Assessment of long-term molecular dynamics calculations with experimental information on protein shape from X-ray scattering-SOD1 as a case study

作者：Yong C W; Glab J; Strange R W; Smith W; Hasnain S S; Grossmann J G^*

来源：Chemical Physics Letters, 2009, 481(1-3): 112-117.

DOI：10.1016/j.cplett.2009.09.042

Predicting protein plasticity with molecular dynamics (MD) calculations requires experimental assessment. Using small-angle X-ray scattering (SAXS) we compare scattering profiles computed from MD structures with experimental profiles from Cu-Zn superoxide dismutase (SOD1) in its metal- loaded and metal-free form. Forty-nanosecond MD calculations provide a sizeable pool of conformational states yielding a neat agreement with experiments for the metal- loaded enzyme and an exploration of flexible polypeptide segments in the metal- free dimer. This flexibility leads to a discrepancy between SAXS and MD which can be resolved proficiently by partial protein metallation highlighting the potential of this approach for examining overall conformational protein dynamics.

• 出版日期2009-10-19