The Basics of Protein Folding

Protein folding is a vital cellular process that shapes proteins into their functional three-dimensional shape. When it goes wrong, sticky misfolded proteins evade systems like chaperones and the proteasome to clump together in the cell, contributing to diseases such as Alzheimer’s and Parkinson’s.


Four forces drive the tertiary fold of proteins, including Hydrophobic interactions, Van der Waals interactions, hydrogen bonding, and disulfide bonds between adjacent cysteine residues.

Hydrophobic Interactions

The protein folding process is controlled by the hydrophobic interactions between amino acid side chain groups. The hydrophobic amino acids are buried in the interior of the protein away from the aqueous environment they are found in while the more polar amino acids interact with water molecules through hydrogen bonds, ionic bonds and dipole-dipole interactions (also known as London dispersion forces).

Proteins have a large amount of hydrophobic surface area compared to their polar volume. Therefore, they have the potential to form weak Van der Waals interactions with water molecules.

In the presence of these interactions, a protein has more stability than if all the side chains are exposed to the aqueous environment. These interactions also contribute to the formation of ionic bonds between oppositely charged amino acids, which increase a protein’s compactness.

It is a well-known fact that the entropy of an unfolded protein is lower than the entropy of its folded counterpart. This is attributed to the strong hydrophobic interaction between amino acid side chains.

The hydrophobic effect is most likely responsible for the shift from the CDS to the HTS in the folding process. It has been shown that the number of hydrogen bonds per surface water molecule in the HTS is larger than the one in the CDS. This suggests that the hydrophobic effect drives the proteins to bury their nonpolar surfaces.

Van der Waals Interactions

The tertiary structure of proteins is stabilized by interactions between functional groups in different parts of the protein (Figure 8). These interactions include hydrophobic interaction, hydrogen bonding, ionic bonding and van der Waals interaction. Hydrophobic interaction between the non-polar amino acid side chains largely contributes to stabilizing the tertiary structure.

Similarly, the non-polar surface of protein is packed with many hydrophobic residues that are capable of forming weak van der Waals interactions with one another. The strength of these interactions scales with the total surface area over which they occur. Because all of the buried hydrophobic residues in proteins have nonpolar properties, they provide large areas of surface over which these interactions can occur.

In addition, nonpolar surfaces of proteins can become transiently polarized by the random motion of electrons. The resulting instantaneous dipoles can attract each other. Proteins tend to contain numerous such regions of surface, providing a significant contribution to the stability of tertiary structures.

In the unfolded state of a protein, atoms on the Phe sidechain of a particular residue can make hydrogen bonds with solvent water molecules (left). During protein folding, however, these interactions are replaced by van der Waals interactions that have more optimal geometry and lead to a net decrease in enthalpy.

Hydrogen Bonds

In proteins, hydrogen bonds bind the amino acids to each other and to the protein’s tertiary structure. The bonds are formed by the transfer of a hydrogen ion from an electronegative atom (donor) to an electropositive atom (acceptor) within a protein molecule. This creates a covalent bond and confers rigidity to the structure and specificity to intermolecular interactions.

Hydrogen bonding also provides most of the directional interactions that determine protein structure and molecular recognition. The most stable conformations of a protein are helixes and beta sheets that maximize intrachain hydrogen bonding between polar amino acid side chains. This binding also requires the burial of hydrophobic side chains within the protein core away from aqueous water molecules. The buried side chains then interact with each other through van der Waals forces and London dispersion forces.

The dominant enthalpic force in protein folding is the hydrophobic effect, aided by van der Waals and hydrogen bonding interactions. Combined, these interactions balance the favorable change in conformational entropy associated with the folding process to stabilize the native state.

Despite these dominances, there are many other contributions to the overall free energy of protein folding. These include weak interactions involving the protein’s internal cavities, as well as strong and moderate individual interactions that are not captured by any of these major mechanisms. The latter are often characterized by a large magnitude of individual interaction energies and may be important for specifying nonlocal intermolecular contacts and ligand binding.

Ionic Bonds

Proteins are held together by several forms of molecular interactions. The dominant forces that drive protein folding are hydrophobic effects, Van der Waals interactions and hydrogen bonds.

Hydrogen bonding is the weakest force in protein folding but can still play a significant role in protein stability and conformational selection. These bonds form between the hydrogen atoms of two adjacent amino acid side chains or between a nonpolar protein-water molecule and a more polar molecule.

Ionic bonding is a stronger force than hydrogen bonding, and it is important for the formation of a protein’s tertiary structure. These bonds result from electrostatic attractions between the negatively charged carboxylate groups of polar amino acids and positively charged water molecules. They can also result from the forming of disulfide linkages or from other non-covalent interactions such as London dispersion forces.

All of these forces contribute to the overall stability of proteins. However, they are not sufficient to explain why and how proteins fold into their native structures. This is because the energy landscape of a protein is not entirely deterministic and there are many pathways to the same native state. For this reason, scientists have developed methods to trigger the protein folding process and observe its dynamics. These techniques include ultrafast mixing of solutions, laser temperature jump spectroscopy and photochemical methods.