Proline containing lipopeptides aggregates as weak acids: Insights from Constant pH molecular dynamics

Molecular Dynamics (MD) is commonly used to investigate complex molecular assemblies such as bilayers, vesicles, micelles, and lamellar structures. Lipopeptides that contain proline (PRO) and serine (SER) self-assemble to form aggregates with varied polymorphism depending on peptide sequence, concentration and pH. They have found recent applications in aldol catalysis and sensing1,2. In this work, we investigate using constant pH molecular dynamics (CpHMD)3 the N terminal protonation equilibria of two lipopeptide systems, namely PRWGC18 and SPRWGC18, in their micellar phase. Such a method enables the study of pH effects in complex environments.

According to our simulations, the average pKa of proline head groups present in the PRWGC18 micelle decreases from 10.6 to 6.5 pKa units. As a result, the system possesses an active protonation equilibrium in a neutral pH, with around half of its terminal nitrogen atoms deprotonated, which is the environment where the majority of catalysis studies were conducted. Similar results were observed for the SPRWGC18 micelle, with serine’s N terminal being more acidic. The typical observed pKa of serine on the micelle was 3.85. Therefore, we observed that the large number of positively charged species in the aggregate strongly influences the N-termini protonation state, turning it into a weak acid. Simulation results are consistent with our previous hypothesis that the micellar environment is needed to enable proline’s aldol catalysis in an aqueous environment. In a previous investigation1, we proposed that the pKa shift of proline could enable a proton shuffling mechanism between proline and trifluoro-acetic acid that is relevant to an efficient catalysis. Moreover, our results suggest that the change in the fractions of protonated head groups with pH can be related to changes in morphology as observed in experiments.