In this Lab, the effect of amino acid availability as regulating factor of every protein synthesis is investigated
Knowing that a number of proteins have a similar content of the same AA means to be able to predict that the expression
of these proteins will depend on the same environmental conditions controlling AA availability. From this consideration
arises the need to create a tool capable of quickly calculating the AA content of proteins and compare groups of protein
based on their AA content. The information gleaned from this comparison may help to solve many biological and
The studies based on the principle
Based on this approach, we carried out some research focused on AA composition of human proteins. The first study
compared human proteins on the basis of their AA content by a hierarchical, agglomerative clustering method. Proteins
with similar tissue expression, even though with different function, were very close in the cluster, and this was
suggestive that the local availability of AAs was a major driver of protein expression, conditioned by tissue context
Moreover, in a second study we calculated the absolute and the relative frequencies of all AA contained in the proteins
expressed selectively by distinct cellular populations. Our analysis demonstrated that the estimation of
glutamate/glutamine ratio can give information on tissue oxygenation. Interestingly, this study suggested that the
similar content in single AAs of proteins codified by the same chromosome could be one of the reasons for gene
clustering (Vernone 2019).
The relationship between gene clustering and AA content of human proteins warrants further studies, which require the
knowledge of both position in chromosome and AA content of the proteins. The position of the codifying gene becomes
relevant when analysing common features of groups of proteins, such as amino acid content, in gene clusters, loci or
other specific regions of human chromosomes. To perform this analysis there is a need for a bioinformatics tool able to
provide details on the position of the codifying gene and on the AA sequence and length of the translated protein.
HERE AND NOW: PROTEIN ANALYSIS TOOL, CHROMOSOME ANALYSIS TOOL
In PROTEIN section, a tool has been created with the aim of calculating the AA content of proteins and compare groups of
protein based on their AA content.
In CHROMOSOME section, a tool has been created with the aim of providing lists of proteins based on the position of
their codifying gene, also supplying the AA sequence and length of the translated protein.