Protein dynamics via computational microscope

Figure 4 Five different metastable states (S0 to S4) identified for the benzamidine-trypsin complex[47]. The relative free energy between the unbound S0 and the bound S4 states is -6 kcal/mol. The most probable transition to the bound state S4 is from S3, since the barrier between two states is just 1.5 kcal/mol. In states S1 and S2, benzamidine is stabilized by π-π stacking interactions with Y151 and Y39 side chains. In S3, a hydrogen bond may be formed between the NH2 groups of benzamidine (only heavy atoms shown for clarity) and Q175 side chain, or by a cation-π interaction between the Q175 side chain and the benzamidine’s benzene ring. Reproduced with permission (Copyright 2011, PNAS).