Protein Cycling Diet: 11

Designing the Diet



Chapter 11
Describes the diet in terms of cytoplasm replacement rates and their implications for counter-acting protein aggregate accumulation.

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Designing the Diet

With the goal of preventing or delaying neurodegenerative diseases by promotion of autophagy, we now must design a suitable diet plan. For this, certain questions must be answered: how much protein restriction is necessary and for how long and how often.

For the first question, how much protein restriction is necessary, the reasonable answer is that calories from protein as delivered to the bloodstream must be reduced to less than what the body normally needs for its own protein synthesis needs, namely 4% of total calories. When that level is achieved, the cells must then perform autophagy to obtain the amino acids they need to carry on.

Ideally most of the protein in your normal diet should be replaced by starches rather than by sugars or fats. Both proteins and starches are long polymers that take time to digest in a time-release manner so to speak. Sugars on the other hand digest very quickly and are more disruptive to your metabolism as a result. Likewise changing the balance of fat to non-fat can be disruptive as well. Realistically though, you will likely find it more practical to increase fat and sugar during periods of protein restriction. If these periods are of short duration, it should hardly matter. We will talk more specifically on this subject in later chapters in more detail.

For the second question, how long should a period of protein restriction last, we can consider the results of two areas of study. In free cell culture, starvation autophagy begins within two hours following transfer to a medium lacking in amino acids. And as will be discussed in the next chapter, there is a form of the Calorie Restriction diet where the dieter alternates days of fasting and eating. In both humans and mice this regime produces the benefits of the other forms of calorie restriction which are proposed to result from autophagy promotion. It is then reasonable to conclude that a single day of near total protein restriction is sufficient to initiate starvation autophagy.

The final question is how often should protein restriction be practiced. The answer to that is a little more involved.

First we must consider what the purpose of promoting autophagy is. It is to clear the cell of degraded and aggregated proteins that are not being handled by the other recycling mechanisms of the cell. To prevent the accumulation we must clear them at a least the same rate as they are produced. We do not really know the production rate of these aggregates but we can infer them from the known usual courses of the diseases we are trying to forestall.

We can calculate the rate of clearing by autophagy from certain known values. We know a 70,000g (154lb) male requires about 25g of protein per day to meet his own protein synthesis needs. Perhaps the body conserves a bit when protein is restricted so, to be conservative as well, we will say 20g of protein is the minimum. We know that cell contents account for about 2/3 of body weight*. We know that the body is about 17% protein and 17% fat by weight. 70,000g x 17% x 2/3 = 8000g of cell protein. When autophagy is induced by protein starvation, at least 20g per day of protein must then be recycled. 20g/8000g = 0.25% per day recycled. As long as that value exceeds the rate of accumulation of aggregates, a neurodegenerative disease produced by those aggregates can in theory be prevented.

Measured values for cytoplasm recycling by autophagy are actually much larger than 0.25% per event. When mouse cancer cells are deprived of amino acids for 2 hours, 2% of the cytoplasm is seen to be recycled30. Of course we are concerned about the value in human neurons which could be much smaller. So we will stick with the 0.25% value. Even then it may be that some other tissue such as muscle is preferentially sacrificed to provide amino acids to the brain, and thus the real value could be less. 0.25% is only an educated guess.

Late-onset AD with 26.6 million sufferers worldwide in 2006 tops the list of diseases we would want to prevent. The numbers for AD are clouded by historical and cultural factors but, nevertheless, its real incidence rate seems to be rising over the decades. For the common non-genetic form, about 3 people per thousand will develop it in their 65 th year. For every five to six years thereafter, the risk of acquiring the disease approximately doubles. From onset to death takes about 7 years on average. After age 90 the incidence may even decline.

Fig. 7

Lewy-body associated diseases including PD are next with about 8 million sufferers worldwide extrapolating from North American values.

The other recognized neurodegenerative diseases: prion diseases, frontotemporal dementia, Pick’s disease, progressive supranumeral palsy, ALS, HD, and spinocerebrellar ataxias altogether account for only around 800,000 cases worldwide by extrapolation from North American values. Compared to AD and PD, they may be of small concern. In many cases, however, the cause is genetic and people know they are at risk or even are certain of developing them should they live long enough.

