pKaTool

pKaTool — Titratable Groups, Made Intuitive pKaTool is a hands-on lab for exploring how acids and bases behave when they're not alone. Real proteins pack titratable groups close together in active sites, and their pKa values shift because of it — coupling that's easy to state on paper but hard to feel until you can play with it. Built for the classroom as much as the lab bench. Set up a system of titratable groups, assign each an intrinsic pKa and an acid or base identity, then adjust the pairwise interaction energy between them. pKaTool solves the exact Boltzmann partition function for every protonation state — no approximation, no Monte Carlo sampling — and redraws the titration curve live as you move the sliders. NEW: pH-activity profiles Mark which protonation state of an active site is catalytically competent, and pKaTool overlays the resulting pH-activity profile on the chart — the same calculation behind published pH-dependent enzyme activity curves. Watch how coupling between two or three residues can shift an enzyme's pH optimum by a full pH unit. NEW: Six systems from the literature Load real, published active-site electrostatics instead of only synthetic examples — intrinsic pKa values and interaction energies transcribed directly from an NMR/GloFTE study of enzyme active sites (Sondergaard et al., J. Mol. Biol. 2008), including a wild-type xylanase and its N35D mutant reproducing a published pH-activity optimum shift (5.7 to 4.6), ribonuclease A, and both oxidation states of thioredoxin. Initial version based on Analysing the pH-dependent properties of proteins using pKa calculations, Jens Erik Nielsen J Mol Graph Model. 2007 Jan;25(5):691-9. doi: 10.1016/j.jmgm.2006.05.007. https://pubmed.ncbi.nlm.nih.gov/16815056/ What you can explore: • Intrinsic pKa vs. effective pKa — watch a group's apparent pKa shift as neighboring charges turn on and off • Repulsive vs. attractive coupling, applied automatically from each group's acid/base identity, just like real electrostatics • Back-titration — the counterintuitive case where a group re-protonates partway through a titration because its neighbors' charge state changes the energetics • pH-activity profiles for enzyme active sites, and net charge and isoelectric point across your full pH range Why it's useful for teaching: • See, in real time, why two nearby acidic or basic residues almost never titrate independently — the classic Henderson-Hasselbalch curve is the special case, not the rule • Build intuition for back-titration, charge inversion, and buffering plateaus by dragging sliders instead of reading about them • Reproduce a real published figure from the primary literature, not a toy example Built for exploration: • One live screen — sliders, interaction matrix, and titration curve all update together, no "calculate" button • Save and switch between named systems to compare setups, including the six built-in literature examples • Adjustable pH scan range and resolution • No account required — systems stay on your device • Occasional non-personalized ads support development; Remove Ads turns them off Whether you're teaching enzyme active-site behavior, building intuition before a kinetics experiment, or just curious why a catalytic residue's pKa never matches the textbook value, pKaTool lets you turn the knobs yourself and watch the physics respond. Original code license: # pKaTool - analysis of systems of titratable groups # Copyright (C) 2010 Jens Erik Nielsen # # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details.