Get Yourself Into Folding At Home---it's Scientific!

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It's Just What Proteins Do & We Can Help the Scientific World Use Our Computers

If it were up to me, I would have named this process "Protein Spiraling," but the scientists got to it before I did! So a relatively formless, flat-like, cooked-spaghetti looking, polypeptide string suddenly can't resist "folding" and it springs into action and the result looks like this.

What do I care about protein folding? My ears have been picking up on medical talk over the media, regarding new discoveries that might solve some puzzling and devastating medical conditions - why they happen, how they happen, and why so many of us get a condition called Peripheral Neuropathy that is wreaking havoc in my life! Read about my discoveries here. peripheral-neuropathy-barbed-wire-in-legs-feet-hands It's not a cool condition - pains are many, complicated and hot!

Now, back to Protein Folding. This is the name of the physical process that grips that polypeptide, and results in its "folding" (spiraling) into a characteristic 3-d structure that performs and functions like that particular protein. This and every protein exists in that stringy polypeptide form, what they call a random-coil after it has converted from its mRNA sequence into a 1-d amino acid chain.

It is Amino Acids that act on the polypeptide that cause it to curl up into a 3-d form with a dependable complexity. Now I would call the "stringy" part on the left the native state of this polypep, but I'd be wrong. The native state of the protein is the curlique on the right.

The result of the "folding" is a particular 3-d form, and irregularities or bends where they don't belong, termed "failure to fold into native structure produces inactive proteins" and these inactive gems are likely to be toxic proteins. (Is this what makes parts of some potato skins green?)

Seriously, we don't want inactive proteins; we want the 3-d structure indicative of functional proteins. (for the most part, nearly every element of functional proteins "folds," however some parts do not. Specifically, the build-up of amyloid fibrills, resulting from wrongly folded proteins, leads to neurodegenerative (and other) diseases, studies are leading scientists to believe. Even allergies require misfolded proteins, to activate, because the immune system provides antibodies that only recognize properly folded proteins.

A public domain illustration of the process of protein folding - Chymotrypsin inhibitor 2.

Why & How? Does this Protein Folding Occur?

in the presence of water,

These proteins exist in their primary structure (this is their amino-acid sequence), also called native conformation. During the Biosynthesis process the protein molecule does its involuntary folding.

Necessary components of the convolusion are H2-0, both in the solvent (water or a lipid bilayer), the salt concentration, hot warm or cold it is, and the presence of specialized molecules which either help or hinder the folding.

Public domain illustration of a lipid bilayer (made of phospholipids in the highest congregation), that - once they are doused with a water bath - form up with their double-tailed ends pointing into the center of their gathering ground (sheet) .

These active little fellas squiggle in close to each other and help provide an impermeable barrier to offensive substances that might prevent the Protein Folding from taking place.

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Protein Folding Video

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Water's Role in Protein Folding

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Protein Folding Occurs During or After Biosynthesis

in biosynthesis cells produce or construct proteins

Protein Biosynthesis is a step once-taken, seldom to be reversed, and that is why protein types can be studied at all. It is rather like dressing for success, all suited up, and stepping into a puddle that turns out to be a pond which swallows you, white suit and all. You can climb out, but you can't undo the fact that you will be forever skittish about stepping into a puddle again - well, it's not quite like that.

Protein Biosynthesis is more like a human body's process of puberty - depends on the production of hormones - and once the sexual-maturity-folding happens - it has happened! There's no becoming a kid again; however, both proteins and people can suffer from disruption in their proper functioning, people from too little or too much hormone, proteins of temperatures that rise or fall out of the optimum range for folding, and other extremes. But, for normal processes to take place and remain strong in the new folded form certain conditions are necessary for proper use of the protein in question.

Primarily, in folding the particular protein's amino-acid-sequence stipulates the confederation of: 1) native state, and 2) the proclivity to reach the native state.

Visualize These Project Images 

See Likeness of Project Images Above

if you like the looks of these complicated strings - give it a try

The videos show you how to grab parts and sections of the images and attach features, which you then manipulate and run through the game's system, all to the accompaniment of rising or lowering scores. Pretty Nifty! Diagram by Yikrazuul commons.wikimedia.org

Oxidative Folding of Peptides and Proteins

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Look at How This Game Project Works on Your Home Computer

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Structure & Mechanism of Protein Folding

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iTunes

Track Artist Album  
Synthesize Kwod Sonik Punk No Justice No Peace (A Protest Song for a Revolution) - EP
Folding Proteins (Reset! Remix) Depressed Buttons Qwerty Remix - EP
One and Amino Acids When In But Out But Alvin Curran Electric Rags II
The Amino Acids Song Biscuithead & the Biscuit Badgers The Greatest Show On Toast

Secondary & Tertiary tRNA Structure 

Foldit Project Explanations & Games

learn about protein folding and this opportunity to play

I heard about Foldit on NPR and since I'm not a gamer, at first I thought it didn't have any resonance to me, until I heard the part about Protein Folding. Well, I've become slightly acquainted with Protein Folding due to my interest in revering polyneuropathy (nerve damage), in some cases caused by toxic chemotherapy drugs (they are all toxic). So I listened more attentively.

