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Conjugate peak refinement (CPR) calculations Calculations were performed using the CPR algorithm in the CHARMM molecular dynamics program. Polar and aromatic hydrogens were included explicitly, and a non-bond cutoff of 8.5Å was used to minimize calculation of long-range interactions. Since the CPR method does not allow the inclusion of explicit solvent, a distance-dependent dielectric was used. The starting structures of deoxy HbA and oxy HbA were obtained from the Protein Data Bank (PDB) . Each hemoglobin structure was energy minimized to alleviate bad atomic contacts. Cross-linkers were built using the modeling program QUANTA (Molecular Simulations, Inc.) and energy minimized. The cross-linker was positioned in the central cavity so the carboxyl groups were within 3Å of the side chain nitrogen of the αLys99. CPR was run with a step size of 0.002Å and a required saddle gradient RMS of 0.001Å. |
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