Residual interactions in the denatured states of proteins affect thermodynamics and kinetics of protein folding. To understand their roles, we used all-atom, explicit-solvent, replica-exchange molecular dynamics to simulate two fragments from a �-hairpin in the native structure of the N-terminal domain of ribosomal protein L9 (NTL9). Simulations started from extended conformations and were performed with two different force fields (CHARMM22/CMAP and AMBER99SB-ILDN). �-sheet structure formed occasionally for the long fragment while the short fragment was always a random coil. Consistent with previous studies, Lys12 strongly interacted with Asp8 and Glu17. In addition, Asp8 and Glu17 formed strong interactions with other lysine residues. These interactions occurred for both force fields but with different preference. In agreement with experiments, the calculated pKa's of Asp8 and Glu17 in the denatured states were depressed. This study highlights the importance of electrostatic interactions in the stability and folding of NTL9.

Characterization of electrostatic interactions in the denatured states of NTL9

244th National Meeting (2012)

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