Regensburg 2025 – scientific programme
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DY: Fachverband Dynamik und Statistische Physik
DY 38: Focus Session: Innovations in Research Software Engineering (joint session BP/DY)
DY 38.9: Talk
Thursday, March 20, 2025, 17:15–17:30, H44
Estimation of pKa values in membrane bound proteins — •Jesse Jones1, Nereu Montserrat i Busquets1,2, Ana Gamiz Hernandez3, Ville Kaila3, and Maria Andrea Mroginski1 — 1Technische Universität Berlin, Berlin — 2Freie Universität Berlin, Berlin — 3Stockholm Universität, Stockholm
Many key bioenergetic processes involving electron and proton reactions take place in membrane bound protein complexes, generating a proton motive force. Yet the ionizable groups which facilitate these reactions are often buried in hydrophobic pockets in the membrane. These processes are mainly described through pKa values, which continue to be poorly understood and difficult to obtain despite structural, biochemical and computational advances. Hence, estimating pKa values of these residues without the need for weeks of work in a laboratory, is important to describe the dynamics of the system, providing information on possible proton pathways. In this work we preview Karlsberg3, a software which uses a Poisson Boltzmann Equation solver (APBS) for proteins and calculates pKa values. Karlsberg3 is, in contrast to its predecessor Karlsberg2+, parallelized, running in modern software environments, and able to take membranes into consideration.
Keywords: pKa; Protonation; Poisson-Boltzmann; Monte-Carlo; Software Engineering