FIGURE 10.

The artificially generated (a) hairpin and (b–d) partially folded hairpin conformations used to investigate the folding pathway. The hairpin conformation (a, ) was constructed as described in the text in connection with Fig. 2 c; conformation (b, ) was obtained by protonating the three cytosines on the extended arm of the hairpin and running a 3-ns MD simulation; conformations (c, ) and (d, ) were artificially constructed from the hairpin conformation by changing dihedral angles in the TTTT tetraloop and equilibrating the structures (see the text for additional details).