Research Article
Simulated Annealing Method for the Automated Simulation of DNA Dynamics in the HhaI Protein Binding Site
Figure 2
Line shape simulations include two independent motions. (a) A slow, uniform rotation of the DNA molecule occurs about the helical axis, labeled Zhelical. Local motion of the backbone is referenced to a local coordinated system, where the z axis is indicated by the vector Zlocal defined by the angle . (b) The 2H5′/5″ and 2H2″ deuterons move through an elliptical trajectory as the furanose ring puckers between the C2′ -endo and C3′-endo conformations.
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