Excess protein gets converted into glucose by the liver then stored as glycogen and/or fat. So the body does store excess protein, just not in a way that allows it to be converted back into protein.
Yes, this business of the protein metabolism in the liver can be very confusing and I've seen this account many times, but it's important to see the difference between protein breakdown (proteolysis) and glucose synthesis (gluconeogenesis) because they are completely different metabolic pathways. If protein gets converted into glucose by the liver, then a diet high in protein would tend to eventually deposit fat, it would be a lipogenic diet. But as Fung, Taubes and others have pointed out, that doesn't generally happen - though it is possible to engineer it to happen. Protein breakdown produces intermediates that can feed into fatty acid metabolism, glucose metabolism, or ketone metabolism. For those interested in the details... and of course, not everyone is even in the slightest bit interested in the details... but for those who are:
The process of protein catalysis involves breaking down the proteins into their individual amino acids, removing the nitrogen through a process called deamination/transamination, to produce a range of breakdown products, none of which can be converted into glucose - their chemistry renders that impossible. Instead, the amino acids enter a cycle of reactions called the Citric Acid cycle. This produces a compound called oxalocitrate which again isn't glucose or directly related to it. The oxalocitrate is converted to something called phosphoenolpyruvate and that enters another distinct pathway in which fructose phosphate is eventually synthesised which is then finally converted to glucose. The conversion has nothing to do with amino acids - phosphoenolpyruvate is simply one of the metabolic products of carbohydrate metabolism. The intermediates in the Citric Acid cycle feed into the production of ketones, fatty acids, and glucose. The amine groups from the amino acids are converted into urea in the urea cycle and will be excreted.
It's complicated, of course, but each of the intermediate chemicals have been isolated and identified and the details of the pathways and how they are controlled are not at all controversial. I'm not aware that anyone challenges this very well-established and evidenced account. In any case, it can be checked up easily enough. The body cannot store proteins nor amino acids. The two energy stores we have are triglycerides and glycogen and that's it. The path from proteins to ketones, fats, and glucose involves the complete degradation of the amino acids into simple substrates and these feed back into very different anabolic pathways. If we misunderstand this, we misunderstand the role of protein in the diet. There are plenty of sources online where we can dig further into the details of all this. Of course, it's rather pedantic to worry about this stuff (and to pick up on it, for which apologies to those irritated by such nerdiness on my part) and as long as we stick to the plan, we should see the results. For me, it's important to avoid the potential confusion about how things work, but for very many people, it really doesn't matter too much, and certainly not at this level of detail.
Good luck and every success to everyone else starting the ND this new year.
