Protein Structure

You might not know, but protein is the most abundant substance in your body water. Every single cell in your body consists of a protein. Proteins have a unique 3-D structure, enabling it to perform a variety of functions. Protein structures refer to a condensation of amino acids which forms peptide bonds. There are four types of structure in proteins. They are the primary structure of protein, the secondary structure of protein, tertiary, and quaternary. The primary structure is nothing but the sequence of amino acids in the protein. Secondary structure refers to dihedral angles of peptide bonds, and tertiary structure refers to the folding of protein chains. In this article, we have explained the essential protein structure in an easy-to-digest format.

Protein Structure Definition

Proteins are nothing but biological polymers. They are polymers of amino acids joined together by amino acids. You must know that amino acids are the building blocks of proteins. It means that proteins have a chain-like structure, where amino acids are the primary ingredient.  The term structure, when it is used in relation to proteins, goes on to have a much more complex meaning than it generally does for small molecules. Proteins are macromolecules and it has four different levels of structure – i.e. primary, secondary, tertiary and quaternary.

These amino acids get linked together with peptide bonds. When such a few bonds get linked together, it becomes a polypeptide chain. When one or more of these polypeptide chains get twisted or folded, it forms a protein.  

The size of the protein varies significantly. It is dependent on the number of polypeptide molecules it holds. Insulin is one of the smallest protein molecules out there. Titin is the largest protein molecule, having 34,350 amino acids.  

Classification of protein: Fibrous and globular are two types of proteins, decided by their molecular shape. When polypeptide chains run parallel, bonded by hydrogen and disulfide, you get a fiber-like structure. And when chains coil around, they give out a spherical shape.  

Also, four types of structure make up a protein molecule. You can learn about them below. The image below can help you with understanding protein structures. 

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Primary Protein Structure 

The primary structure of a protein refers to a unique formation and sequence in which amino acids get combined. They all get linked together to produce a protein molecule. The primary structure is responsible for giving particular properties to protein. Depending on the side-chain substituent, an amino acid can be classified into being acidic, basic or neutral. Although twenty amino acids are required for the synthesis of various proteins found in humans, we can synthesize only ten. The remaining ten are called essential amino acids and must be obtained in a diet.

The amino acid sequence of a protein is kind of encoded in the DNA. Proteins are synthesized by a series of steps called transcription and translation. Often, post-translational modifications, such as glycosylation or phosphorylation which occur are necessary for the biological function of the protein. While the amino acid sequence makes up the primary structure of the protein, the chemical and biological properties of the protein are very much dependent on the three-dimensional or tertiary structure.

In total, there are 20 amino acids in the human body. They all have two groups – carboxyl and amino group. However, each one has a variable group, called an ‘R’ group. That R group is accountable for lending a unique structure to a protein. 

All the protein gets determined by the sequencing of the amino acids. This formation and sequence of amino acids in proteins is exceptionally unique. If you change even a single amino acid in the chain, then you can end up with a non-functioning protein.

Secondary Protein Structure 

This secondary protein structure gives a unique shape to the protein. It’s where the peptide backbone of a protein structure gets folded onto itself. The folding of the polypeptide chains occurs because of the interaction between the carboxyl group and amine groups of the peptide chains. 

Secondary protein structure gives out two types of shapes; they are α-helix and β-pleated sheets.

• α-helix – The backbone of protein follows a helical structure. Across different layers of the helix, the hydrogen forms bonds with oxygen, rendering a helical structure.  The side-chain substituents of the amino acid groups in an α helix extend to the outside. Hydrogen bonds form between the oxygen of each C = O bond in the strand. The hydrogen of each N - H group four amino acids below it in the helix. The hydrogen bonds make this structure very much more stable. The side-chain substituents of the amino acids always fit in beside those N-H groups. 

• β-pleated sheet – In this shape, polypeptide chains get stacked next to each other. The external hydrogen molecules of these chains form intramolecular bonds, giving it a sheet-like structure. The hydrogen bonding occurs between strands, rather than within strands. The sheet conformation consists of pairs of strands that are lying side by side.  The carbonyl oxygen in one strand bonds with the amino hydrogen of the adjacent strand. The two strands can either be parallel or antiparallel depending on whether the strand directions are the same or opposite. The antiparallel ß-sheet is more stable due to the more well-aligned hydrogen bonds. 

Tertiary Protein Structure 

Tertiary structure is responsible for the formation and 3-D shape of the protein. As amino acids form bonds during secondary structure, they give out shapes such as helices and sheets. Further, the structure can coil or fold randomly, and that’s what you call the tertiary structure of proteins. When the structure gets disturbed, the protein becomes denatured. Such a protein gets chemically affected, and the structure becomes distorted. The protein molecule will bend and twist in such a way so as to achieve the maximum stability or lowest energy state. The three-dimensional shape of a protein may seem to be irregular and random. It is fashioned by many stabilizing forces due to the bonding interactions between the side chain groups of the amino acids.

Quaternary Protein Structure 

The spatial arrangement of two or more peptide chains leads you to a quaternary protein structure. You should know that proteins don’t necessarily need to have a quaternary structure. Also note that primary, secondary, and tertiary structures of proteins are available in all-natural proteins. But, that’s not the case for quaternary structure. Thus, when a particular protein has the first three structures, it can qualify to be a protein. 

Analysis of Protein Structure

The complexities of a protein structure do make the elucidation process of a complete protein structure extremely difficult, even with the most advanced analytical equipment.  An amino acid analyzer can be used to determine which amino acids are present and their molar ratios. The sequence of the protein can then be analyzed by means of peptide mapping, and the use of Edman degradation. This process is routine for peptides and small proteins but more complex for large multimeric proteins. 

One method which is used to characterize the secondary structure of a protein is called circular dichroism spectroscopy. The different types of secondary structure, α-helix, ß-sheet, and random coil, all have characteristic circular dichroism spectra in the far-UV region of the spectrum. To determine the three-dimensional structure of a protein by X-ray diffraction, a large and well-ordered single crystal is required. X-ray diffraction allows the measurement of the short distance between atoms and it yields a three-dimensional electron density map, which can be used to build a model of the protein structure.  

The use of NMR to determine the three-dimensional structure of a protein has some advantages over X-ray diffraction. It can be carried out in solution form, and thus the protein is free from the constraints of the crystal lattice. The two dimensional NMR techniques generally used are NOESY which measures the distance between atoms through space, and COESY which measures distance through bonds. The variety of methods for determining protein stability emphasizes the complexity of the nature of protein structure and the importance of maintaining that structure for a successful pharmaceutical product.