Understanding protein

Understanding protein

A few considerations about Protein from a nutritionist perspective:

Contrary to popular belief, the bioavailability of protein is not just about the presence of the essential amino acids in a food and how they relate to the body’s requirements. It's also dictated by the structure of the protein and cofactors. Some proteins are more easily broken down (digested) and used than others.  To better understand let’s consider the structure of proteins, how proteins are assembled from amino acids and the various shapes those proteins take.

Roughly 500 amino acids have been identified in nature, but just 20 amino acids make up the proteins found in the human body. Let's learn about all these 20 amino acids and the types of different amino acids. Each amino acid has an α-carboxyl group, a primary α-amino group, and a side chain called the R group. Each and every protein is made from these amino acids appearing in varying order and in varying amounts and combinations, thus providing the possibility of almost limitless combinations. That said, most proteins are large molecules that may contain several hundred to many thousand amino acids arranged in branches and chains.

The assembly of amino acids into proteins is actually determined and directed by information encoded in your genes. Each protein has its own unique amino acid sequence as specified by the gene encoding that particular protein. Protein synthesis takes place inside cellular cytoplasm and can achieve the synthesis of 20 amino acids per second in a given cell. In fact, the assembly of amino acids is responsible for more than just the creation of protein. It is also responsible for the creation of peptides and polypeptides, which can be thought of as "short" or "incomplete" proteins. Polypeptides, and peptides chains have multiple amino acids, as do protein.  However, the term protein, usually applies to a complete, longer chain of biological molecules in a stable structure.

The size of a synthesized protein can be measured by the number of amino acids it contains and by its total molecular mass. Some proteins may contain just a few hundred amino acids strung together, but the largest can contain close to 30,000 amino acids all chained together.

Structure is important for stability. A chain of 30,000 amino acids for example achieves stability through its structure. These long chains fold in on themselves to form stable structures. A protein can also be identified by its structure.  The primary structure is comprised of a linear chain of amino acids called a polypeptide chain, and its structure is defined by sequence of the amino acids. Every protein has at least a primary, secondary and tertiary structure.  (The secondary structure relates to the spatial arrangement of a polypeptides main chain- the backbone, and the tertiary structure is the three dimensional structure of the whole peptide chain.) Most proteins fold into unique 3-dimensional structures. Some proteins even have quaternary structure.

The shape into which a protein naturally folds is known as its native state, although proteins may shift between several related structures during the course of performing their biological functions.

Structures typically related to the function of the protein in the human body. And, bringing us back to our initial point, protein structure plays a major role in determining how readily it can be broken down into its constituent amino acids during the digestive process. In other words, the structure of a protein plays a major role in determining the bioavailability of the protein (and also its inclination to elicit allergic responses).

Amino acids are further classified into 3 groups depending on the structure of the R-group—neutral, acidic, and basic.

Types of amino acids and their relevance to nutrition:

Nutritionally, amino acids are divided into 3 groups—essential, nonessential, and semi-essential. Semi-essential amino acids are synthesized by the body but are designated essential during periods of stress. 

Nine amino acids, including histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine, are classified as essential amino acids because they cannot be synthesized by human or other mammalian cells. Therefore, these amino acids must be supplied from your diet. Non-essential amino acids not primarily derived from the diet are synthesized by the body. Semi-essential amino acids are growth-promoting amino acids. They are essential in children, pregnant women, and lactating women, because they are required for growth. In addition to serving as the building block of proteins and peptides, amino acids play crucial roles in various important functions.

Protein digestion:

The majority of dietary proteins are fully degraded and absorbed in the small intestine: after a meal, proteins are denatured by acid and hydrolyzed by gastric pepsin in the stomach, further hydrolyzed by pancreatic proteases, subsequently degraded by small intestinal enterocyte membrane exopeptidases and absorbed across the small intestinal enterocytes into the bloodstream as individual AA for use in the body.

What you eat protein with, affects its bio-availablity:

Naturally protein doesn’t typically exist on its own.  Whether from animal or vegetable sources, protein usually is found imbedded in or alongside various fats or carbohydrates. The presence of these compounds can affect the digestibility of the protein. For example, some accompanying nutrients can inhibit proteolytic enzymes that would normally break down the protein, or can suppress the release of stomach acid necessary for the digestion of the protein, or simply cover the protein so that enzymes and stomach acid cannot reach it.

