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Kasahara, Kento ; Re, Suyong ; Nawrocki, Grzegorz ; Oshima, Hiraku ; Mishima-Tsumagari, Chiemi ; Miyata-Yabuki, Yukako ; Kukimoto-Niino, Mutsuko ; Yu, Isseki ; Shirouzu, Mikako ; Feig, Michael ; et al ( , Nature Communications)
Abstract The inside of a cell is highly crowded with proteins and other biomolecules. How proteins express their specific functions together with many off-target proteins in crowded cellular environments is largely unknown. Here, we investigate an inhibitor binding with c-Src kinase using atomistic molecular dynamics (MD) simulations in dilute as well as crowded protein solution. The populations of the inhibitor, 4-amino-5-(4-methylphenyl)−7-(
t -butyl)pyrazolo[3,4-d]pyrimidine (PP1), in bulk solution and on the surface of c-Src kinase are reduced as the concentration of crowder bovine serum albumins (BSAs) increases. This observation is consistent with the reduced PP1 inhibitor efficacy in experimental c-Src kinase assays in addition with BSAs. The crowded environment changes the major binding pathway of PP1 toward c-Src kinase compared to that in dilute solution. This change is explained based on the population shift mechanism of local conformations near the inhibitor binding site in c-Src kinase.