Almost everything in the smali language has a direct analogue in dalvik bytecode/dex format. In this case, the .prologue directive corresponds to the DBG_SET_PROLOGUE_END debug opcode that is part of the debug_info_item.
From http://s.android.com/tech/dalvik/dex-format.html:
sets the prologue_end state machine register, indicating that the next position entry that is added should be considered the end of a method prologue (an appropriate place for a method breakpoint). The prologue_end register is cleared by any special (>= 0x0a) opcode.