Abstract for non-specialists.

This theory proposes that biological aging is driven by the thermodynamic transition of proteins from high-energy states to a rigid, structural minimum. Newly synthesized proteins possess the significant potential energy and flexibility required to perform essential cellular functions. However, as these proteins operate, they transfer their energy into the broader, organized proteome, which acts as a heat sink or refrigerator. This process causes the entire system to become increasingly structured and inflexible, eventually stripping the proteins of their functional capabilities. Consequently, the body loses its vitality over time because the energy necessary for life is absorbed by an increasingly static cellular environment.

Introduction.

This text is based on experimental results. All conclusions were drawn from the interpretation of previously obtained data on normal human cells and the corresponding macromolecules used to improve cellular function. Therefore, the protocol described below as point 5 has been tested, validated, and continually refined. This is not an idea, not a hypothesis; it is a working clinical approach. In a word: it works.

The classic and most natural view of aging is loss of function. Loss of function, loss of somatic identity, is always mentally and logically linked to a damaged biological unit. This could be a macromolecule, DNA, or protein; it could be a higher-level unit, such as a cellular organelle (proteasome, mitochondria, membraneless organelle, etc.), or it could be an organ or even an organism. The organism is the most beloved unit/target of all doctors, both in the US and in Russia. Doctors don't believe in silly molecular mechanics; that's "reductionism." They dream of organisms, but each organism ages individually, and... In short, we're all going to die. Incidentally, the key words in the emotional passage above are "believe" and "dream," not practical, methodological, or experimental approaches to solving the problem of aging.

Let's get back to the topic. So, the obvious way to mitigate the effects of aging is to stimulate cell, tissue, and organ renewal. Ultimately, to renew the body.

I will try to challenge this dogma: do we really need "...regulation of cell renewal processes in the body as the basis for long-term maintenance of the functional activity of organs and tissues?"

According to the latest data on protein half-life, the average half-life of mitochondrial proteins, even in the brain, is few weeks (Fornasiero et al., 2018).

Almost all proteins in the ovaries of mice are replaced within 6 months. This estimate was obtained after labeling the animals with the isotope 15N and then consuming a normal, unlabeled diet for 6 months (Bomba-Warczak, 2024). Certainly, there are proteins that retain the 15N label after 6 months. Nuclear pore proteins, for example. But collagen was not among them. Collagen was completely replaced in the ovaries after 6 months. The ovaries are so-called parenchymatous organs, and collagen is a ubiquitous structural component of this organ. Collagen is found outside the organ, inside, and even within cells. However, it was completely replaced quite quickly. Therefore, I strongly recommend forgetting about collagen cross-links; there are no cross-links in a protein with a high turnover rate.

Based on this, it can be concluded that all parenchymatous organs are completely renewed at the protein level within 6 months.

Figure 1. A schematic energy landscape for protein folding. The energy of the protein chain is represented by the deepness of the wells, and the configurational entropy of the states is represented by their width. Unfolded states showing varied conformations and residual structures which may possess several distinct morphologies. The competition between unimolecular folding and aggregate formation is intricately balanced by the cellular proteostasis network. Samreen Amani, Aabgeena Naeem, Understanding protein folding from globular to amyloid state: Aggregation: Darker side of protein, Process Biochemistry, Volume 48, Issue 11, 2013, Pages 1651-1664,

Systems biology, evolutionary theory, and, I would say, fundamental biology suggest that similar processes can, will, and are observed in all organisms. In archaeology, the use of isotope content in human bones to assess dietary intake is limited to 10-15 years, no more (Lamb 2024). This means that even in bone, ribs, and hard tissue, proteins are renewed quite efficiently.

Thus, we have a paradox: macromolecules, cellular organelles, cells, organs and the organism are completely replaced within months, and sometimes even days, but the biological unit weakens, loses its functions and ages.

Interim conclusion: The molecular replcement does not provide functional restoration.

What's missing? It's the protein conformation.

First statement.

