Exploring the energy surface of protein folding by structure-reactivity relationships and engineered proteins: observation of Hammond behavior for the gross structure of the transition state and anti-Hammond behavior for structural elements for unfolding/folding of barnase

Abstract

The structure of alpha-helix 1 (residues 6-18) in the transition state for the unfolding of barnase has been previously characterized by comparing the kinetics and thermodynamics of folding of wild-type protein with those of mutants whose side chains have been cut back, in the main, to that of alanine. The structure of the transition state has now been explored further by comparing the kinetics and thermodynamics of folding of glycine mutants with those of the alanine mutants at solvent-exposed positions in the alpha-helices of barnase. Such "Ala-->Gly scanning" provides a general procedure for examining the structure of solvent-exposed regions in the transition state. A gradual change of structure of the transition state was detected as helix 1 becomes increasingly destabilized on mutation. The extent of change of structure of helix 1 in the transition state for the mutant proteins was probed by a further round of Ala-->Gly scanning of those mutants. Destabilization of the helix 1 was found to cause the overall transition state for unfolding to become closer in structure to that of the folded protein. This is analogous to the conventional Hammond effect in physical-organic chemistry whereby the transition state moves parallel to the reaction coordinate with change in structure. But, paradoxically, the structure of helix 1 itself becomes less folded in the transition state as helix 1 becomes destabilized. This is analogous, however, to the rarer anti-Hammond effect in which there is movement perpendicular to the reaction coordinate. These observations are rationalized by plotting correlation diagrams of degree of formation of individual elements of structure against the degree of formation of overall structure in the transition state. There is a relatively smooth movement of the degree of compactness in the transition state against changes in activation energy on mutation that suggests a smooth movement of the transition state along the energy surface on mutation rather than a switch between two different parallel pathways. The results are consistent with the transition state having closely spaced energy levels. Helix 1, which appears to be an initiation point and forms early in the folding of wild-type protein, may be radically destabilized to the extent that it forms late in the folding of mutants. The order of events in folding may thus not be crucial.