Substrate binding changes conformation of the α-, but not the β-subunit of mitochondrial processing peptidase

Lifetime analysis of tryptophan fluorescence of the mitochondrial processing peptidase (MPP) from Saccharomyces cerevisiae clearly proved that substrate binding evoked a conformational change of the α-subunit while presence of substrate influenced neither the lifetime components nor the average lifetime of the tryptophan excited state of the β-MPP subunit. Interestingly, lifetime analysis of tryptophan fluorescence decay of the α-MPP subunit revealed about 11% of steady-state fractional intensity due to the long-lived lifetime component, indicating that at least one tryptophan residue is partly buried at the hydrophobic microenvironment. Computer modeling, however, predicted none of three tryptophans, which the α-sub-unit contains, as deeply buried in the protein matrix. We conclude this as a consequence of a possible dimeric (oligomeric) structure.