Direct phosphorylation of the GluR1 subunit of postsynaptic AMPA receptors by Ca(2+)/calmodulin-dependent protein kinase II (CaM-KII) is believed to be one of the major contributors to the enhanced strength of glutamatergic synapses in CA1 area of hippocampus during long-term potentiation. The molecular mechanism of AMPA receptor regulation by CaM-KII is examined here by a novel approach, silence analysis, which is independent of previously used variance analysis. I show that three fundamental channel properties-single-channel conductance, channel open probability, and the number of functional channels-can be measured in an alternative way, by analyzing the probability of channels to be simultaneously closed (silent). Validity of the approach was confirmed by modeling, and silence analysis was applied then to the GluR1 AMPA receptor mutated at S831, the site phosphorylated by CaM-KII during long-term potentiation. Silence analysis indicates that a negative charge at S831 is a critical determinant for the enhanced channel function as a charge carrier. Silence and variance analyses, when applied to the same sets of data, were in agreement on the receptor regulation upon mutations. These results provide independent evidences for the mechanism of AMPA receptor regulation by CaM-KII and further strengthens the idea how calcium-dependent phosphorylation of AMPA receptors can contribute to the plasticity at central glutamatergic synapses.