Comparative Protein Dynamics by Simulation

We simulated four folded proteins for comparison of dynamic properties to NMR. First was the third Igg-binding domain of protein G (GB3). The native structure was defined as a liquid crystal NMR structure (PDB ID: 1P7E^{40 (link)}). Second was the bovine pancreatic trypsin inhibitor (BPTI). The native structure was defined as a joint neutron/X-ray diffraction structure (PDB ID: 5PTI^{41 (link)}). Third was ubiquitin (Ubq), with the native structure defined as a crystal structure (PDB ID: 1UBQ^{42 (link)}). Fourth was hen egg white lysozyme (HEWL), with the native structure defined as a crystal structure (PDB ID: 6LYT⁴³ ). Owing to their larger size, the proteins were equilibrated as above, but with the unrestrained step extended to a full nanosecond, rather than 500 ps.