| simulated annealing |
Structures were calculated using a simulated annealing protocol within Xplor-NIH with torsion angle molecular dynamics in the presence of experimentally determined restraints. Solid-state NMR experiments on static oriented lipid bilayer samples allowed for the measurements of anisotropic backbone 15N chemical shifts and 15N-1H dipolar couplings, which were used as the experimental restraints. The initial structure was an alpha helix with ideal phi/psi angles (-61/-45). The calculations also included the Xplor-NIH potential for knowledge-based torsion angles and the routine terms ANGL, BOND and IMPR. A total of 100 structures were generated and the 10 lowest energy structures were accepted for analysis and representation. By convention, the bilayer normal for all of the oriented samples is aligned along the z-axis of the calculated structures. |
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