Biochemistry, Tertiary Protein Structure

Fundamentals

The structure of proteins is fundamental to their diverse functions in living organisms. This structure encompasses four levels—primary, secondary, tertiary, and quaternary, each contributing to the overall shape and function of the protein.

Primary Structure of Proteins

A protein's primary structure, defined by its unique sequence of amino acids, is essential to its function. For example, a single mutation in hemoglobin that replaces glutamic acid at residue 6 in β-globin with valine (Β6Glu→Val) results in sickle-cell anemia.[5] This primary structure forms the foundation for higher levels of protein structure, including secondary, tertiary, and quaternary.

Secondary Structure of Proteins

The secondary structure of proteins is formed by interactions between functional groups in the peptide-bonded backbone. These structures are distinctively shaped segments stabilized mainly by hydrogen bonding between the oxygen on the C=O group of one amino acid residue and the hydrogen on the N-H groups of another amino acid.

In most proteins, these polar groups form hydrogen bonds when the backbone bends, resulting in either an α-helix, where the polypeptide's backbone is coiled, or a β-pleated sheet, where segments of a peptide chain bend 180° and then fold in the same plane. In both α-helix and β-pleated sheet structures, hydrogen bond residues are often located close together in the linear sequence of a polypeptide's primary structure.

In an α-helix, hydrogen bonds are formed between residues, which are only 4 linear positions apart. The distance between residues that form a β-pleated sheet can be more significant as folds in the chain bring them close enough to bond in a 3-dimensional space.

The primary structure of a protein determines whether a segment forms α-helix or β-pleated sheet structures. Certain amino acids are more likely involved in α-helices than in β-pleated sheets, and vice versa. For instance, proline is rarely found in α-helices due to its unusual R-group, which forms bonds with the alpha carbon and the nitrogen of the core amino group.

Tertiary Structure of Proteins

A protein's distinctive 3-dimensional configuration, or tertiary structure, arises from interactions between residues as the chain bends and folds in a 3-dimensional space. These interacting residues are often distant from each other in the linear sequence.

Unlike secondary structures, which involve only hydrogen bonds between backbone components, tertiary structures result from diverse bonds and interactions between R-groups or between R-groups and the backbone. The key chemical bonds involved include hydrogen bonding, which occurs between polar side chains and opposite partial charges either in the peptide backbone or other R-groups; hydrophobic interactions in an aqueous solution, where water molecules interact with the hydrophilic polar side chains of a polypeptide, forcing the hydrophobic nonpolar side chains to merge into globular masses; and van der Waals interactions. Once hydrophobic side chains are close, their association is further stabilized by electrical attractions known as van der Waals interactions.[6][7][8]

Covalent bonding can occur between the side chains of 2 cysteines through a reaction involving their sulfhydryl groups. These disulfide bonds are often called bridges because they create strong links between distinct regions of the same polypeptide or 2 separate polypeptides. Ionic bonding, on the other hand, forms between groups with full and opposing charges, such as the ionized acidic and basic R groups.

As a polypeptide folds into its correct shape, amino acids with nonpolar side chains typically cluster at the core of the protein, avoiding contact with water. Once these nonpolar amino acids have formed the core, weak van der Waals forces stabilize the protein. In addition, hydrogen bonds and ionic interactions between polar, charged amino acids contribute to the tertiary structure. Although individually weak in the cellular environment, their cumulative effect is crucial in determining the protein's distinctive shape.[9]

The primary structure plays a critical role in determining the tertiary structure and the protein's overall function. Experiments have convincingly demonstrated that protein denaturation is a reversible process. Proteins denatured by heat, extreme pH, or denaturing reagents regain their native structure and original biological function when returned to conditions favoring the native conformation.

For example, ribonuclease undergoes denaturation in the presence of urea and mercaptoethanol, where disulfide bridges break apart in the reducing environment. However, after removing urea and mercaptoethanol, ribonuclease regains its native conformation. This example underscores how the primary structure determines the tertiary structure.

Most proteins likely undergo several intermediate structures as they progress toward achieving their most stable conformation. However, these intermediates are not visible in the final folded protein. Chaperonins, protein molecules that assist in proper protein folding, are crucial in this process. These molecules keep proteins away from disruptive chemical conditions in the cytoplasmic environment and allow polypeptides to fold spontaneously. Defects in protein folding provide the molecular basis for several genetic disorders.

Quaternary Structure of Proteins

The primary, secondary, and tertiary structures of proteins involve single polypeptides. However, some proteins contain multiple polypeptides that interact to form a single functional structure. These combinations of polypeptides, called subunits, give some proteins a quaternary structure, where individual polypeptides are held together by the same types of bonds and interactions found in the tertiary level of structure.

Clinical Significance

The structure of proteins determines their function. Therefore, incorrectly folded proteins in the human body can have catastrophic effects. Misfolding or alterations in a protein's primary structure can affect its tertiary structure. Protein misfolding can lead to conditions such as type 2 diabetes, Alzheimer's disease, Huntington's disease, and Parkinson's disease. In these conditions, a normally soluble protein is misfolded and secreted as an insoluble form called an amyloid fiber, collectively known as amyloidoses.

Mutations in the gene encoding a specific protein can lead to incorrect tertiary structure of the protein. One example of a disease resulting from this mechanism is cystic fibrosis, an inherited disorder characterized by thick and sticky mucus. Typically, the mucus secreted by epithelial cells is watery and serves as a lubricant to protect tissues. However, the thick and sticky mucus associated with cystic fibrosis does not move easily, leading to infections, difficulty absorbing nutrients in children, and infertility in men. All these issues stem from a single misfolded protein.

Cystic fibrosis arises from mutations in the gene that codes for a protein called cystic fibrosis transmembrane regulator. Individuals with cystic fibrosis produce abnormal cystic fibrosis transmembrane regulator protein or sometimes none at all. Consequently, the body produces thick, sticky mucus instead of the thin, watery type.[10][11]

The primary structure of a protein determines its secondary and tertiary structure. Mutations in the gene encoding a protein can occur due to environmental factors such as ultraviolet radiation or errors in DNA replication. Furthermore, the primary structure can be altered if the translation process on the ribosome does not occur entirely accurately. Understanding that a protein's entire structure and function rely on its primary structure is essential; if incorrect, it can potentially devastate the human body.