Dictionary Definition: 

“Transfer a proton to (a molecule, group, or atom) which forms a coordinate bond to the proton.”

Selected from OxfordDictionaries.com

Functional Definition: 

When something is protonated it gains a proton. The idea is simple enough but it relates to the acidity (pH) of the surrounding environment of a molecule. In proteins ionizable groups are protonated and deprotonated as pH rises and falls according to their respective pKa values  Protonated forms of a molecule or functional group are considered acidic forms which the deprotonated form is considered the basic form.