Improving the Estimation of p K a Values for All Titratable Amino Acids at the Water/Membrane Interface

Understanding how pH-sensitive molecules behave when incorporated into lipid bilayers is a challenging problem that requires specialized methods and robust sampling. Techniques based on constant-pH molecular dynamics (CpHMD) can be employed to investigate the effects of pH on molecules at the water-membrane interface. Here, we compare the performance of enhanced sampling protocols coupled with CpHMD in describing protonation and pKa values of model Ala pentapeptide systems inserting into a DMPC membrane. From regular CpHMD, replica exchange (pHRE), and umbrella sampling (US-CpHMD), the latter provides more reliable and complete pKa profiles along bilayer insertion, in particular, at deeper regions of the membrane. Overall, there is a consistent trend for pKa values to shift toward the molecules' neutral state, a crucial effect that enables a (de)protonation-assisted increase in membrane permeability. Building on US-CpHMD, we have successfully coupled an umbrella replica exchange scheme (REUS), which significantly improved the reliability of results for our Asp pentapeptide by enhancing configurational sampling between the umbrellas, albeit at a substantial computational cost.