Protein Domains

Protein Domains

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protein domains

Proteomics is known as the study of protein structures and these structural units are distinguished as protein domains. The overall functional role of a protein depends on its structure. Most proteins comprise of multiple structural domains. Similarly, a specific domain may appear in one or more different proteins. In a nutshell, a protein domain is best described as a conserved part of a protein chain or a protein sequence.

A crucial feature of any protein domain is that they exist independently and can successfully establish a stable form. It is because of this noted feature of protein domains, processes to discover chimeric proteins can easily be executed by using genetic engineering between two proteins.

How is a protein domain measured?

Protein domains are part of tertiary structures. As a result, each domain is unique with a special three-dimensional structure. This structure is again very contributing in nature as these domains are highly stable independently. Did you know that modification of proteins is possible? Well, thanks to the stable protein domains that can be easily swapped and recombined with different domains to create proteins with differing functions.

The entire process is termed as ‘Molecular Evolution’. Speaking about the length of protein domains, they are measured by their counts of amino acids. Not all protein domains are of equal length. The length of protein domains can range anywhere between 25 to 500 amino acids. An example of the shortest protein domain is the zinc finger. Another example of a short protein domain is the SR3 or the ‘Src Homology 3’ that is just 50 amino acids in length.

‘Residue’ is another chief factor determining the size of structural domains. 32 residues in E-selectin to 692 residues in lipoxygenase-1 mark the scale of variation. Shorter the protein domains, specifically less than 40 residues, easier they are to stabilize using disulfide bonds and metal ions.

On the contrary, larger domains of more than 300 residues comprise of multiple hydrophobic cores.

How is the study of protein domain useful?

Since proteins are building blocks and perform the activities of a living cell, studying about the protein domains benefit us in a number of ways.

  • They help duplicate and figure out DNA datas.
  • The same domain can be used to create other proteins with varying functions.
  • It contributes to the technique of X-Ray Crystallography.

CDD

A Conserved Domain Database and Search Service.

DOMO

DOMO is a database of homologous protein domain families. It was obtained from successive sequence analysis steps including similarity search, domain delineation, multiple sequence alignment and motif construction. 83054 non redundant protein sequences from SWISSPROT and PIR have been analysed yielding a database of 99058 domains clustered into 8877 multiple sequence alignments.

Pfam

Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains. Pfam version 7.7b (October 2002) contains alignments and models for 4832 protein families, based on the Swissprot 40 and SP-TrEMBL 18 protein sequence databases.

ProDom

The Protein Domain database.

PROSITE

PROSITE is a database of protein families and domains. It consists of biologically significant sites, patterns and profiles that help to reliably identify to which known protein family (if any) a new sequence belongs.

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