Individual differences:  You can impact your ability to digest protein.

Who is eating the protein, can affect its ability to be used or digested!

Beyond variations in basic protein requirements, consumers vary in their ability to digest protein, particularly across disease states. Host proteolytic capacity depends on a number of facets of gut health and function, including the concentration and activity of endogenous luminal proteases (partially determined by certain gastrointestinal hormones such as gastrin and cholecystokinin (CCK)) and brush border peptidases, luminal pH and transit time. Across conditions, variations in these factors lead to differences in overall proteolytic capacity. Lowered protein digestion can be observed with techniques beyond traditional protein digestibility measurements such as examining the residual peptides, microbiota, microbial metabolites and protein biomarkers.

Protein malabsorption has been observed or supposed in different situations such as bariatric surgery, short bowel syndrome (SBS), pancreatic insufficiency, inflammatory bowel disease (IBD) and environmental enteric dysfunctions (EED).

Chemical and physical structure affect digestibility:

Dietary proteins vary greatly in their susceptibility to digestive processes in the human gut due to size, charge, AA sequence, tertiary structure and post-translational modifications, especially glycosylation and phosphorylation.

In normal physiological conditions, when digestive capacities are not impaired, the main determinant of digestive bioavailability is the nature of the protein as well as the food matrix in which it is incorporated – protein isolates being generally more digestible than proteins in their crude matrices.

Optimise protein bioavailability to optimize nutrition:

Proteins differ in their digestibility and consumers differ in their ability to digest, particularly across disease state. Incomplete protein digestion stimulates the growth of putrefactive colonic microbes and the production of toxic metabolites. Therefore, it is clear that the future of optimizing nutrition must include monitoring individual protein digestive capacity, especially in diseases that reduce digestive capacity.

Protein bioavailability is affected by the sum of three factors:

1. The combination of amino acids in the protein ingested (or in the combination of proteins eaten during the day). The shortage of an essential amino acid provides a limiting factor on how much of the overall protein can be utilized by the body.

2. The structure and size of the protein molecule. The larger and more tightly folded the molecule, the less able the body is to break it down. Large proteins that frequently undergo incomplete digestion include those found in wheat, corn, dairy, and soy. (Wheat, dairy and soy are also among the top allergy foods.)

3. The other foods (or components in the protein source itself) that inhibit the breakdown of the protein.

4. Support digestion when there are specific diseases that may affect protein digestion. (Such as in the case of inflammatory bowel diseases or Chronic malnutrition which may reduce protein degradation. A few disorders, including chronic pancreatitis and cystic fibrosis, can cause near complete loss of pancreatic enzymes. Medications such as antacids, proton pump inhibitors and H2 blockers reduce gastric acidity and may negatively impact protein digestion.)

Protein utilization can be measured

There are several tests for measuring protein utilization, or bioavailability, although they're a bit like the story of the blind men describing an elephant -- each one gives an incomplete picture. The blind man who feels the trunk says an elephant is like a snake. The one who feels its legs says an elephant is like a tree. The one who feels the ears says an elephant is like a giant fan. And the one who feels its body says an elephant is like a massive wall. Each one provides useful information; but each one also provides an incomplete picture.  It’s best to consider all together:

The Kjeldahl method is the standard for measuring the total protein concentration in food. It provides the number that you normally see on nutrition labels on the side of food packages. Unfortunately, it tells you nothing about how much of that protein is actually available or utilised by the body.  

Biological value (BV) measures how much of the protein that you eat gets incorporated into your body tissue. It does so by measuring how much of the nitrogen in the protein you eat is absorbed by the body and then how much is excreted. The assumption is that the difference is what got incorporated into your body protein. Its weakness is that BV varies greatly depending on how food is prepared and according to what other foods were eaten in the recent diet that can alter nitrogen measurements. Although the following three methods all provide better measures of protein utilization, BV is still commonly used by nutritionists out of force of habit.

Net protein utilization (NPU) is the ratio of amino acids converted to proteins to the ratio of amino acids supplied in the protein source. Experimentally, this value is calculated by determining the amount of dietary protein you are consuming and then measuring how much nitrogen is excreted. It is significantly affected by the limiting amino acids (as discussed earlier) in the particular food.

