Gene and Protein Virtual Lab

In this Lab, the effect of amino acid availability as regulating factor of every protein synthesis is investigated

The local availability of amino acids (AA) may be a limiting factor in protein biosynthesis.

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 biochemical questions.

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 (Vernone 2013). (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3617222/) 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). (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6502398/)

Further studies

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.