Dietary protein does not become body fat if you are on a low carbohydrate diet

By definition LC is about dietary carbohydrate restriction. If you are reducing carbohydrates, your proportional intake of protein or fat, or both, will go up. While I don’t think there is anything wrong with a high fat diet, it seems to me that the true advantage of LC may be in how protein is allocated, which seems to contribute to a better body composition.

LC with more animal protein and less fat makes particularly good sense to me. Eating a variety of unprocessed animal foods, as opposed to only muscle meat from grain-fed cattle, will get you that. In simple terms, LC with more protein, achieved in a natural way with unprocessed foods, means more of the following in one's diet: lean meats, seafood and vegetables. Possibly with lean meats and seafood making up more than half of one’s protein intake. Generally speaking, large predatory fish species (e.g., various shark species, including dogfish) are better avoided to reduce exposure to toxic metals.

Organ meats such as beef liver are also high in protein and low in fat, but should be consumed in moderation due to the risk of hypervitaminosis; particularly hypervitaminosis A. Our ancestors ate the animal whole, and organ mass makes up about 10-20 percent of total mass in ruminants. Eating organ meats once a week places you approximately within that range.

In LC liver glycogen is regularly depleted, so the amino acids resulting from the digestion of protein will be primarily used to replenish liver glycogen, to replenish the albumin pool, for oxidation, and various other processes (e.g., tissue repair, hormone production). If you do some moderate weight training, some of those amino acids will be used for muscle growth.

In this sense, the true “metabolic advantage” of LC, so to speak, comes from protein and not fat. “Calories in” still counts, but you get better allocation of nutrients. Moreover, in LC, the calorie value of protein goes down a bit, because your body is using it as a “jack of all trades”, and thus in a less efficient way. This renders protein the least calorie-dense macronutrient, yielding fewer calories per gram than carbohydrates; and significantly fewer calories per gram when compared with dietary fat and alcohol.

Dietary fat is easily stored as body fat after digestion. In LC, it is difficult for the body to store amino acids as body fat. The only path would be conversion to glucose and uptake by body fat cells, but in LC the liver will typically be starving and want all the extra glucose for itself, so that it can feed its ultimate master – the brain. The liver glycogen depletion induced by LC creates a hormonal mix that places the body in fat release mode, making it difficult for fat cells to take up glucose via the GLUT4 transporter protein.

Excess amino acids are oxidized for energy. This may be why many people feel a slight surge of energy after a high-protein meal. (A related effect is associated with alcohol consumption, which is often masked by the relaxing effect also associated with alcohol consumption.) Amino acid oxidation is not associated with cancer. Neither is fat oxidation. But glucose oxidation is; this is known as the Warburg effect.
A high-protein LC approach will not work very well for athletes who deplete major amounts of muscle glycogen as part of their daily training regimens. These folks will invariably need more carbohydrates to keep their performance levels up. Ultimately this is a numbers game. The protein-to-glucose conversion rate is about 2-to-1. If an athlete depletes 300 g of muscle glycogen per day, he or she will need about 600 g of protein to replenish that based only on protein. This is too high an intake of protein by any standard.

A recreational exerciser who depletes 60 g of glycogen 3 times per week can easily replenish that muscle glycogen with dietary protein. Someone who exercises with weights for 40 minutes 3 times per week will deplete about that much glycogen each time. Contrary to popular belief, muscle glycogen is only minimally replenished postprandially (i.e., after meals) based on dietary sources. Liver glycogen replenishment is prioritized postprandially. Muscle glycogen is replenished over several days, primarily based on liver glycogen. It is one fast-filling tank replenishing another slow-filling one.

Recreational exercisers who are normoglycemic and who do LC intermittently tend to increase the size of their liver glycogen tank over time, via compensatory adaptation, and also use more fat (and ketones, which are byproducts of fat metabolism) as sources of energy. Somewhat paradoxically, these folks benefit from regular high carbohydrate intake days (e.g., once a week, or on exercise days), since their liver glycogen tanks will typically store more glycogen. If they keep their liver and muscle glycogen tanks half empty all the time, compensatory adaptation suggests that both their liver and muscle glycogen tanks will over time become smaller, and that their muscles will store more fat.

One way or another, with the exception of those with major liver insulin resistance, dietary protein does not become body fat if you are on a LC diet.