First we shall look at AD. If the disease in fact results from an accumulation of aggregated proteins, what can we infer about the rate of the accumulation?

The simplest model assumes a steady rate accumulation over a life-time. When the accumulation reaches some threshold value, the disease manifests. When the accumulation reaches a second threshold, death occurs. Variation in age of onset is then due to personal variation in rate of accumulation and most people do not live long enough to reach this threshold..

Fig. 8

Applying this model to AD, we infer a worst case maximum increase of 1/65 of the manifest threshold per year or (1/65)/365=0.0042%. To delay the disease indefinitely, we must replace at least 1/65 of our cytoplasm year or (1/65)/365=0.0042% per day. Since autophagy replaces 0.25% per day, the minimum number of days in the year where protein should be restricted is (0.0042%/0.25%)*365days = 6.2 days.

The following illustrates what might happen when more intensive protein cycling is used against an aggregating protein that reaches its manifest threshold at age 50.

Fig. 9

If at age 30 protein cycling is initiated at a 50% cytoplasmic replacement rate per decade, by age 40, the accumulation is knocked back to the same level as at age 20. We can break this down into two processes. In the decade after initiation the existing aggregate is cut down by half, the equivalent of 15 years of accumulation. At the same time, 10 years of new aggregate is added at half its normal rate resulting in 5 years of accumulation. 15 plus 5 is 20.

Since autophagy replaces 0.25% per day, one might think we could calculate the number of days per year of protein fasting required as days = (50%/decade / 0.25%/day) = 200 days/decade=20 days/year. The error in such a calculation, of course, is that each autophagy event consumes not just old cytoplasm, but also some fraction of the new cytoplasm that replaced what was lost in previous autophagy episodes. I will give the correct calculations in a table below after discussion of some other models of aggregate accumulation that imply a much larger number than just 20 days a year of protein restriction.

Next we will consider a slightly more complex model where the aggregate protein is again produced at a constant rate, but the cell employs a mechanism to recycle the aggregate. As long as the recycling rate exceed the production rate, no accumulation occurs. However, in this model over time, the protein cycling mechanism of the cell declines and aggregate accumulation eventually begins. As the recycling capacity decays, the net rate of production minus recycling grows.

Fig. 10

In this example we have the recycling capability declining by half every 20 years. As long as the rate of recycling is greater than the rate of accumulation of aggregate, no accumulation occurs. At the point where the rates are equal, accumulation begins and accelerates towards but never exceeds its constant rate of production.

In the next model we consider what happens when the rate of aggregate protein production is not constant but increasing with time. This is what would be expected with the protein mis-folding theory of degenerative diseases discussed in previous chapters where the accumulation of aggregate protein itself causes its production rate to increase. This is a true exponential increase.

Fig. 11

The 1x line represents the aggregate accumulating at a constant rate. For the 10y line, the rate doubles every decade. For the 5y line, the accumulation rate doubles every 5 years. . Likewise the 2.5y and the 1.25y lines double every 2.5 and 1.25 years respectively.

This model overcomes one of the problems with the other models, the relatively small difference between the level of aggregate at which the disease manifests and the level at which the disease proves lethal.

When a new drug is developed, two dose levels are determined: the therapeutic dose and the LD50 dose. The therapeutic dose is the level where the benefits of the drug manifest. The LD50 dose is the level where 50% of the test subjects die. Usually there is more than a ten-fold difference between the two values. neurodegenerative diseases generally manifest about a decade before death. In this chart, if 100% is the death threshold at age 50 then 80% is the manifest level at age 40 with the 1x constant increase model. Rarely would the therapeutic dose of a drug be as large as 80% of the LD50. If the aggregate follows similar dynamics as a drug, it would seem doubtful that the constant production 1x model really applies.