I wasn't the only one who had any amount of skepticism about this game concept, and the others held science smarts superior to me. The Scientist, Magazine of the Life Sciences, features Andrea Gawrylewski's 5/23/08 article, "Foldit for fun" about the then recent phenomenon. The game is a result of co-founder David Baker's team of scientists at the University of Washington, coupled with computer programmers, garnering info from Rosetta@home.

The premise of Foldit is simple: See protein floating on screen. Drag parts of protein around to get it to the optimal energy state. The better the energy, the more points you get. But in order to make that happen, you must rearrange amino acid chains attached to the protein backbone, making sure they aren't hitting, or "clashing," each other and sending out spinning red stars on the screen.

Read more: Foldit for fun - The Scientist - Magazine of the Life Sciences
the-scientist.com

From Foldit!! Competitive Protein Folding

this is real science you play like a game

Use the tools to enter into a game to solve a Protein Folding puzzle while you earn points for all your smart moves. Expert players demonstrate their skills as you watch them earn points.
Fold.it tutorial
by goldennick | video info

16 ratings | 14,668 views
curated content from YouTube

Protein Folding, Misfolding, and Disease

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iTunes

Track Artist Album  
Folding Protein Depressed Buttons Qwerty - EP

Protein Folding Science & Game at Once!

do real science, solve problems, help out

If you have good visual memory, good spatial vision, this may be the game for you. Although this idea is new to me, you may have some acquaintance with the idea, but have never got into puzzling. This session was done at UW in 2009.
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Molecular Chaperones and Protein-Folds Catalysts

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Online Gamers Rapidly Solved Med Problem

gamers went to town and solved this challenging problem

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VIRTmac Protein Folding/Enzyme Structure

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Science in the News

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Proteins Background for Understanding

getting started with the foldit games project

Proteins are the operative factors in every living cell, numbering over 1 to the 12th, 13th, on up. Proteins utilize the carbs we ingest prior to exercising, but not before they break them down and send the food through our digestive systems, in the smallest increments. No matter what the kind, all proteins consist of long amino acid strings.

Each protein chain folds up on itself in a unique set of bends. Occasionally a protein mis-folds, leading to release of toxins, allowing illness or other conditions that lead to ill health or even death.

Healthy chains consist of molecules joins one to another, and periodically dangling a small string of atoms. The main string is called the "backbone" and the side string is called a "sidechain."

Characteristic of each variety of protein is the "fold" into which they bend themselves, the same shape every time (with few malfunctions), due to their proclivity to resist remaining in a straight line.

I always thought a protein was a protein, and an enzyme was an enzyme, but it turns out that proteins can do the work of enzymes, acting as catalysts to help chemicals zip through their reactions, doing their jobs.

Proteins serve our bodies in so many functions:

Begins to convert food starch into usable forms
Converts alcoholic beverages into the form the human body can metabolize for energy
Transports oxygen through our bloodstreams
Scabs over a wound providing protection for healing
Collagen provides foundation for everything from skin to bones
Serves as muscle protein
It's also the growth hormone that creates adults out of kids
In potassium channels, signals circulate through the nervous systems
As insulin, they govern blood sugar levels, both positive and negative aspects


The Foldit game provides players an opportunity to predict the structure of various proteins. Knowing the structure that is just right is a critical challenge in fighting and correcting the problems associate with diseases and conditions that afflict millions.

Gamers can even try their hands at designing "new" proteins that could be helpful in disease prevention or remediation. How? By clicking and dragging, and submitting their trials into the program so it can do its trick. The three main areas of concentration are HIV/AIDS, Cancer and Alzheimer's Disease.

Learn a certain amount of science as you build your gaming skills, and get rapid feedback.

Magnetic Folds / Enzyme Structure Manipulatives

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Foldit!! Supercomputer Folding Project - Go Get It Now!!!

that's an asymmetrical retroviral structure you're looking at

I downloaded Foldit., 46.5MB for the Mac, in a few minutes. Now if I can stop.

I downloaded BOINC at boinc.berkeley.edu

BAM, or BOINC Account Manager, makes it easier to manage a player's preferences, teams and project choices. I considered creating a BAM account here boincstats.com

I went through a number of steps, agreed to the rules of the road, and can begin working on a project at my leisure.

Diagram at en.wikipedia.org/wikia>

Macs Serve You Right for Folding Gaming

I can't imagine not having a Mac

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The Right PC for This Science Project

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Apple MacBook Air for Easy Gaming

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Misfolding & neurodegenerative diseases

Kindle Edition

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Folding Protein Music Album Available Now!

from Mad Decent and Downtown Music, LLC

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Project Gaming Brings Scientific Advance

gaming that really counts

What do gaming and degenerative nerve diseases have in common with chiropractic? Protein-Folding Gamers work on online games, seeking solutions to scientific puzzles - to which the answer is not yet known. Through gaming some of the same type of discoveries on mis-folding that causes neuropathies - as have been made on AIDS puzzles.

Many individuals with diabetes, HIV, and those exposed to chemo-like toxins are some of those who can benefit from results of these games. This link takes you to my 4th Peripheral Neuropathy lens, that explains some modalities chiropractors use to treat PN in patients. squidoo.com/treatPNchiro

What Do You Think of This Idea of Online Gaming for Science?

  • Wordwinder Jan 2, 2012 @ 1:54 am | delete
    It is a great idea for those interested in science.

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