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Structural refinement by restrained molecular‐dynamics algorithm with small‐angle X‐ray scattering constraints for a biomolecule
Author(s) -
Kojima Masaki,
Timchenko Alexander A.,
Higo Junichi,
Ito Kazuki,
Kihara Hiroshi,
Takahashi Kenji
Publication year - 2004
Publication title -
journal of applied crystallography
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.429
H-Index - 162
ISSN - 1600-5767
DOI - 10.1107/s0021889803026165
Subject(s) - small angle x ray scattering , scattering , molecular dynamics , crystallography , algorithm , crystal (programming language) , small angle scattering , materials science , physics , chemistry , mathematics , computer science , optics , computational chemistry , programming language
A new algorithm to refine protein structures in solution from small‐angle X‐ray scattering (SAXS) data was developed based on restrained molecular dynamics (MD). In the method, the sum of squared differences between calculated and observed SAXS intensities was used as a constraint energy function, and the calculation was started from given atomic coordinates, such as those of the crystal. In order to reduce the contribution of the hydration effect to the deviation from the experimental (objective) curve during the dynamics, and purely as an estimate of the efficiency of the algorithm, the calculation was first performed assuming the SAXS curve corresponding to the crystal structure as the objective curve. Next, the calculation was carried out with `real' experimental data, which yielded a structure that satisfied the experimental SAXS curve well. The SAXS data for ribonuclease T 1 , a single‐chain globular protein, were used for the calculation, along with its crystal structure. The results showed that the present algorithm was very effective in the refinement and adjustment of the initial structure so that it could satisfy the objective SAXS data.