(IJCH) Protein Folding for Dummies (or Understanding How Protein Mechanics can improve the Lives of every Human Being on Earth!)

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IJCH - Inside JaiChai's Head (Meaning: My Warped, Personal Opinions and Musings)

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From the Author:

Salutations.

I am JaiChai.

And if I haven't had the pleasure of meeting you before, I'm delighted to make your acquaintance now.

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I invite you to interact with everyone, learn, and have as much fun as possible!

For my returning online friends, "It's always great to see you again!"

Please Note:

To fully understand every aspect of the protein molecule requires a lot of education, time, effort and countless observations of recognized, validated (repeatable) experimentation.

I don't possess a PhD in Molecular biology, Biochemistry or Biophysics.

Consequently, the following will be a VERY SIMPLIFIED explanation of how proteins actually function.

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Nevertheless, the title of this article is "Protein Folding for Dummies" and my only objective is to present the material in such a way that is both true AND simple enough for non-experts to easily understand.

I've taken great pains to present analogies and metaphors that truthfully portray the basics (especially in the "Protein Mechanics 101" section) sans the intimidation factor of complex theories and confusing scientific jargon.

And if I've successfully done that, I'll be overjoyed - mission accomplished.

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Introduction: Protein - NOT Just a Macronutrient and Fitness Supplement

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Until I heard of "Protein Machines and Protein Folding", all I knew (or cared to know) about protein were the answers to these questions:

• What nutritional/energy impact does it have on the body? Answer: 4 Kcal/gm - just like carbohydrates.

• Why does everyone need it? Answer: Optimum health and fitness.

• How much of it is required to ingest on a daily basis?

  Answer: Depends on many factors, such as:

  • Lifestyle (Sedentary, Moderate, or Active)

  • Current weight, health, and age

  • Chronic illnesses

  • Traumatic Injury (MVAs, GSRs, Bomb and Burn Victims, etc.)

  • Genetics (Predisposition for degenerative or debilitating diseases)

  • Heredity (Body Type and less commonly, metabolic rate)

  • Type of chosen physical activity

  • Intensity and duration of training

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Instead of the RDA of 1 gm/kg of body weight, I was groomed on the one gram per pound of body weight per day philosophy - and even more if I was doing multiple sessions of hard training that resulted in extended periods of metabolic catabolism (muscle cell breakdown).

(Of course, these days if I go on a cycle of very high protein intake, I make sure that my renal system is functioning properly. In some individuals, the stress of processing large amounts of daily protein can wreak havoc on their liver and kidneys.)

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For me, the 1 gm/1 lb body weight formula was a simple daily goal and that was that (easy-peasy).

Other than shopping around for protein powder that didn't make me gag, throw up, or spend half a day on the toilet (I am lactose intolerant), I didn't bother knowing anything else about protein.

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Strange fact:

Did you know that for decades, the dairy industry thought the substance identified as "whey" was a useless, smelly and annoying byproduct of processing cheese or milk?

(Hence, the children's rhyme of "Little Miss Muffet eating her curds and whey"...)

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In other words, back in the old days before Bally's Fitness Centers and Gold's Gyms, the same whey protein we look for in today's high-quality protein supplements was actually discarded as filthy waste!

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(Warning: Tangent Incoming)

Ah, the wonders of "marketing-meeting-demand", no?

It's almost like that cheap Mexican beer that was exported as "Premium Beer" (with premium prices) and marketed to rich and stupid American Yuppies. I'm sure you've heard of it.

It's called Corona beer.

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(Leaving tangent and coming back on topic now).

But recently I've learned that protein is so much more than just a macronutrient and fitness supplement.

In fact, the current advances in our understanding of the protein molecule is paving the way for tiny, specialized Protein Machines.

These machines will impact every living thing on Earth; while simultaneously reducing (or halting) the harmful, accumulated effects on the Biosphere from using today's Traditional Machines.

In short, Protein Folding (manipulating the shape of protein molecules) will be a significant, far-reaching, and civilization-changing technology.

