Monday, July 18, 2016

Standard and non-standard amino acids

Amino acids are molecules that, from a chemical standpoint, are characterized by the presence of an amine group and a carboxylic group (acid), and hence its name: amino acid. Its main function is to serve as monomers for the synthesis of peptides and proteins. Of all the amino acids in nature, there is a set of 20 amino acids which are designated by standard amino acids, and that are used as building blocks for most of the proteins produced by any living being. These amino acids are widely studied and have been the central elements in my last posts. Just to remember, the standard amino acids are:

- glycine
- alanine
- proline
- valine
- leucine
- isoleucine
- methionine
- phenylalanine
- tyrosine
- tryptophan
- serine
- threonine
- cysteine
- asparagine
- glutamine
- lysine
- arginine
- histidine
- aspartate
- glutamate
However, besides the standard amino acids, there are many others that are found in some proteins and are called non-standard amino acids. The idea of ​​using these non-standard amino acids is simple to understand. By having a composition different from the standard amino acids, they present different physicochemical properties. Therefore, when it is necessary to introduce in a protein a local with certain properties, if they cannot be provided by the standard amino acid, it is incorporated in the sequence a non-standard amino acid. With regard to translation, in these cases, at these sites are introduced standard amino acids, which suffer post-translation covalent modifications to give amino acids with other features. I would like to highlight something that I think it is important. How you will notice below, several of the non-standard amino acids are found in the extracellular matrix proteins. As the extracellular matrix is a very complex structure, establishing numerous interactions with many different molecules (extracellular and cellular molecules), it is necessary that the proteins that make up the matrix may present a high versatility in the interactions that they establish, hence the need to specifically include some amino acids that have different characteristics. Some non-standard amino acid examples include:
- Cystine, desmosine and isodesmosine, which are amino acids found in extracellular matrix proteins such as elastin;


- Hydroxyproline and hydroxylysine, found in the most abundant protein of  the extracellular matrix – collagen;


- Gamma-carboxyglutamate, found in osteocalcin which is an extracellular matrix protein of bone, but also in the pro-thrombin, which is important for the coagulation cascade;
- Phosphoserine, phosphothreonine and phosphotyrosine, which are found in many different proteins, as protein phosphorylation is the most common post-translational modification, and always involves amino acids with hydroxyl groups in their side chains;

- N-acetillysine, which is fundamental to the structure of histones:
- Methyllyisine, which is found in myosin, a motor protein of our cytoskeleton, more specifically of actin filaments.

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