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A strategy based on thermal flexibility to design triosephosphate isomerase proteins with increased or decreased kinetic stability

Quezada, Andrea G., Cabrera, Nallely, Piñeiro, Ángel, Díaz-Salazar, A. Jessica, Díaz-Mazariegos, Selma, Romero-Romero, Sergio, Pérez-Montfort, Ruy, Costas, Miguel
Biochemical and biophysical research communications 2018 v.503 no.4 pp. 3017-3022
Trypanosoma brucei, Trypanosoma cruzi, activation energy, denaturation, differential scanning calorimetry, evolution, half life, molecular dynamics, mutation, parasites, proteins, simulation models, temperature, triose-phosphate isomerase
Kinetic stability of proteins determines their susceptibility to irreversibly unfold in a time-dependent process, and therefore its half-life. A residue displacement analysis of temperature-induced unfolding molecular dynamics simulations was recently employed to define the thermal flexibility of proteins. This property was found to be correlated with the activation energy barrier (Eact) separating the native from the transition state in the denaturation process. The Eact was determined from the application of a two-state irreversible model to temperature unfolding experiments using differential scanning calorimetry (DSC). The contribution of each residue to the thermal flexibility of proteins is used here to propose multiple mutations in triosephosphate isomerase (TIM) from Trypanosoma brucei (TbTIM) and Trypanosoma cruzi (TcTIM), two parasites closely related by evolution. These two enzymes, taken as model systems, have practically identical structure but large differences in their kinetic stability. We constructed two functional TIM variants with more than twice and less than half the activation energy of their respective wild-type reference structures. The results show that the proposed strategy is able to identify the crucial residues for the kinetic stability in these enzymes. As it occurs with other protein properties reflecting their complex behavior, kinetic stability appears to be the consequence of an extensive network of inter-residue interactions, acting in a concerted manner. The proposed strategy to design variants can be used with other proteins, to increase or decrease their functional half-life.