A January 2012 JAMA study reports that people eating 40% more calories than they expended for eight weeks gained the same amount of body fat regardless whether they ate protein at 5% (low protein), 15% (normal protein), or 25% (high protein) of calories.

But the amount of lean (muscle) weight gain (and thus total weight gain) and resting energy expenditure were influenced by the amount of protein eaten.

The weight gain in the low protein diet group was 3.16 kg, about half that of the other 2 groups (normal protein diet: 6.05 kg; high protein diet: 6.51 kg; P = .002). The rate of weight gain in the low protein diet group was significantly less than in the other 2 groups (P < .001). The failure to increase lean body mass in the low protein group accounted for their smaller weight gain [emphasis added]. …

Resting energy expenditure, total energy expenditure, and body protein did not increase during overfeeding with the low protein diet. In contrast, resting energy expenditure … and body protein (lean body mass) … increased significantly with the normal and high protein diets.

Weirdly, although all excess calories were fed as fat and were equal in all groups, and although all groups gained the same amount (3.51 kg) of body fat, the authors state that the low-protein group stored more than 90% of the extra calories as fat, while the normal- and high-protein diet groups stored about 50% of the excess calories as fat.

There were no significant differences between energy intake and energy expenditure between the 3 diets. We can account for all excess energy consumed through energy stored in fat and in protein or expended in higher total energy.  With the low protein diet, more than 90% of the extra energy was stored as fat.

With the normal and high protein diets, only about 50% of the excess energy was stored as fat with most of the rest consumed (thermogenesis). The high total energy expenditure probably reflects the higher cost of protein turnover and storage.

What accounts for the increased energy expenditure in the normal- and high-protein groups? The work of building extra muscle mass.

Resting energy expenditure responded differently to low vs high protein intake. Neither resting energy expenditure, nor lean body mass increased in the low protein group. In contrast, the accretion of lean body mass in the normal and high protein groups was the principal contributor to the increase in resting energy expenditure [emphasis added].

Two important conclusions of this study:

Extra energy intake [calories] predicted both the increase in lean body mass and body fat. In contrast, protein intake predicted the increase in lean body mass, but not the change in fat storage.

Calories alone … contributed to the increase in body fat. In contrast, protein contributed to the changes in energy expenditure and lean body mass, but not to the increase in body fat.

Author George Bray, MD, talks about the study in this video.

Bray GA et al. Effect of Dietary Protein Content on Weight Gain, Energy Expenditure, and Body Composition During Overeating. JAMA. 2012;307(1):47-55. doi: 10.1001/jama.2011.1918