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Protein folding and structure

To understand how the protein gets its final shape or conformation, we need to understand the four levels of protein structure: primary, secondary, tertiary, and quaternary. For a short (four minutes) introduction video on protein structure click here.

Primary structure

The unique sequence of amino acids in a polypeptide chain is its primary structure. The linear sequence of amino acids in the polypeptide chain are held together by peptide bonds and result in the N-C-C-N-C-C patterned backbone. The primary structure is coded for in the DNA, a process you will learn about in the "Transcription" and "Translation" modules.

Figure 1. The peptide bond between two amino acids is depicted. The shaded quadrilateral represents planar nature of this bond.
Attribution: Marc T. Facciotti (own work)

Figure 2. The primary structure of a protein is depicted here as "beads on a string" with the N terminus and C terminus labeled. The order in which you would read this peptide chain would begin with the N terminus as Glycine, Isoleucine, etc., and end with methionine.
Source: Erin Easlon (own work)

Secondary structure

The local folding of the polypeptide in some regions gives rise to the secondary structure of the protein. The most common shapes created by secondary folding are the α-helix and β-pleated sheet structures. These secondary structures are held together by hydrogen bonds forming between the backbones of amino acids in close proximity to one another. More specifically, the oxygen atom in the carboxyl group from one amino acid can form a hydrogen bond with a hydrogen atom bound to the nitrogen in the amino group of another amino acid that is four amino acids farther along the chain.

Figure 3. The α-helix and β-pleated sheet are secondary structures of proteins that form because of hydrogen bonding between carbonyl and amino groups in the peptide backbone. Certain amino acids have a propensity to form an α-helix, while others have a propensity to form a β-pleated sheet.

Tertiary structure

The unique three-dimensional structure of a polypeptide is its tertiary structure. This structure is in part due to chemical interactions at work on the polypeptide chain. Primarily, the interactions among R groups creates the complex three-dimensional tertiary structure of a protein. The nature of the R groups found in the amino acids involved can counteract the formation of the hydrogen bonds described for standard secondary structures. For example, R groups with like charges are repelled by each other and those with unlike charges are attracted to each other (ionic bonds). When protein folding takes place, the hydrophobic R groups of nonpolar amino acids lay in the interior of the protein, whereas the hydrophilic R groups lay on the outside. These types of interactions are also known as hydrophobic interactions. Interaction between cysteine side chains forms disulfide linkages in the presence of oxygen, the only covalent bond forming during protein folding.

Figure 4. The tertiary structure of proteins is determined by a variety of chemical interactions. These include hydrophobic interactions, ionic bonding, hydrogen bonding, and disulfide linkages. This image shows a flattened representation of a protein folded in tertiary structure. Without flattening, this protein would be a globular 3-D shape.

All of these interactions, weak and strong, determine the final three-dimensional shape of the protein. When a protein loses its three-dimensional shape, it may no longer be functional.

Quaternary structure

In nature, some proteins are formed from several polypeptides, also known as subunits, and the interaction of these subunits forms the quaternary structure. Weak interactions between the subunits help to stabilize the overall structure. For example, a multi-subunit protein called insulin (a globular protein) has a combination of hydrogen bonds and disulfide bonds that hold the multiple subunits together. Each of these subunits went through primary, secondary, and tertiary folding independently of one another.

Figure 5. The four levels of protein structure can be observed in these illustrations. 
Source: modification of work by National Human Genome Research Institute

Denaturation and protein folding

Each protein has its own unique sequence and shape that are held together by chemical interactions. If the protein is subject to changes in temperature, pH, or exposure to chemicals, the protein structure may change, losing its shape without losing its primary sequence. This process is known as denaturation. Denaturation is often reversible because the primary structure of the polypeptide is conserved in the process if the denaturing agent is removed, allowing the protein to resume its function. Sometimes denaturation is irreversible, leading to loss of function. One example of irreversible protein denaturation is when an egg is fried. The albumin protein in the liquid egg white is denatured when placed in a hot pan and the heat causes the strands of protein present to unravel and stick together in less ordered blobs. Not all proteins are denatured at high temperatures; for instance, bacteria that survive in hot springs have proteins that function at temperatures close to boiling. The stomach is also very acidic, has a low pH, and denatures proteins as part of the digestion process; however, the digestive enzymes of the stomach retain their activity under these conditions.

Protein folding is critical to its function. It was originally thought that the proteins themselves were responsible for the folding process. Only recently was it found that they often receive assistance in the folding process from protein helpers known as chaperones (or chaperonins) that associate with the target protein during the folding process. They act by preventing aggregation of polypeptides that make up the complete protein structure, and they disassociate from the protein once the target protein is folded.

Khan Academy link

Protein structure.