Protein Structure – Properties of Primary, Secondary, Tertiary and Quaternary Structure

Protein Structure

Introduction

Proteins are polymers of amino acids. The biosynthesis of proteins occurs in every living cell at some point of its life. Proteins perform a variety of functions by the virtue of their structure. Protein structure has four levels: primary, secondary, tertiary (globular) and quaternary.

In this article, we will go through the details of different types of protein structures. We shall also see the different bonds involved in creating these structures and also denaturation of proteins.

Primary Structure

The amino acids in polypeptides are held together by peptide bonds. A dipeptide is formed by a reaction between the α-carboxyl and α-amino groups of two amino acids. For example, Adding more amino acids produces oligopeptides and finally polypeptides.

Each peptide has an amino terminus, conventionally written on the left side, and a carboxyl terminus, written on the right side. The peptide bond is not ionizable, but it can form hydrogen bonds. Therefore peptides and proteins tend to be water soluble.

Many proteins contain disulfide bonds between the side chains of cysteine residues. Disulfide bond formation is an oxidative reaction in which hydrogen is transferred to an acceptor molecule.

The disulfide bond can be formed between two cysteines in the same polypeptide (intrachain) or in different polypeptides (interchain). The reaction takes place in the endoplasmic reticulum (ER), where secreted proteins and membrane proteins are processed.

Therefore, most secreted proteins and membrane proteins have disulfide bonds. Most cytoplasmic proteins, which do not pass through the ER, have no disulfide bonds.The enzymatic degradation of disulfide-containing proteins yields the amino acid cysteine.

The covalent structure of the protein, as described by its amino acid sequence and the positions of disulfide bonds, is called its primary structure.

Nature of Peptide Bonds

The peptide bond is conventionally written as a single bond, with four substituents attached to the carbon and nitrogen of the bond. This can be shown as:

A C—N single bond, like a C—C single bond, should show free rotation. The triangular plane formed by the O=C—C₁ portion should be able to rotate out of the plane of the C₂—N—H portion. Actually, however, the peptide bond is a resonance hybrid of two structures as follows:

protein structure
Fig 5. Representation of peptide bond as resonance hybrid of two structures.

Its ‘real’ structure is between these two extremes. One consequence is that, like C=C double bonds, the peptide bond does not rotate. Its four substituents are frozen in space with the two α-carbons in trans configuration, opposite each other.

The other two bonds in the polypeptide backbone, those formed by the α-carbon, are ‘pure’ single bonds with the expected rotational freedom. Rotation around the nitrogen—carbon bond is measured as the φ (phi) angle, and rotation around the peptide bond carbon—α-carbon bond as the ψ (psi) angle.

This rotational freedom turns polypeptides into contortionists capable of forming U-turns and spirals. Globular proteins have compact shapes. Most are water soluble, but some are embedded in cellular membranes or form supramolecular aggregates, such as the ribosomes.

Hemoglobin and myoglobin, enzymes, membrane proteins, and plasma proteins are globular proteins. Fibrous proteins are long and threadlike, and most serve structural functions. The keratins of hair, skin, and fingernails are fibrous proteins, as are the collagen and elastin of the extracellular matrix.

Secondary Structure

A secondary structure is a regular, repetitive structure that emerges when all the φ angles in the polypeptide are the same and all the ψ angles are the same. Only a few secondary structures are energetically possible.

α-Helix

In the α-helix, the polypeptide backbone forms a right-handed corkscrew. ‘Right-handed’ refers to the direction of the turn: When the thumb of the right hand pushes along the helix axis, the flexed fingers describe the twist of the polypeptide.

The threads of screws and bolts are right-handed, too. The α-helix is very compact. Each full turn has 3.6 amino acid residues, and each amino acid is advanced 1.5 angstrom units (Å) along the helix axis (1 Å = 10⁻¹ nm = 10⁻⁴ μm = 10⁻⁷ mm).