But before we can understand the "Why" and "How" of Protein Machines and Protein Folding, we must first review (very quickly) the "What" of protein...

The Life Supporting Functions of Protein

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As you can see below, protein is responsible for a myriad of critical physiological functions:

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Protein - Function Follows Form

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The SHAPE (Form) of a protein molecule determines its function.

If it is shaped one way, it can store things. If it's shaped another way, it can transport things. If it's shaped still another way, it can hold things in place, etc.

The SHAPE is determined by its number and sequence of the various, fundamental building blocks of protein called amino acids.

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There are 20 different kinds of amino acids to build a protein molecule. They are arranged in a string-like configuration, like the different color pearls on a necklace.

This translates into thousands upon thousands of unique combinations that can possibly manifest - factorial 20 ( 20! = 2.4329 to the 18th power).

And each of these combinations represent a different type of protein molecule.

Protein - The Amazing Molecular Machines

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Make no mistake, proteins are real machines.

They perform many observable/measurable mechanical tasks.

Here's a short list of their mechanical capabilities:

• moving levers.

• pumping substances in and out of molecular structures.

• rotating or spinning themselves and/or parts of other molecules.

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• "walking" (called "gliding") along a path - commonly used for muscle contraction.

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Traditional Machines vs. Protein Machines

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Here are some major differences between Traditional Machines and Protein Machines:

• Traditional Machines are noisy; Protein Machines are noiseless.

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• Many Traditional Machines burn fossil fuels and pollute the environment; Protein Machines do not (Protein Mechanics explained in the next section).

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• Other Traditional Machines are powered by electricity; Protein Machines are not.

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• When Traditional Machines become obsolete or broken, they accumulate huge amounts of non-reuseable waste; Protein Machine parts (amino acids) can be reused to make other Protein Machines.

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Protein Mechanics 101

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A protein molecule is like a super-microscopic version of the Great White Shark.

It is constantly on the lookout for, attacking, and latching onto other things in its environment.

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But it has a soft spot for the Ramora Fish.

They have a symbiotic relationship. The Ramora cleans parasites off of the shark, while the shark's proximity provides protection and his feeding frenzies produce scraps for the Ramora.

So, one could say that the Ramora perfectly "fits" into a special place on the shark.

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It's likened to a key to a lock.

If the right key is put in place, it causes the lock to perform an action - most commonly, to open or "release" the locking mechanism.

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Keep in mind that there are many other actions that can be caused with these same basic steps. In one instance the action inhibits a process. In another, the action accelerates it.

It all depends on the players (types of protein machine) involved, what an acceptable key may (or may not) be, and what action is desired.

The main thing is to remember is that whatever action occurs, it is because something fit (or was blocked from fitting) into a special area on the host (owner of the lock, landlord of the whole establishment, etc.).

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Using the Great White Shark/Ramora Fish analogy, let's describe what is happening with the protein molecule during a molecular mechanical process.

(1) Shark bites and holds onto his prey - (Protein molecule bites onto and captures his "molecular prey").

(2) A Ramora Fish comes along and settles into his special place on the Great White - (The right molecular "key" appears and fits into the special place on the protein molecule.).

(3) After the Ramora is securely into that special area on the shark's back, it causes the shark to release his prey - (After the "key" is firmly in place, the protein molecule releases his "molecular prey").

That's it!

No electricity or gasoline needed for protein machines to work!

Congratulations, you've just passed "Protein Mechanics 101"!

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Pat yourself on the back. You now know more about how Protein Machines work than over 99% of the world's population!

Interesting Side Note:

This "key, receptor site, and unlocking" paradigm of Protein Mechanics is also used in the pharmaceutical industry for developing new drugs to combat a multitude of diseases.

For the chemically curious, here's a more technical explanation:

A drug's efficiency may be affected by the degree to which it binds. The less bound a drug is, the more efficiently it can traverse cell membranes or diffuse.

Common blood proteins that drugs bind to are human serum albumin, lipoprotein, glycoprotein, and α, β‚ and γ globulins.

