Protein Structure

Protein structures are made by condensation of amino acids forming peptide bonds. The sequence of amino acids in a protein is called its primary structure. The secondary structure is determined by the dihedral angles of the peptide bonds, the tertiary structure by the folding of protein chains in space. Association of folded polypeptide molecules to complex functional proteins results in quaternary structure.

Define Protein Structure

Protein structure is defined as a polymer of amino acids joined by peptide bonds.

Related Topics

• Amino acids
• Peptide bond
• Denaturation of Proteins
• Enzymes
• Hormones

Let us see how a peptide bond is established from the following reaction:

Formation of Peptide Bond

We can thus see that the peptide bond (-CO-NH) is formed between the amine group of one molecule and the carboxyl group of the adjacent molecule followed by the elimination of a water molecule. This bond is otherwise an amide linkage. When peptide bonds are established among more than ten amino acids, they together form a polypeptide chain. Very often, when a polypeptide chain has a mass exceeding 10000u and the number of amino acids in the chain exceeding 100, we get a protein.

Also Read: Denaturation of Proteins

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Classification of Proteins

Based on the molecular shape, proteins can be classified into two types.

1. Fibrous Proteins:

When the polypeptide chains run parallel and are held together by hydrogen and disulfide bonds, then the fiber-like structure is formed. Such proteins are generally insoluble in water. These are water-insoluble proteins.

Example – keratin (present in hair, wool, and silk) and myosin (present in muscles), etc.

2. Globular Proteins:

This structure results when the chains of polypeptides coil around to give a spherical shape. These are usually soluble in water.

Example – Insulin and albumins are common examples of globular proteins.

Levels of Protein Structure

1. Primary Structure of Protein

• The Primary structure of proteins is the exact ordering of amino acids forming their chains.
• The exact sequence of the proteins is very important as it determines the final fold and therefore the function of the protein.
• The number of polypeptide chains together form proteins. These chains have amino acids arranged in a particular sequence which is characteristic of the specific protein. Any change in the sequence changes the entire protein.

The following picture represents the primary protein structure (an amino acid chain). As you might expect, the amino acid sequence within the polypeptide chain is crucial for the protein’s proper functioning. This sequence is encrypted in the DNA genetic code. If mutation is present in the DNA and the amino acid sequence is changed, the protein function may be affected.

The protein ‘s primary structure is the amino acid sequence in its polypeptide chain. If proteins were popcorn stringers designed to decorate a Christmas tree, a protein ‘s primary structure is the sequence in which various shapes and varieties of popped maize are strung together.

Covalent, peptide bonds which connect the amino acids together maintain the primary structure of a protein.

All documented genetic disorders, such as cystic fibrosis, sickle cell anemia, albinism, etc., are caused by mutations resulting in alterations in the primary protein structures, which in turn lead to alterations in the secondary , tertiary and probably quarterly structure.

Amino acids are small organic molecules consisting of a chiral carbon with four substituents. Of those only the fourth the side chain is different among amino acids.

2. Secondary Structure of Protein

Secondary structure of protein refers to local folded structures that form within a polypeptide due to interactions between atoms of the backbone.

• The proteins do not exist in just simple chains of polypeptides.
• These polypeptide chains usually fold due to the interaction between the amine and carboxyl group of the peptide link.
• The structure refers to the shape in which a long polypeptide chain can exist.
• They are found to exist in two different types of structures α – helix and β – pleated sheet structures.
• This structure arises due to the regular folding of the backbone of the polypeptide chain due to hydrogen bonding between -CO group and -NH groups of the peptide bond.
• However, segments of the protein chain may acquire their own local fold, which is much simpler and usually takes the shape of a spiral an extended shape or a loop. These local folds are termed secondary elements and form the proteins secondary structure.

(a) α – Helix: 

α – Helix is one of the most common ways in which a polypeptide chain forms all possible hydrogen bonds by twisting into a right-handed screw with the -NH group of each amino acid residue hydrogen-bonded to the -CO of the adjacent turn of the helix. The polypeptide chains twisted into a right-handed screw.

(b) β – pleated sheet: 

In this arrangement, the polypeptide chains are stretched out beside one another and then bonded by intermolecular H-bonds. In this structure, all peptide chains are stretched out to nearly maximum extension and then laid side by side which is held together by intermolecular hydrogen bonds. The structure resembles the pleated folds of drapery and therefore is known as β – pleated sheet

3. Tertiary Structure of Protein

• This structure arises from further folding of the secondary structure of the protein.
• H-bonds, electrostatic forces, disulphide linkages, and Vander Waals forces stabilize this structure.
• The tertiary structure of proteins represents overall folding of the polypeptide chains, further folding of the secondary structure.
• It gives rise to two major molecular shapes called fibrous and globular.
• The main forces which stabilize the secondary and tertiary structures of proteins are hydrogen bonds, disulphide linkages, van der Waals and electrostatic forces of attraction.

4. Quaternary Structure of Protein

The spatial arrangement of various tertiary structures gives rise to the quaternary structure. Some of the proteins are composed of two or more polypeptide chains referred to as sub-units. The spatial arrangement of these subunits with respect to each other is known as quaternary structure.

The exact amino acid sequence of each protein drives it to fold into its own unique and biologically active three-dimensional fold also known as the tertiary structure. Proteins consist of different combinations of secondary elements some of which are simple whereas others are more complex. Parts of the protein chain, which have their own three-dimensional fold and can be attributed to some function are called “domains”. These are considered today as the evolutionary and functional building blocks of proteins.

Many proteins, most of which are enzymes contain organic or elemental components needed for their activity and stability. Thus the study of protein evolution not only gives structural insight but also connects proteins of quite different parts of the metabolism.

Also Read: Laboratory Test of Proteins

Rules of Protein Structure

• The type determines the function of a protein.
• A protein’s shape is determined by its primary structure (the amino acid sequence).
• The amino acid sequence within a protein is determined by the encoding sequence of nucleotides in the gene (DNA).

Summary of Protein Structure

Linderstrom-Lang (1952) in particular first suggested a hierarchy of protein structure with four levels: central, secondary, tertiary , and quaternary. You are already familiar with this hierarchy, because the most useful starting point for teaching basic protein structure is this structural grouping.

• The primary structure of protein is the hierarchy’s basic level, and is the particular linear sequence of amino acids comprising one polypeptide chain.
• Secondary structure is the next level up from the primary structure, and is the regular folding of regions into specific structural patterns within one polypeptide chain. Hydrogen bonds between the carbonyl oxygen and the peptide bond amide hydrogen are normally held together by secondary structures.
• Tertiary structure is the next level up from the secondary structure, and is the particular three-dimensional arrangement of all the amino acids in a single polypeptide chain. This structure is usually conformational, native, and active, and is held together by multiple noncovalent interactions.
• Quaternary structure is the next ‘step up’ between two or more polypeptide chains from the tertiary structure and is the specific spatial arrangement and interactions.