Assuming that our measurements on two sets of distinct di- and tri-peptides reflect the stoichiometries in general, our new data add to our previous multiple binding mode model by showing that tri-peptides are transported using three protons, whereas di-peptides are transported using four or possibly even five protons per cycle.
The cluster formation can be characterized by means of equilibrium thermodynamics, applying a multiple-binding model, which allows for structural preformation.
One obvious elaboration is to model multiple binding events in a region.
Conventional motif analysis or a more elaborate model including multiple binding sites might expose the protein-protein interactions, however.
The NEXT-peak program also provides a goodness-of-fit test, automating screening of the spurious binding, and work is in progress to extend its model to locate multiple binding events in a region.
Kalo and coworkers found that many tyrosine residues could be phosphorylated in the EphB2 cytoplasmic domain in retina tissue and 293 cells, including tyrosines 605, 611, 668, 789, and 939 (30), suggesting a model in which multiple binding sites and signaling pathways may act downstream of activated Eph receptors.
However, the inferior potency of neonicotinoids at the vertebrate nAChR model is attributable to multiple binding conformations conflicting in the agonist-binding pocket.
This model suggests the existence of multiple binding sites in these enzymes.
The pinpointing step based on tag-profile modeling does improve the resolution for detecting both single and multiple binding sites.
Likewise, multiple binding events in a region R r cause deviations from the unimodal density of the model.
On the other hand, Hidden Markov Models, which can be thought of as one dimensional statistical mechanics models of multiple proteins binding on DNA, have been applied to study multiple binding sites for protein complexes in a stretch of DNA [ 38, 39].