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But How are these Wonderful Machines Made?

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Earlier I explained that protein molecules consist of a long chain of amino acids.

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And we also established that it is the SHAPE of the molecule that determines what the protein machine actually does.

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But how does each different molecule get its unique shape if they all started as just strings of stuff?

Answer:

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Starting off as building blocks of amino acids, they quickly fold to their proper shape, going through many high-energy transitions along the way.

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Correct folding is crucial for the function of each protein machine, and when it is not done correctly, protein folding diseases can result (e.g., Alzheimer's disease, Lou Gehrig's disease, cystic fibrosis, amyloidosis and many others).

The Protein Folding Problem - Three Questions

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The structure of protein pre-folding and post-folding has been known since the 1950's. And since then, over 80,000 structures have been discovered.

But...

(1) No one has deciphered the protein-folding "code"; that is, which strings of beginning amino acids always result in - AND how do they interact to create - the unique, balled-up ("native") final structure of a particular protein?

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(2) How does one amino acid "find" his partner among a vast sea of other amino acids?

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(3) With all the external factors that affect the very sensitive folding process (e.g., H2O buffeting [turbulence], electromagnetic fields, temperature, pH, chemicals, space constraints, overcrowding and more), how the Hell does protein folding happen in less than a milisecond!?

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But there is a very real possibility that this problem will soon be solved.

Why do I say this?

Because of the simultaneous surge of new interest in the Protein Folding Problem plus the giant leaps in computer technology.

This combination has already yielded greater and faster progress in the last couple years than the aggregate achievements of the last 4 1/2 decades!

See:

"The Protein Folding Problem, 50 Years On"

And:

"The Protein Folding Revolution"

Parting Shots: On the Horizon

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The next revolution in machine design and function is on the horizon. And IMHO, it will be based on a scaled-up version of Protein Mechanics.

When that happens, a new global economy will emerge driven by super-efficient, noiseless, non-polluting, and affordable mechanical technology.

This will solve many problems plaguing the world - least of which is this:

Machine Access/Usage and Poverty - An Ugly Statistical Correlation

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It may not surprise you to hear that there is a fifty-fold difference between the poorest countries and the richest countries.

But did you know that access and usage of modern machines mirrors those same statistical comparisons?

Yup, that's right, the poorest countries are 50x less rich AND have 50x less access to modern machines than the richest countries.

Hmm, imagine that?

This is the sad, but true correlation between access/use of modern machines and worldwide poverty.

Just take a look at this image.

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The dotted areas are the areas around the world that have access and regularly use modern machines.

It is clear that countries without such access also happen to be the poorest ones.

These financially marginalized countries are the ones that stand the most to gain with access to modern, affordable machines that are far superior to machines created by traditional methods and using legacy designs.

As with all modern technology, in order to successfully enter, compete, and thrive in the global economy, people (especially from developing countries) must begin learning about it now, force themselves to embrace new paradigms, and consistently prepare for the arrival of new technology.

"The sooner the paradigm shift, the longer, less steep, and least painful the learning curve..." - Jaichai

By JaiChai

Mighty Kind of You for stopping by.

Truly hope to see you again!

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About the Author

Believing that school was too boring, he dropped out of High School early; only to earn an AA, BS and MBA in less than 4 years much later in life – while working full-time as a Navy/Marine Corps Medic.

In spite of a fear of heights and deep water, he performed high altitude, free-fall parachute jumps and hazardous diving ops in deep, open ocean water.

After 24 years of active duty, he retired in Asia.

Since then, he's been a full-time, single papa and actively pursuing his varied passions (Writing, Disruptive Technology, Computer Science and Cryptocurrency - plus more hobbies too boring or bizarre for most folk).

He lives on an island paradise with his teenage daughter, longtime girlfriend and three dogs.

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(More articles by JaiChai can be found on the Busy.org website. Use this link to visit Busy.org. Better yet, come join the Busy.org community!)

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"My mind was a terrible thing to waste..." - JaiChai

Namaste, Jaichai