With the 10y doubling, the difference between the onset and lethal levels is a more reasonable 2 to 1 for an onset at age 40 in the chart above. Likewise with the 2.5y doubling, the difference is a quite reasonable 10+ to 1. With the 1.25y line, on the other hand, it seems like onset would be more likely around 45 than 40.

The problem with doubling is that there first has to be something to double. We cannot start at zero. In the self-catalyzing protein mis-folding model, there is an initial spontaneous mis-folding or mis-foldings that forms the nucleus to catalyze further future mis-foldings. The question then arises as to whether the number of protein molecules that must mis-fold on their own without ‘direction’ from other mis-folded proteins of the same species is a reasonable number.

A typical nerve cell in the brain has about a 30 micrometer diameter. Such a cell might have around a thousand separate species of proteins. Calculating roughly**, each species on average would have about a billion (10^9) protein molecules of its type. If a single protein molecule mis-folded at age zero and was capable of causing one other of its brethren to mis-fold similarly every 2.5 years, in 75 years, nearly 100% of the billion molecules of that type could be mis-folded. A similar result happens with a doubling every 2 years in 60 years or every 1 year in 30 years. Such is the power of exponential growth.

So it seems that the exponential model of aggregate accumulation passes the test and well approximates the actual dynamics of the neurodegenerative diseases. Unfortunately, this model implies a much higher accumulation rate than the previously discussed models, as much as a doubling every 2.5 years. A successful response would have to diminish aggregate at nearly the same rate. The following table shows the rates to be expected from various protein cycling regimes:

Estimated Annual Cytoplasm % Replacement with Various Protein Cycling Regimes***

Years 1/week 2/week 3/week 3.5/wk 4/week 3/month 5/month 7/month
1 12 23 32 37 41 09 14 19
2 23 41 54 60 65 16 26 34
2.5 28 48 62 68 73 20 0.31 41
5 48 73 86 90 93 36 53 65
10 73 93 98 99 99 59 78 88

Table 4

From the table we can see that 3 days a week of protein restriction would be sufficient to counteract an exponential accumulation that doubles every 2.5 years. This then is my most recommended regime: three 24 hour periods each week where very little protein is consumed.

Of course it is not necessary to match or exceed the rate of aggregate accumulation since a lower rate, though not preventing disease development, can delay its onset past the expected date of death from other natural causes.

It is not necessary to align the periods with day boundaries. One could say restrict protein from Saturday evening through Sunday afternoon, Monday evening through Tuesday afternoon, and Wednesday evening through Thursday afternoon every week.

Nor is it necessary to stick tightly to the schedule as long as, over time, the necessary numbers are achieved. If, for example, a social eating event came up on a scheduled no-protein period, one could just shift the period a few hours to accommodate the event.

Since the protein cycling diet is is a life-long commitment, it needs to be as unobtrusive as possible. The remainder of the book will deal with ways to achieve this goal without turning your life completely upside down.

Note that after neurological disease symptoms appear, it may be too late to prevent further disease progression since the doubling rate may conceivably already exceed the maximum halving rate obtainable with protein cycling. If you are at particularly high risk of a neurodegenerative disease, you should commence protein cycling as soon as practical if you believe and intend to use it.

If you already have a neurological disease, you should be under the care of a physician and should clear with him or her before undertaking protein cycling, ADCR or any other diet.



Excluding blood (unnucleated cells), lymph and dead skin and hair


(30um^3)/(2*10^-6) ≈ vol of cell in (cc = ml) ≈ 1.35*10^-6grams. 17% of 1.35*10^-6g = 2.3*10^-7g protein/cell. ~110 daltons/amino acid * ~1000 amino acids/ protein molecule = 110000g/Avogadro’s number of molecules = 110000/6.023*10^23 =1.83*10^-19g/molecule. (2.3*10^-7g protein/cell) / (1.83*10^-19g/molecule) = 1.26*10^12 molecules protein/cell. 1.26*10^12/ 1000 species = 1.26*10^9 molecules protein/ species/ cell.


=100*(1-((8000g-20g)/8000g)^(years*((days/week)*52))) 8000g=(17%*70kg lean man)*(2/3)

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