Originally posted February 18, 2011

Proteins and the Workings of Unfulfilled Bonds

February 18, 2011

Push and stretch.
Fold.
Turn.

Push and stretch.
Fold.
Turn.

Push and stretch.
Fold.
Turn.

If you happen to bake bread at home, you know this rhythm.¹ If you have enough practice with it, it becomes natural. You get started and, rather mindlessly, set to the task of kneading your dough. Push and stretch. Fold. Turn. Do this properly and you will have carried out a rather profound transformation.

From top to bottom

It all starts with some flour and water. The flour, fine and powdery on its own, becomes a sticky mass when you pour water on it. It’s a mess. The dough sticks to everything. It sticks to the bowl. It sticks to the table. And, it certainly sticks to your hands. But, you proceed because humans have been doing this for the past 30,000 years. And you are rewarded for your efforts. After a couple minutes of kneading, the dough starts to take shape. It becomes a little more solid. It doesn’t stick to your hands so much. It starts to look like what you expect a ball of dough to look like. But, you keep pushing on. 30,000 years of practice tells you that your dough just isn’t ready yet. So you knead some more. And the dough becomes satiny and smooth. It stretches without breaking when you pull it. It is ready. It is a beautiful thing.

All of these big physical changes – things that you can see, things that you can feel – come about because you are changing the molecular structure inside of the dough. The simple acts that you perform with your hands: push and stretch, fold, turn are translated all the way down to the molecular scale.

Before you add water to the flour, the wheat starch is really pretty similar to the corn starch molecules I wrote about last week. The granules of wheat starch are made up of amylose and amylopectin (long strings of sugar molecules) that are held together by hydrogen bonds. These starch particles are so stable because the OH groups on each of the individual sugar molecules attract one another through hydrogen bonding. The particles are also surrounded by a protein coat, helping them to hold their form and resist decomposition.

Image of wheat starch molecules from the wonderful food chemistry blog Delicious News written by Dr. Andrew Ross of Oregon State University.

A protein coat is just that. Various proteins use hydrophobic (water-loving) and hydrophilic (water-fearing or greasy) interactions to cloak and stabilize the starch particle. As you add water, you destroy many of the hydrophilic interactions – hydrogen bonding among the starch molecules and between these molecules and the protein coat – leading to unfulfilled bonding. In fact, after you pour water on the flour, the starch particles completely shed their protein coats. (Like they are having a little wet t-shirt competition or something.) The proteins float around adrift from the granules until they start running into one another. As the proteins start to come into contact with one another, they can reform some of those hydrophilic and hydrophilic interactions that had been disrupted. The proteins start to aggregate. This aggregation of proteins in dough is called gluten.

Cartoon of a stable protein structure on the right. In this shape, the protein has all of its hydrophobic pieces interacting with each other and all of its hydrophilic pieces interacting with water. When the protein unfolds, these interactions disappear, and the protein must find new hydrophobic and hydrophilic things to come into contact with.

The wetted gluten proteins form sticky sheets of stickiness. They very quickly find a way to satisfy some of their hydrophobic and hydrophilic pieces. But, they still have unfulfilled bonds. It is this mass of proteins that sticks to our hands/the bowl/the wooden spoon when we start to handle the dough (because all of these objects: hands, bowl, spoon have hydrophobic and hydrophilic parts that the dough can bind to). When we knead the dough, we help each little, itty, bitty, teeny, tiny protein find its way so that it can position itself and have a) all of its hydrophobic parts interacting with hydrophobic parts of some other molecule and b) all of its hydrophilic parts interacting with hydrophilic parts of some other molecule. It seems almost too strange to believe that pushing some dough around can orient individual proteins, but it most certainly does.

On the left is a scanning electron microscope (SEM) image of freshly wetted dough. Image Source Notice how flat and amorphous the gluten appears to be. On the right is an SEM image of kneaded dough. Image Source Notice that after kneading, the gluten aligns into very structured fibers. There are also excellent images of this effect in Harold McGee’s On Food and Cooking (p. 537)

As the individual gluten fibers are developed, your dough also comes together. It takes form from the initial mess of stickiness. All of that happens because you are just squishing the dough together with your hands.

Diseases related with old-age

It seems almost too easy to disrupt the proteins in wheat starch. A little water and a little pushing around and they go from stable individual units to a vast network of fibers that hold its shape and trap gas bubbles. This is what happens in bread dough. Try to imagine what happens to the proteins inside of your body.

We spend our lives putting our bodies through loads of physical stress. Good habits. Bad habits. Exercise. Sloth. Eating. Eating the wrong foods. Drinking. Thinking. Breathing. Working. Playing. Etc. etc. ad infinitum. Compared to kneading, we must be seriously torturing our proteins. And these are all of the actions that we see and feel. There are all of the un-noticed things that the proteins in our body do all day, every day, for our entire lives. They open and close. They carry information. They unravel DNA. They build new structures inside of our cells. They carry energy. And the list goes on and on. Thankfully we have evolved with ways to counteract damage in our bodies. Protein folding chaperones, which make sure that proteins have a supportive and nurturing environment for taking on the right shape, and ubiquitin modifications, which tell the cell to destroy damaged proteins, are just two of the ways that we handle proteins that have gone bad.

However, as we age, our proteins (having been battered for a life-time) are more likely to be damaged. And, our mechanisms for coping with damaged proteins don’t work nearly as well as they used to. When these two factors converge, we start to develop the initial stages of what may turn into Alzheimer’s, Parkinson’s, Huntington’s, Creutzfeldt-Jacob, amytrophic lateral sclerosis (Lou Gehrig’s Disease), or any number of other protein mis-folding diseases.

Just like the proteins in our bread, when the proteins in our body unfold, they start to look for ways to satisfy the bare hydrophobic and hydrophilic pieces that had once held the protein together. The unfolded proteins start to aggregate. (This process is shown in the image below.) Image Source.

The unfolded proteins aggregate into larger and larger fiber structures shown in the image below. Image Source

Note how these fibers look an awful lot like the fibers formed during gluten development. While seemingly surprising, Chris Dobson of the University of Cambridge has found that fiber formation from unfolded proteins is a generic characteristic of all proteins, not just those involved with disease.

Also characteristic of these fibers are ways to break them apart, which is useful knowledge when trying to destroy these disease-causing protein aggregates. Unfortunately it takes harsh conditions – like the acids in your stomach, which can digest the gluten fibers – to make this happen. And since these protein unfolding diseases mainly impair the function of our brains, we can’t just apply concentrated acids to these affected areas.

Don’t be a downer, dude.

Sorry to gloom your day with a discussion of disease. Since I am a doctor (well, not that kind of a doctor but a doctor nonetheless), I am going to prescribe that you go home and bake yourself a loaf of bread. I promise that your spirits will lift and you will find comfort in the enjoyable side of the science of protein unfolding.

Cheers

-mrh

Note:

1. One of my favorite recipes of all time, and one that makes the first few stanzas of this blog entirely unnecessary, is Jim Lahey’s no-knead bread recipe. It is so simple. It requires very little “work” on your part. And it results in all of the wonderful aromas and flavors of freshly baked bread in your own home.