Biophys J, December 1998, p. 2637-2646, Vol. 75, No. 6

Role of Hydrophobicity and Solvent-Mediated Charge-Charge Interactions in Stabilizing -Helices

 ^*Universidad Nacional de San Luis, Facultad de Ciencias Físico Matemáticas y Naturales, and Instituto de Matemática Aplicada San Luis, Consejo Nacional de Investigaciones Científicas y Técnicas, 5700 San Luis, Argentina;  ^#Baker Laboratory of Chemistry and Chemical Biology and  ^§Cornell Theory Center, Cornell University, Ithaca, New York 14853 USA; and  ^¶Department of Biochemistry, FLOB, The University of North Carolina, Chapel Hill, North Carolina 27599 USA

A theoretical study to identify the conformational preferences of lysine-based oligopeptides has been carried out. The solvation free energy and free energy of ionization of the oligopeptides have been calculated by using a fast multigrid boundary element method that considers the coupling between the conformation of the molecule and the ionization equilibria explicitly, at a given pH value. It has been found experimentally that isolated alanine and lysine residues have somewhat small intrinsic helix-forming tendencies; however, results from these simulations indicate that conformations containing right-handed -helical turns are energetically favorable at low values of pH for lysine-based oligopeptides. Also, unusual patterns of interactions among lysine side chains with large hydrophobic contacts and close proximity (5-6 Å) between charged NH₃⁺ groups are observed. Similar arrangements of charged groups have been seen for lysine and arginine residues in experimentally determined structures of proteins available from the Protein Data Bank. The lowest-free-energy conformation of the sequence Ac-(LYS)₆-NMe from these simulations showed large pK shifts for some of the NH₃⁺ groups of the lysine residues. Such large effects are not observed in the lowest-energy conformations of oligopeptide sequences with two, three, or four lysine residues. Calculations on the sequence Ac-LYS-(ALA)₄-LYS-NMe also reveal low-energy -helical conformations with interactions of one of the LYS side chains with the helix backbone in an arrangement quite similar to the one described recently by Groebke et al., 1996 (Proc. Natl. Acad. Sci. U.S.A. 93:4025-4029). The results of this study provide a sound basis with which to discuss the nature of the interactions, such as hydrophobicity, charge-charge interaction, and solvent polarization effects, that stabilize right-handed -helical conformations.

Biophys J, December 1998, p. 2637-2646, Vol. 75, No. 6
© 1998 by the Biophysical Society   0006-3495/98/12/2637/10  $2.00

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