Protein Folding - Online Tutor, Practice Problems & Exam Prep

Protein folding is a complex process influenced by non-covalent interactions, particularly the hydrophobic effect, which drives non-polar amino acids to the protein's interior while polar amino acids remain on the exterior. Leventhal's paradox highlights that protein folding is not random; instead, it follows predictable pathways due to cooperative interactions among amino acids, allowing proteins to achieve their native conformation in less than one second. Understanding these mechanisms is crucial for grasping protein structure and function in biological systems.

Protein Folding

So now that we've covered the Anfinsen experiment, in this video, we're going to talk about protein folding. Protein folding has many different contributing factors, but it heavily relies on noncovalent interactions such as the hydrophobic effect, which we can see in our example of protein folding below. Recall from our previous lesson on the Anfinsen experiment that the final protein conformation ultimately depends on the primary level of protein structure and the final protein conformation. Typically, protein folding leads to nonpolar hydrophobic amino acids being found on the interior of the protein, and polar hydrophilic amino acids on the perimeter. We see this in our example below.

On the left over here, we have an unfolded polypeptide chain. The black line represents the peptide backbone. Each of these red balls represents hydrophobic amino acid residues that are nonpolar. On the other hand, the blue balls represent hydrophilic amino acid residues that are polar. This is our unfolded polypeptide chain. But after it undergoes protein folding, the tendency is for the nonpolar hydrophobic amino acid residues in red to be tucked away into the interior because they are water-fearing. The clumping of these hydrophobic amino acid residues is initiated by the hydrophobic effect. The hydrophilic polar amino acid residues, which want to interact with the aqueous water environment surrounding the protein, are likely to be found on the perimeter of the protein.

In our image on the right, we show the 20 amino acids and where we are likely to find these proteins after protein folding, in terms of being on the inside or the outside of the protein. Within our neutral amino acid residues, we've divided them into nonpolar and polar amino acid groups. We don't have our aromatic amino acid group because we've distributed the aromatic amino acids—phenylalanine, tyrosine, and tryptophan—amongst the nonpolar and polar groups. For our nonpolar amino acids, our mnemonic is GAV LIMP. Adding tryptophan and phenylalanine, we can remember this by saying that our buddy Gavin, who is limping away on crutches from the water fast, forms the mnemonic GAV LIMP way fast. These nonpolar amino acids are hydrophobic and will be tucked into the interior of the protein, as we see with these red hydrophobic residues.

To the opposite extreme, we have amino acids with full charges at physiological pH. The mnemonic to remember these is "dragons eat knights riding horses." We have negatively and positively charged amino acids that are very hydrophilic or very water-loving. They interact with the water molecules surrounding them thus, they are found on the perimeter of the protein. In the middle, we have polar amino acids. They are neutral at physiological pH but are still polar, though not as much as the charged ones. As they are somewhat hydrophilic, they can be found either on the inside or the outside of the protein, which means they are distributed throughout the protein. The mnemonic for the polar amino acids is "Santa's team crafts new quilts," and the "y" for Tyrosine can be added to this mnemonic.

This concludes our lesson on protein folding and how the amino acids are distributed throughout a protein. We'll be able to practice these concepts in our next practice video. I'll see you guys there.

Which of the following is the greatest contributor to spontaneous protein folding?

• A. Decreased chain conformational entropy.
• B. Increased chain conformational entropy.
• C. Decreased entropy of the solvent due to folding.
• D. Increased entropy of the solvent due to folding.

Protein Folding

So now that we've covered the basics of protein folding, we can talk about Levinthal's paradox. And so, this guy, Cyrus Levinthal, actually disproved the popular belief that protein folding was a random trial and error process. The protein would have to test all of its possible conformations before it could actually achieve its final native conformation. And so, all Levinthal did was he made a pretty simple realization. He realized that testing all the possible conformations would simply take way too long and he knew that protein folding was super fast and was a non-random process, not a random process. And what that means is that protein folding must have predictable folding pathways. And so today, scientists are able to actually predict the folding pathways for some small proteins, and this field is actually growing as we speak today. And so, like we said earlier, protein folding is super fast and really, it has to do with the cooperative stepwise interactions between amino acids that make the protein folding so fast. So, they speed up the protein folding and these cooperative stepwise interactions pretty much act like protein folding shortcuts.

