A DESIGNED CAVITY IN THE HYDROPHOBIC CORE OF A 4-ALPHA-HELIX BUNDLE IMPROVES VOLATILE ANESTHETIC BINDING-AFFINITY

The structural features of protein binding sites for volatile anesthet ics are being explored using a defined model system consisting of a fo ur-alpha-helix bundle scaffold with a hydrophobic core. Earlier work h as demonstrated that a prototype hydrophobic core is capable of bindin g the volatile anesthetic halothane. Exploratory work on the design of an improved affinity anesthetic binding site is presented, based upon the introduction of a simple cavity into a prototype (alpha(2))(2) fo ur-alpha-helix bundle by replacing six core leucines with smaller alan ines. The presence of such a cavity increases the affinity (K-d = 0.71 +/- 0.04 mM) of volatile anesthetic binding to the designed bundle co re by a factor of 4.4 as compared to an analogous bundle core lacking such a cavity (K-d = 3.1 +/- 0.4 mM). This suggests that such packing defects present on natural proteins are likely to be occupied by volat ile general anesthetics in vivo. Replacing six hydrophobic core leucin e residues with alanines results in a destabilization of the folded bu ndle by 1.7-2.7 kcal/mol alanine, although the alanine-substituted bun dle still exhibits a high degree of thermodynamic stability with an ov erall folded conformational Delta G(H2O) = 14.3 +/- 0.8 kcal/mol. Cova lent attachment of the spin label MTSSL to cysteine residues in the al anine-substituted four-alpha-helix bundle indicates that the di-alpha- helical peptides dimerize in an anti orientation. The rotational corre lation time of the four-alpha-helix bundle is 8.1 +/- 0.5 ns, in line with earlier work on similar peptides, Fluorescence, far-UV circular d ichroism, and Fourier transform infrared spectroscopies verified the h ydrophobic core location of the tryptophan and cysteine residues, show ing good agreement between experiment and design. These small syntheti c proteins may prove useful for the study of the structural features o f small molecule binding sites.