first approach uses all-atom explicit-solvent molecular dynamics (MD) simulations. The second, far less computationally expensive method involves prediction of the hydration density around a protein using our new HyPred solvation model, which is applied without the need for additional MD simulations. The SWAXS patterns obtained from the HyPred model compare well to both experimental data and the patterns predicted by the MD simulations. Both approaches exhibit advantages over existing methods for analyzing SWAXS data. The close correspondence between calculated and observed SWAXS patterns provides strong experimental support for the description of hydration implicit in the HyPred model.

SUBMITTER: Virtanen JJ

PROVIDER: S-EPMC3192974 | biostudies-literature | 2011 Oct

REPOSITORIES: biostudies-literature

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Modeling the hydration layer around proteins: applications to small- and wide-angle x-ray scattering.

Virtanen Jouko Juhani JJ Makowski Lee L Sosnick Tobin R TR Freed Karl F KF

Biophysical journal 20111001 8

Small-/wide-angle x-ray scattering (SWAXS) experiments can aid in determining the structures of proteins and protein complexes, but success requires accurate computational treatment of solvation. We compare two methods by which to calculate SWAXS patterns. The first approach uses all-atom explicit-solvent molecular dynamics (MD) simulations. The second, far less computationally expensive method involves prediction of the hydration density around a protein using our new HyPred solvation model, wh ...[more]

PMID: 22004761

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