And so in our example below, what we have is an image for Levinthal's Paradox. And so what you'll see is on the far left over here, what we have is our unfolded protein which has 100 amino acids in it, "aa" represents amino acids. And then on the far right, what we have is our native protein structure. And so again, before Levinthal's paradox, the popular belief was that the protein, the unfolded protein, would have to randomly test all of its possible conformations in a random trial and error process until it achieved its native structure. And so, you can see all of these different folding pathways and possibilities; 100 amino acids, the time that it would take for a protein with 100 amino acids to explore all of its possible conformations was 1027 years which is a massive number in a huge amount of time. And so, it's predicted that the age of the entire universe is just 109 years. So the time that it would take for a protein with 100 amino acids to explore all of its possible conformations is way longer than the length or the age of the entire universe. There's no way that it could take that long for it to test, for it to achieve its native conformation. And today, we know that the actual time for a protein to fold into its native conformation is actually less than one second. So that's a drastic, a massive difference in time. And so, of course, what that means is that there has to be a predictable folding pathway that can be achieved to reach the native structure. And, again, this pathway is dictated by cooperative stepwise interactions between amino acids

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This concludes our lesson on Levinthal's paradox and we'll be able to get more practice with these concepts in our practice video. So I'll see you guys there.

Draw each amino acid & determine which is most likely found in the blue regions of the folded protein below?

• A. Asp.
• B. Glu.
• C. Ile.
• D. Gln.

Which of the following occurs when myoglobin folds into its native conformation?

• A. Myoglobin adopts its lowest energy state form.
• B. Most of the nonpolar, hydrophobic amino acid residues are found buried in myoglobin's core.
• C. Most polar, charged, hydrophilic residues are found on the outside of myoglobin.
• D. b and c.
• E. All the above.

In general, which option contains the major cooperative interactions driving spontaneous protein folding?

• A. Hydrophobic interactions in the protein core & formation of hydrogen bonds in secondary structures.
• B. Formation of salt bridges & disulfide bonds between R-groups that stabilize key interactions.
• C. Reduced chain conformational entropy.
• D. Restricting surrounding solvent molecules to have less rotational/conformational possibilities.

Here’s what students ask on this topic:

What is the hydrophobic effect in protein folding?

The hydrophobic effect is a key driving force in protein folding. It refers to the tendency of non-polar, hydrophobic amino acids to avoid contact with water and cluster together in the interior of the protein. This minimizes their exposure to the aqueous environment. Conversely, polar, hydrophilic amino acids are more likely to be found on the exterior of the protein, where they can interact with water molecules. This segregation helps stabilize the protein's three-dimensional structure, ensuring that it folds into its native conformation efficiently.

What is Leventhal's paradox and how does it relate to protein folding?

Leventhal's paradox highlights the improbability of proteins folding through a random trial-and-error process. Cyrus Leventhal calculated that if a protein with 100 amino acids were to explore all possible conformations, it would take longer than the age of the universe. However, proteins fold in less than a second, indicating that folding is not random but follows predictable pathways. These pathways are guided by cooperative stepwise interactions among amino acids, allowing the protein to achieve its native conformation quickly and efficiently.

How do non-covalent interactions influence protein folding?

Non-covalent interactions play a crucial role in protein folding. These include hydrogen bonds, ionic interactions, van der Waals forces, and the hydrophobic effect. Hydrogen bonds and ionic interactions help stabilize the protein's secondary and tertiary structures. Van der Waals forces contribute to the overall stability by optimizing the packing of amino acid side chains. The hydrophobic effect drives non-polar amino acids to the protein's interior, while polar amino acids remain on the exterior, interacting with the aqueous environment. Together, these interactions ensure the protein folds into its functional native conformation.

What are the mnemonics for remembering non-polar and polar amino acids?

Mnemonics can help remember the classification of amino acids. For non-polar amino acids, the mnemonic is 'GAV LIMP way fast,' where GAV stands for Glycine, Alanine, Valine; LIMP stands for Leucine, Isoleucine, Methionine, Proline; and 'way fast' adds Tryptophan and Phenylalanine. For polar amino acids, the mnemonic is 'Santa's team crafts new quilts,' where Santa's team stands for Serine, Threonine; crafts stands for Cysteine, Asparagine; new stands for Glutamine; and quilts adds Tyrosine. These mnemonics help in quickly recalling the amino acids' properties and their likely positions in a folded protein.

Why is understanding protein folding important in biochemistry?

Understanding protein folding is crucial in biochemistry because the three-dimensional structure of a protein determines its function. Misfolded proteins can lead to diseases such as Alzheimer's, Parkinson's, and cystic fibrosis. Knowledge of protein folding pathways and mechanisms helps in designing drugs and therapies to correct or prevent misfolding. Additionally, it aids in the development of synthetic proteins with specific functions, advancing biotechnology and medical research. Overall, insights into protein folding enhance our understanding of cellular processes and the molecular basis of health and disease.