FREE ENERGIES FOR FOLDING AND REFOLDING OF FOUR TYPES OF BETA TURNS - SIMULATION OF THE ROLE OF D/L CHIRALITY

摘要

Rational protein design would benefit from quantitative estimates of the free-energy differences (Delta G among beta turn conformers. We have simulated a chirally representative set of nine loop dipeptides of the form CH3CO-L1-L2-NHCH3, where L1 and L2 were Gly, L-Ala, or D-Ala. The Delta G value for each glycine (type-II) and inverse-glycine (type-II') beta-turn conformer (relative to the Gly-Gly conformers) was estimated in an explicit water environment by the slow-growth method, in which an alpha-hydrogen atom of a Gly residue is replaced by a methyl group to give L-Ala or D-Ala. The Delta G values ranged from 0.9 to 6.5 kcal/mol. The molecular symmetry of this model system allowed estimation of the Delta G values for II --> II' refolding, which were spread from -4.6 to 4.6 kcal/mol. The relative free-energy change (Delta Delta G(f)) for folding of each loop dipeptide from its extended (epsilon) conformer into its type-II or type-II' beta-turn conformer (relative to folding of the Gly-Gly loop dipeptide) was calculated from a thermodynamic cycle. The Delta Delta G(f) values for epsilon --> II or epsilon --> II' folding ranged from -2.2 to 2.5 kcal/mol, and those for epsilon --> I Or epsilon --> I' folding spanned from -2.1 to 0.9 kcal/mol. The contribution of an L-Ala or D-Ala residue to the Delta Delta G(f) for folding of the loop dipeptides into four beta-turn conformations (I, I', II, II') ranged from -1.1 to 1.7 kcal/mol. The Delta Delta G(f) values for folding of Gly-Gly, Gly-L-Ala, and L-Ala-Gly into each of these beta-turn conformations correlated with the relative occurrences of these beta-turn conformations in natural proteins, suggesting that formation of a beta rum during protein folding is mainly guided by local interactions. During rational design of a synthetic protein, placing-D-Ala at L1 alone should favor the type-II' beta turn, D-Ala at L2 alone should favor the type-II beta turn, and D-Ala at both L1 and L2 should favor the type-I' beta turn. Using Gly at L1 should favor either a type-I' or -II' beta turn and Gly at L2 should favor either a type-I or -II beta turn. [References: 49]