What is the Difference Between Motif and Domain in Protein Structure

The main difference between motif and domain in protein structure is that a motif is a super secondary structure whereas a protein domain is a tertiary structure of proteins. Furthermore, motifs perform similar biological functions through a particular protein family, while protein domain evolves, functions, and exists independently of the rest of the protein chain.  

Motif and domain are to types of structural components that can occur in a protein chain. Moreover, they have structural and functional importance in proteins. 

Key Areas Covered 

1. What is a Motif in Protein Structure
     – Definition, Structure, Importance
2. What is a Domain in Protein Structure
     – Definition, Structure, Importance
3. What are the Similarities Between Motif and Domain in Protein Structure
     – Outline of Common Features
4. What is the Difference Between Motif and Domain in Protein Structure
     – Comparison of Key Differences

Key Terms 

Protein Domain, Protein Motif, Protein Structure, Supersecondary Structure, Tertiary Structure

What is a Motif in Protein Structure 

A motif is a super secondary structure of a protein. Generally, the first evolving 3D structure of a protein is the secondary structure, which can be either an alpha-helix or beta-sheet. Also, this secondary structure is formed to neutralize the natural polarity of different amino acids in the primary protein structure, which is a sequence of amino acids. Typically, this neutralization occurs through the formation of hydrogen bonds. Further, these secondary structures combine with each other to form these motifs. The combining occurs through small loops. 

Figure 1: Zinc Fiber Motif

Furthermore, sometimes, motifs of a particular protein family perform a similar function. For example, Zinc fiber motif performs a DNA binding function. Some other examples of motifs in protein structure are the beta-hairpin motif, Greek key motif, Omega loop motif, helix-loop-helix motif, helix-turn-helix motif, nest motif, niche motif, etc. 

What is a Domain in Protein Structure 

A domain in protein structure is the tertiary structure of a protein. Moreover, it forms, exists, and functions independently from the other components of the protein. Although a motif is formed through the interaction of secondary structural elements in a protein, the interactions that occur between secondary structural elements are stronger in a domain. Here, several kinds of bonds can form between these secondary structural elements. Out of that, the main type of bonds formed are the disulfide bridges. They are the most stable interactions as well. 

Figure 2: Three Domains of Pyruvate Kinase

Moreover, ionic bonds or salt bridges can also form between the positively and negatively charged amino acids in the secondary structures. Additionally, hydrogen bonds can form to stabilize the tertiary structure. On the other hand, protein domains typically have a globular structure, and it is soluble in water. Also, a protein domain performs a unique function of a protein. Generally, four classes of protein domains can be identified; all-α domains, all-β domains, α+β domains, and α/β domains. 

Similarities Between Motif and Domain in Protein Structure 

• Motif and domain are two components of a protein structure. 
• They have both structural and functional importance in the protein structure.  
• Also, both are made up of a chain of amino acids linked by peptide bonds. 
• Moreover, they are made up through the interactions of alpha-helices and beta-sheets. 
• Besides, both are 3D structures. 

Difference Between Motif and Domain in Protein Structure 

Definition 

A motif in protein structure refers to a chain-like biological structure made up of connectivity between secondary structural elements while a domain in protein structure refers to an independent folding unit of the three-dimensional protein structure. Thus, this is the main difference between motif and domain.

Type of Structure 

Another difference between motif and domain is that a motif is a super secondary structure of a protein, while a domain is a tertiary structure of the protein.  

Formation 

Moreover, a motif is formed by the connected alpha-helices and beta-sheets through loops, while a domain is formed by the formation of disulfide bridges, ionic bonds, and hydrogen bonds between amino acid side chains. 

Significance 

Motifs mainly have a structural function in the protein structure, while domains mainly have functional importance. 

Function 

Furthermore, motifs have similar functions through protein families, while domains have unique functions. 

Stability 

Additionally, motifs are not stable independently, while domains are independently stable. Hence, this is also an important difference between motif and domain.

Conclusion 

A motif in protein structure is a super secondary structure of a protein. Connectivity between alpha-helices and beta-sheets produce motifs. Also, they have similar functions in a particular protein family. On the other hand, a domain is the tertiary structure of a protein. Significantly, it can form and exist independently in the protein structure. Also, it has a unique function in the protein structure. Therefore, the main difference between motif and domain is the structure and importance. 

References:

1. “Protein 3D Structure: Structural Levels, Motifs and Folds.” Basic Principles of Protein Three-Dimensional Structure: Levels of Protein Structure, Motifs, Domains and Databases, Available Here.

Image Courtesy:

1. “Zinc finger rendered” By Thomas Splettstoesser (www.scistyle.com) – self-made, based on PDB structure 1A1L, the open source molecular visualization tool PyMol and Cinema 4D (CC BY-SA 4.0) via Commons Wikimedia  
2. “Pyruvate kinase protein domains” By Thomas Splettstoesser (www.scistyle.com) – Own work (CC BY-SA 3.0) via Commons Wikimedia