Domain and Motif in Protein
1.1 Domain: Shorter polypeptide chain like that of Myoglobin and Hemoglobin fold into a single compact globular structure. However, Examination of the structure of proteins has revealed that larger polypeptides consist of several independently folded regions, each separated by a short polypeptide sequence. Those independently folded regions are called domains. They assume a convenient 3d structure. Well defined domains often act as independent folding units and retain at least part of their normal biological activity even if they are split off from rest of the protein.
A domain may consist of about 50-350 amino acids. Short proteins may have a single domain and extremely long proteins may occasionally have upto a dozen. Zinc finger is an example of shortest protein domain.
Usually domains are responsible for a particular function or interaction contributing to overall role of the protein. Similar domains can be found in protein with different functions. For example: Src Homology 3 (SH3) domains are smaller domains of about 50 amino acid residues. They occur in a diverse range of proteins with different functions including adaptor proteins, phosphatidylinositol 3-kinases, phospholipases and myosin. A particular domain may appear in a variety of evolutionarily related proteins.
Protein modification is possible due to independently stable nature of proteins domains that can be easily swapped and recombined with different domains to create proteins with different function. Thus. Domains are considered as building blocks in molecular evolution.
1.2 Motif: In case of proteins, use of term motif refers to a set of contiguous secondary structural elements, which is also referred to as super secondary structure. They are made up of connectivity between secondary structural pieces like helices and sheets in different combinations. In other words, protein motifs are small region of proteins, three dimensional structure or amino acid sequence shared among different proteins. Some common motifs are HTH, HLH, and Hairpin etc.
Motifs are recognizable regions of protein structure. They may or may not be defined by a unique chemical or biological functions. They are typically only between 3-23 amino acids long. They are spatially close but not necessarily adjacent in the sequence. Proteins with similar functions often have same motif. As they are so short and mostly function independently of the rest of the protein sequence or structure, they play an essential role in protein evolution.
Some of the small motifs are independently stable domains such as Zn fingers or EGF domains. Other may act as a part of larger domain such as helix-turn-helix motifs or omega loop.
1.3 In Summary: Comparison between Domain and Motif
| Motif | Domain |
| Motif is supersecondary structure of protein. | Domain is tertiary structure of protein. |
| They are formed by the connected alpha-helices and beta-sheets through loops. | They are formed by the formation of disulphide bridges, ionic bonds, and hydrogen bonds between amino acids side chain. |
| They are biological structure made up of connectivity between secondary structural elements. | They are independently folded region of protein. |
| They are not stable independently. | They are stable independently. |
| Motifs are composed of 3-23 amino acids. | Domains are composed of 50-350 amino acids. |
| They have mainly structural function in protein structure. | They have mainly functional importance. |
| They perform similar biological functions through a particular protein family. | Similar domains may have different functions in different proteins. |
Reference:
- Burton E. Tropp . Molecular Biology : Genes to Proteins 78-80 Jones and Bartlett publication (2008)
- George M. Malacinski. Essentials of Molecular Biology 126-128 Jones and Bartlett publication (2002)
- Elliott J Stollar, David P Smith; Uncovering protein structure. Essays Biochem 8 October 2020; 64 (4): 649–680. doi: https://doi.org/10.1042/EBC20190042
- https://bio.libretexts.org/Bookshelves/Cell_and_Molecular_Biology/Book
- https://www.cambridge.org/core/books/abs/essential-bioinformatics/protein-motifs-and-domain-prediction
- https://bio.libretexts.org/Bookshelves/Biochemistry/Fundamentals_of_Biochemistry
- https://www.uniprot.org/help/domain
- https://www.ebi.ac.uk/training/online/courses/protein-classification-intro-ebi-resources/protein-classification/what-are-protein-domains/
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