K+ binding and proton redistribution in the E2P state of the H+, K+-ATPase

Abstract

The H+, K+-ATPase (HKA) uses ATP to pump protons into the gastric lumen against a million-fold proton concentration gradient while counter-transporting K+ from the lumen. The mechanism of release of a proton into a highly acidic stomach environment, and the subsequent binding of a K+ ion necessitates a network of protonable residues and dynamically changing protonation states in the cation binding pocket dominated by five acidic amino acid residues E343, E795, E820, D824, and D942. We perform molecular dynamics simulations of spontaneous K+ binding to all possible protonation combinations of the acidic amino acids and carry out free energy calculations to determine the optimal protonation state of the luminal-open E2P state of the pump which is ready to bind luminal K+. A dynamic pKa correlation analysis reveals the likelihood of proton transfer events within the cation binding pocket. In agreement with in-vitro measurements, we find that E795 is likely to be protonated, and that E820 is at the center of the proton transfer network in the luminal-open E2P state. The acidic residues D942 and D824 are likely to remain protonated, and the proton redistribution occurs predominantly amongst the glutamate residues exposed to the lumen. The analysis also shows that a lower number of K+ ions bind at lower pH, modeled by a higher number of protons in the cation binding pocket, in agreement with the ‘transport stoichiometry variation’ hypothesis.

Clinical significance of P‑class pumps in cancer (Review)

“…The HKA expresses characteristic structural changes once activated, known as E1 and E2 conformations, leading to the transportation of H+ into the lumen while K + is removed and released into the cytoplasm side of the enzyme ( 94 – 96 ). Therefore, when the protein is open to the cytoplasmic side then it is in the E1 phase, when it is open to the extracellular environment then it is in the E2 phase ( 92 ).…”

Modeling MesoBioNano systems with MBN Studio made easy

“…CHARMM (Chemistry at HARvard Macromolecular Mechanics) is the name of a widely used library of force fields that can be used for molecular dynamics as well as the name for the molecular dynamics simulation and analysis package associated with them [50]. The MM form of potential is widely used for the description of the potential energy of biomacromolecules, such as polypeptides, proteins, and DNA [13,[54][55][56][57][58][59][60][61][62]. The same type of potential can also be used to model other liquids, such as for example ethanol, featured in Fig.…”

Syndrome of inappropriate antidiuretic hormone secretion is associated with different proton pump inhibitor use: a pharmacovigilance study

“…Proton pump inhibitors (PPI) block the activity of H + , K + -ATPase in gastric parietal cells and secretion of gastric acid caused by any stimulation [1]. Since the late 1980s when omeprazole entered the clinic, PPIs have been widely used for the treatment of a variety of acidrelated conditions, such as peptic ulcer disease and gastroesophageal reflux disease [2][3][4].…”