The origin of specificity and insight into recognition between an aminoacyl carrier protein and its partner ligase

Abstract

Acyl carrier proteins (ACPs) are among the most promiscuous proteins in terms of protein–protein interactions and it is quite puzzling how ACPs select the correct partner between many possible upstream and downstream binding proteins. To address this question, we performed molecular dynamics simulations on dimeric Bradyrhizobium japonicum Gly:CP ligase 1 to inspect the origin of its selectivity towards the three types of carrier proteins, namely holoCP, apoCP, and holoCP–Gly, which only differ in the attached prosthetic group. In line with experiments, MM-GBSA analysis revealed that the ligase preferentially binds the holoCP form to both subunits with the binding free energies of −20.7 and −19.1 kcal mol⁻¹, while the apoCP form, without the prosthetic group, is also recognized, but the binding values of −9.2 and −3.6 kcal mol⁻¹ suggest that there is no competition for the ligase binding as long as the holoCP is present. After the prosthetic group becomes glycylated, the holoCP–Gly dissociates from the ligase, as supported by its endergonic binding free energies of 2.9 and 20.9 kcal mol⁻¹. Our results indicate that these affinity differences are influenced by three aspects: the form of the prosthetic group and the specific non-polar hydrophobic interactions, as well as charge complementarity dominantly manifested through Arg220–Glu53 ion pair within the binding region among proteins. A careful examination of the bonding patterns within the ligase active site elucidated the interactions with Arg258, Asp215 and Tyr132 as being predominant in stabilizing the prosthetic group, which are significantly diminished upon glycation, thus promoting complex dissociation.