Less than 60 years ago, it was proposed that each protein can adopt up to 2E100 conformations, the so-called Levital paradox. It was soon recognized that no protein undergoes every possible conformation and that there are clearly defined "pathways" governing protein folding. Each protein exists in several conformations. More accurately, each protein domain exists in several (tens, hundreds?) conformations. Among these, some are the most stable (units), and it is these conformations that determine the protein's function. More details can be found in an unpublished article about BioEmu—software that predicts, constructs, and evaluates the conformations of working, functional proteins. In short, each protein conformation exists on a three-dimensional surface: the higher the energy of a conformer, the less stable it is. This surface has several energy minima, the most stable conformations. Incidentally, stability does not guarantee functionality. Some functions require an "unstable" protein conformation, at least for the duration of the function.

Figure 2. Protein folding and energy landscape.

Second statement.

It's been well documented that prions can cause protein conformational changes and associated diseases, as well as a non-DNA-mediated mode of inheritance. It seems that prions aren't an isolated, merely interesting phenomenon, but a general trend.

Indeed, amyloid-prone proteins can contribute to the development of amyloidosis. About 45% of the proteome is amyloid-prone due to the presence of so-called intrinsically disordered domains in these proteins. These domains readily fold into beta sheets, leading to amyloidosis or protein aggregate formation. The rest of the proteome can also aggregate into amyloid, but these proteins require non-physiological conditions for this to occur.

I was surprised to learn that poly-lysines or poly-glutamines can form beta sheets and the corresponding ordered aggregates. Even single amino acid artificial "proteins" can fold into amyloid fibrils.

Third statement.

Sliding down the energy hill of protein conformations is not spontaneous. Mitochondria are to blame. Both cardiolipins, the main component of the mitochondrial inner membrane, and polyphosphates, the most ancient means of energy storage, induce amyloidogenesis in various types of proteins. Proteome at a stable, energetically lower level will convert every newly synthesized protein to that level, thereby limiting the functional characteristics of fresh proteins, hence AGING...

Conclusion:

1. Any protein tries to find energy minima during folding.
2. Structurally well-organized proteins can, and seem to actively force, structurally flexible proteins to lower energy levels.
3. Functional performance requires energetically higher structures.
4. If the proteome is at a stable, energetically lower level, it will convert every newly synthesized protein to that level, thereby limiting the functional characteristics of fresh proteins => loss of function => AGING
5. Molecules (polyions) that can prevent/stabilize protein conformations at higher energies can stabilize protein function and prevent sliding down energy minima to well-structured, well-organized, but dysfunctional conformations, thereby slowing or preventing aging.

References

Fornasiero, E.F., Mandad, S., Wildhagen, H. et al. Precisely measured protein lifetimes in the mouse brain reveal differences across tissues and subcellular fractions. Nat Commun 9, 4230 (2018). doi.org/10.1038/s4...

Bomba-Warczak EK, Velez KM, Zhou LT, Guillermier C, Edassery S, Steinhauser ML, Savas JN, Duncan FE. Exceptional longevity of mammalian ovarian and oocyte macromolecules throughout the reproductive lifespan. Elife. 2024 Oct 31;13:

Lamb AL. Multi-isotope analysis demonstrates significant lifestyle changes in King Richard III,

Journal of Archaeological Science, V 50, 2014, Pages 559-565,

Levinthal, Cyrus (1968). "Are there pathways for protein folding?" (PDF). Journal of Physical Chemistry and Biological Physical Chemistry. 65: 44–45.

www.microsoft.com/en-us/rese...

The influence of zwitterionic and anionic phospholipids on protein aggregation. Biophysical Chemistry, V. 306, 2024

Protein-to-lipid ratio uniquely changes the rate of lysozyme aggregation but does not significantly alter toxicity of mature protein aggregates. Biochim Biophys Acta Mol Cell Biol Lipids. 2023           

J Biol Chem. 2021 Jan-Jun:296:100510. Polyphosphates induce amyloid fibril formation of α-synuclein in concentration-dependent distinct manners