Protein

Protein is a consumable item which can be purchased from each Region's League, or traded for Berries with the Berry Master of each region from Johto onwards. It can be fed to a Pokémon to increase the amount of attack that Pokémon gains by 1 per protein per hatch. Each Pokémon can consume a total of 5 proteins per unlocked region.

How to Use
Go to Start Menu > Items > Item Bag, select the protein and select a Pokémon to use it on. Once used, the effect is permanent and cannot be removed by any means.

New Efficiency
Below is a list of the most efficient Pokémon to breed after they have been fed the max amount of proteins for that region unlock. The first table for each region ignores non-native damage reduction and event Pokémon. The second (collapsed) table takes those into account and is suggested for use at the beginning of a new region. Breeding efficiency is determined by the following formula:

$$\text{Egg Cycles} = \frac{\text{Egg Steps}}{40}$$

$$\text{Breeding Efficiency} = \frac{0.25 \times \text{Base Attack} + \text{Proteins Used}}{\text{Egg Cycles}} $$

Kalos
=Price=

When bought from the Indigo Plateau / Pokémon League, the price for Protein rises irreversibly, similar to Masterballs. It starts off at 10,000, increments by a factor of 1.1 every purchase, and caps at 1,000,000 after 49 purchases.