here's some more discussion on this that I thought was interesting. This isn't mine. I'm cutting/pasting from elsewhere.
Bomb calorimetry is how calories in food are determined. A bomb calorimeter measures the amount of heat generated by heating a substance until it is ash and no longer produces heat. A piece of wood has calories by bomb calorimetry. Calories in food have nothing to do with biochemistry. (not sure if this is correct). A calorie is not a calorie or we could eat like termites. About protein; Protein is thermogenic.
Quoting from Preddon-Jones et al., The American Journal of Clinical Nutrition, Volume 87, Issue 5, May 2008, Pages 1558S–1561S, There are 3 areas that contribute:
"1) increased satiety—protein generally increases satiety to a greater extent than carbohydrate or fat and may facilitate a reduction in energy consumption under ad libitum dietary conditions; 2) increased thermogenesis—higher-protein diets are associated with increased thermogenesis, which also influences satiety and augments energy expenditure (in the longer term, increased thermogenesis contributes to the relatively low-energy efficiency of protein); and 3) maintenance or accretion of fat-free mass—in some individuals, a moderately higher protein diet may provide a simulatory effect on muscle protein anabolism, favoring the retention of lean muscle mass while improving metabolic profile."