AlphaFold 3: How Does Proteins Misfolding Cause Neurodegenerative Diseases?

If an individual is sleep deprived, at what minimum can certain functions continue without getting any sleep? If someone sees something from a distance, but it is just clear enough to be roughly interpreted by the mind in terms of kind, but not specificity, is there an input configuration requirement to guarantee an optimum interpretation of the external world by the human mind?

\ If functions are continuously operating at minimums, could there be a likelihood that some of the factors responsible for optimum outputs may start getting the message that they are no longer necessary? If this is the case, could it cascade into a serious condition?

\ Neurons are known to have around 50 billion proteins. Protein misfolding has been established as a major cause of some neurodegenerative diseases. A possible reason for protein misfolding has been identified as [cellular] environmental stress. A theoretical basis for why environmental stress may be responsible could be to look at working minimums and maximums, for functions, over certain intervals.

\ Theorizing protein folding requires a top-down approach, which means that there is a source for which problems might arise, resulting--eventually--in misfolding and degenerative diseases. The closest destination for the top option is the electrical and chemical signals of neurons.

\ It is theorized that the human mind is responsible for all functions that the brain is said to do. The human mind is the collection of all the electrical and chemical signals, with their interactions and features, in sets, in clusters of neurons, across the central and peripheral nervous system.

\ This means that the human mind is the signals with their interactions and features. All the configurations for which representations and interpretations are based, for interoception and exteroception, have just one possible option in the brain, the signals, not genes, proteins, neurons, or other types of cells.

\ This means that whatever is interpreted, accurately or not, or seems represented, accurately or not, is a result of the signals, such that with signals, interpretations, and features, in sets, are at the top, though their work has implications for other cells in the body, and several other molecules, especially proteins, abundant in neurons.

\ Why? Exercise, for example, is an activity where electrical and chemical signals are interacting actively, with varying features applying. This top activity results in relays of electrical signals that, conceptually, for interactions with chemical signals, in sets, have an effect on other parts of the body.

\ Simply, electrical and chemical signals are involved in every function. The consequences of those functions can also be seen elsewhere.

Proteins, Neurons, and Signals

Since neurons are not the human mind, or their proteins, because they do not organize information, it can be theorized that as neurons are involved in clusters, with sets of signals, their proteins assist several interactive processes between electrical and chemical signals.

\ This indicates that when there are extended minimums or maximums, in sets of signals, there are ways that they come to have an effect on some of the proteins of the neurons involved in respective clusters [hence environmental stress].

\ Simply, neurons have proteins, and these proteins contribute to the primary role of signals, but as signals carry out their roles, depending on the pace or direction, they come to also have effects on the protein of some neurons, which may work more or work less, over an interval, which may, for some cases lead to misfolding, and then accumulations and disease, conceptually.

\ It means that the mechanisms of signals can have an effect, conceptually, on the misfolding of proteins, then possibly developing into a degenerative disease for some.

Tracking Possible Paths for Protein Misfolding From Signals

It is possible to develop a number of minimums, maximums, and interactive-feature stretches of signals, with an exploration of how, for some people with Amyloidosis, that may have resulted from cellular [environmental] stress, to look at the roles that signals played.

\ The interaction of signals is the way electrical signals strike at chemical signals, while the features are some of the states of the signals, in sets, at the times of the interactions. If a person drinks cold water but does not feel it as cold, why did the signals not give the experience of cold? There are several examples like this, but what can be looked at is the intensity of certain experiences or the longevity of others, which may have caused the larger protein folding error.

\ Theorizing why proteins misfold may have to center around the major functional operators the electrical and chemical signals, which can then be sought, as the source toward reversal or prevention.

\ There is a recent story in Nature, AI protein-prediction tool AlphaFold3 is now open source, stating that, "AlphaFold3, unlike its predecessors, is capable of modelling proteins in concert with other molecules. But instead of releasing its underlying code — as was done with AlphaFold2 — DeepMind provided access via a web server that restricted the number and types of predictions scientists could make. Crucially, the AlphaFold3 server prevented scientists from predicting how proteins behave in the presence of potential drugs. But now, DeepMind’s decision to release the code means academic scientists can predict such interactions by running the model themselves. The company initially said that making AlphaFold3 available only through a web server struck the right balance between enabling access for research and protecting commercial ambitions. Isomorphic Labs, a DeepMind spinoff company in London, is applying AlphaFold3 to drug discovery."

\ There is a recent press release, Argonne team breaks new ground in AI-driven protein design, stating that, "Harnessing the power of artificial intelligence (AI) and the world’s fastest supercomputers, a research team led by the U.S. Department of Energy’s (DOE) Argonne National Laboratory has developed an innovative computing framework to speed up the design of new proteins. On the heels of this year’s Nobel Prize in Chemistry, which recognized advances in computational protein design, Argonne’s AI-driven approach has been selected as a finalist for the prestigious Gordon Bell Prize. Presented by the Association of Computing Machinery, the annual prize recognizes breakthroughs in using high performance computing to solve complex science problems. Mapping a protein’s amino acid sequence to its structure and function is a long-standing research challenge. Each unique arrangement of amino acids — the building blocks of proteins — can yield different properties and behaviors. The sheer volume of potential variations makes it impractical to test them all through experiments alone. To put this in perspective, modifying just three amino acids in a sequence of 20 creates 8,000 possible combinations. But most proteins are far more complex, with some research targets containing hundreds to thousands of amino acids."