biostudies-literatureFeghhi TNational Institute of Neurological Disorders and StrokeNINDS NIH HHSNational Institutes of Health5575-5591https://www.ebi.ac.uk/biostudies/studies/S-EPMC8715252biostudies-literatureUnknown120(24)At chemical synapses, synaptic vesicles release their acidic contents into the cleft, leading to the expectation that the cleft should acidify. However, fluorescent pH probes targeted to the cleft of conventional glutamatergic synapses in both fruit flies and mice reveal cleft alkalinization rather than acidification. Here, using a reaction-diffusion scheme, we modeled pH dynamics at the Drosophila neuromuscular junction as glutamate, ATP, and protons (H⁺) were released into the cleft. The model incorporates bicarbonate and phosphate buffering systems as well as plasma membrane calcium-ATPase activity and predicts substantial cleft acidification but only for fractions of a millisecond after neurotransmitter release. Thereafter, the cleft rapidly alkalinizes and remains alkaline Biophysical journalComputational modeling predicts ephemeral acidic microdomains in the glutamatergic synaptic cleft.PMC8715252R01 NS103906NS103906R56 NS103906Feghhi TLau AWCStawarski MKamasawa NHernandez RXThomas CIMacleod GTfalseComputational modeling predicts ephemeral acidic microdomains in the glutamatergic synaptic cleft.At chemical synapses, synaptic vesicles release their acidic contents into the cleft, leading to the expectation that the cleft should acidify. However, fluorescent pH probes targeted to the cleft of conventional glutamatergic synapses in both fruit flies and mice reveal cleft alkalinization rather than acidification. Here, using a reaction-diffusion scheme, we modeled pH dynamics at the Drosophila neuromuscular junction as glutamate, ATP, and protons (H⁺) were released into the cleft. The model incorporates bicarbonate and phosphate buffering systems as well as plasma membrane calcium-ATPase activity and predicts substantial cleft acidification but only for fractions of a millisecond after neurotransmitter release. Thereafter, the cleft rapidly alkalinizes and remains alkaline 2021-01-01T00:00:00Z2021 Dec2025-04-05T08:47:39.166Z2025-04-05T08:47:39.166ZS-EPMC87152523477450310.1016/j.bpj.2021.11.011