Protein Efficiency Ratio (PER) is based on the weight gain of a test subject divided by its intake of a particular food protein during the test period. Theoretically, it is a biological assay of the quality of a particular protein, measured as the gain in weight of an animal per gram of a particular protein eaten.  At one time, this was the industry standard, but unfortunately PER is based upon the amino acid requirements of growing rats, which differ noticeably from that of humans.

Protein digestibility corrected amino acid score (PDCAAS) evaluates protein quality based on the amino acid requirements of humans. This is now the preferred standard. Nevertheless, it too has holes.

1. PDCAAS takes no account of where proteins have been digested and cannot account for proteins that are absorbed by bacteria in the digestive tract.

2. PDCAAS is calculated solely on the basis of single protein consumption and therefore once again does not calculate the changes in protein utilization resulting from the intake of complementary protein sources.

Digestible Indispensable Amino Acid Score (DIAAS). In this context, digestibility of each indispensable amino acid (IAA) must be measured at the ileal level because absorption occurs in the small intestine. Amino acids reaching the large intestine are fermented, and molecules are partly transformed into either other amino acids or metabolites that can be absorbed at the colon level, such as ammonia or indoles for nitrogen molecules, or H2S, phenol and branched-chain fatty acids for nonnitrogenous compounds.

On an individual basis, monitoring the diet for the optimal amount of protein is challenging. Therefore, tests for markers of gut putrefaction could aid individuals in controlling their daily protein intake.

Improving protein utilization for optimum health

One key idea to take away from all this is:

Consume more than one type of protein, and consider how the components of the meal may be improving or detracting from its nutrition availability.

When a protein is highly digestible, all individuals display a great capacity to digest the protein, but when the protein is less digestible some of them have a great capacity to digest it while others have a low capacity.

Protein digestibility varies depending on the source, and the digestibility of animal proteins (meat and dairy proteins) is higher (typically >90%) than that of plant proteins (70–90%).

As we've discussed, protein utilization is defined, to a large degree, by the protein consumed in the diet, not just the type but how or specifically what it is consumed with. Even complete proteins (those containing all of the essential amino acids) can still be out of balance and may not achieve maximum utilisation (this is because some amino acids compete with each other for receptor sites). Although dairy and egg tend to be well balanced and therefore offer a high amino acid yield, they also are amongst the high allergy foods group. Meat, chicken, and fish, on the other hand, are usually higher in select amino acids, and benefit from the consumption of other proteins and cofactors to achieve optimal utilisation and protein balance. The same is true of soy and other vegetable protein sources.

For example… eating rice and legumes will give you a complete protein (all the essential amino acids).

Ingesting vitamin B6 helps you maximize the value of your protein. It helps your digestive enzymes do their job to break down proteins and transport the resulting amino acids to the bloodstream.

Some individuals may first need to control intestinal inflammation through consumption of extensively hydrolyzed protein.

Cooking can make protein more digestible. Moderate temperature and short times typically denature proteins and deactivate anti-nutritional factors, which increases their digestibility. With each processing step that involves heat, the degree of denaturation and chemical modifications (hence, changes to digestibility) depend on the temperature, heating time and moisture content. Even when these variables are constant, these effects vary with protein source.  (Note, Too high temperature, and other factors like maillard reaction can negatively impact nutrition.)

In some instances taking digestive enzymes or hormones can be helpful or necessary.

And remember more, is not necessarily better.  Keep your protein intake moderate and varied in order to keep it optimal.

References:

Lopez MJ, Mohiuddin SS. Biochemistry, Essential Amino Acids. [Updated 2024 Apr 30]. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2024 Jan-. Available from: https://www.ncbi.nlm.nih.gov/books/NBK557845/

Hoffman, J. R., & Falvo, M. J. (2004). Protein - Which is Best?. Journal of sports science & medicine, 3(3), 118–130.

Image source: https://www.compoundchem.com/2014/09/16/aminoacids/

Dallas, D. C., Sanctuary, M. R., Qu, Y., Khajavi, S. H., Van Zandt, A. E., Dyandra, M., Frese, S. A., Barile, D., & German, J. B. (2017). Personalizing protein nourishment. Critical reviews in food science and nutrition, 57(15), 3313–3331. https://doi.org/10.1080/10408398.2015.1117412

Gaudichon, C., & Calvez, J. (2021). Determinants of amino acid bioavailability from ingested protein in relation to gut health. Current opinion in clinical nutrition and metabolic care, 24(1), 55–61. https://doi.org/10.1097/MCO.0000000000000708