At room temperature, proteins undergo dynamic excursions away from their average three-dimensional structure. Ensembles obeying the laws of statistical thermodynamics that describe these excursions well are essential for understanding their influence on function. Here we report an unrestrained molecular dynamics ensemble of ubiquitin using the recently refined AMBER99SB force field, which reproduces experimental residual dipolar couplings in multiple alignment media, on the ensemble level, comparable to or better than high resolution averaged structures.
All Science Journal Classification (ASJC) codes
- General Chemistry
- Colloid and Surface Chemistry