Therefore a complete turn advances by 3.6 × 1.5 = 5.4 Å, or 0.54 nm. The α-helix is maintained by hydrogen bonds between the peptide bonds. Each peptide bond C—O is hydrogen bonded to the peptide bond N—H four amino acid residues ahead of it. Each C—O and each N—H in the main chain are hydrogen bonded. The N, H, and O form a nearly straight line, which is the energetically favored alignment for hydrogen bonds.

β-Pleated Sheet

The β-pleated sheet is far more extended than the α-helix, with each amino acid advancing by 3.5 Å. In this stretched-out structure, hydrogen bonds are formed between the peptide bond C—O and N—H groups of polypeptides that lie side by side.

protein structure beta pleated sheet secondary structure
Fig 8. Structure of the β-pleated sheets. A, The parallel β-pleated sheet. B, The antiparallel β-pleated sheet. Arrows indicate the direction of the polypeptide chain.

The interacting chains can be aligned either parallel or antiparallel, and they can belong either to different polypeptides or to different sections of the same polypeptide. Blanketlike structures are formed when more than two polypeptides participate. The α-helix and β-pleated sheet occur in both fibrous and globular proteins.

Tertiary Structure of Proteins

Globular proteins fold themselves into a compact tertiary structure because they have a hydrophobic core.

Sections of secondary structure are short, usually less than 30 amino acids in length, and they alternate with irregularly folded sequences. Unlike the α-helix and β-pleated sheet, which are formed by hydrogen bonds, tertiary structures are formed mainly by hydrophobic interactions between amino acid side chains.

These amino acid side chains form a hydrophobic core. Some polypeptides fold themselves into two or more globular structures that are connected by more flexible and extended portions of the polypeptide. In these cases we say that the protein forms multiple globular domains.

Quaternary Structure of Proteins

Quaternary structures are defined by the interactions between different polypeptides (subunits). Therefore only proteins with two or more polypeptides have a quaternary structure. In some of these proteins, the subunits are held together only by noncovalent interactions, but others have interchain disulfide bonds.

Glycoproteins contain covalently bound carbohydrate, and phosphoproteins contain covalently bound phosphate. Other non-polypeptide components can be bound to the protein, either covalently or noncovalently. They are called prosthetic groups.

Many enzymes contain prosthetic groups that participate as coenzymes in enzymatic catalysis.

Denaturing of Proteins

Proteins lose their biological activities when their higher order structure is destroyed. Peptide bonds can be cleaved by heating with strong acids or bases. Proteolytic enzymes (proteases) achieve the same in a gentle way, as occurs during protein digestion in the stomach and intestine. Disulfide bonds are cleaved by reducing or oxidizing agents.

The non-covalent interactions in proteins are so weak that the higher-order structure of proteins can be destroyed by heating. Within a few minutes of being heated above a certain temperature (often between 50 °C and 80 °C), the higher-order structure unravels into a messy tanglework. This process is called heat denaturation.

Denaturation destroys the protein’s biological properties. Stated another way, the biological properties of proteins require intact higher-order structures. Also the physical properties of the protein change dramatically with denatur-ation. For example, water solubility is lost because the de-natured polypeptide chains become irrevocably entangled.

Generally, protein denaturation is irreversible. A boiled egg does not become unboiled when it is kept in the cold. Not only heat, but anything that disrupts non-covalent interactions can denature proteins. Detergents and organic solvents denature proteins by disrupting hydrophobic interactions. Being nonpolar, they insert themselves between the side chains of hydrophobic amino acids.

Strong acids and bases denature proteins by changing their charge pattern. In a strong acid, the protein loses its negative charges; in a strong base, it loses its positive charges. This deprives the protein of intra-molecular salt bonds.

Also, high concentrations of small hydrophilic molecules with high hydrogen bonding potential, such as urea, can denature proteins. They do so by disrupting the hydrogen bonds between water molecules. This limits the extent to which water molecules are forced into a thermodynamically unfavorable ‘ordered’ position at an aqueous non-polar interface, weakening the hydrophobic interactions within the protein.

Heavy metal ions (lead, cadmium, mercury) can denature proteins by binding to carboxylate groups and, in particular, sulfhydryl groups in proteins. Their affinity for functional groups in proteins is one reason for the toxicity of heavy metals.