LL5ß is a eukaryotic protein 1253 amino acid in length mainly associated with the stabilisation of microtubules and ensuring cell dynamics occur in a single direction.  The distribution of LL5ß is dependent on the cellular concentration of PI(3,4,5)P3 which binds to LL5ß through it’s pleckstrin homology domain (PH domain).  When the concentration of PI(3,4,5)P3 is low, the binding affinity for LL5ß is lost and LL5ß is driven to vesicular compartments. LL5ß has been found to stabilise microtubules through it’s communication with cytoplasmic linker-associated proteins (CLASPS) which in turn bind to the (+) end of microtubules.

 

Through multiple sequence alignment of related proteins using clustal omega we determined that the most conserved region of our protein was close to the c-terminus.  This high rate of conservation suggests that there is a key domain related to the function of the protein present at this location.

 

In order to find out more, using structural analysis we were able to analyse the domains of  LL5ß.  Secondary structural analysis done using Psipred found the structure consists mostly of alpha helices with a few ß strands near to the c-terminus.  To further enhance our understanding of LL5ß, we analysed the structure using programs which would predict the tertiary structure.  Our most promising interpretations of the structure came from Phyre2 and RaptorX.  While the tertiary structure of LL5ß predicted by the two programs is very different, we can clearly see a domain at the c-terminus composed of primarily ß-sheets and a domain in the centre of the protein composed of alpha helices.

 

We can understand these domains more by using our sequence analysis. The use of programs such as BLAST and PFAM allowed us to determine that our protein of interest contained several domains: - a C-terminal PH domain, a SPEC superfamily domain and a DUF2361 superfamily domain.  As shown by it’s high conservation rate between related proteins, the pleckstrin homology domain is crucial to the function of the LL5ß.  This is due to LL5ß being activated through it’s binding with PI(3,4,5)P3.  This binding occurs through the use of the PH domain therefore making the PH domain critical to the function of LL5ß.

 

In summary, LL5ß is crucial in the formation of microtubules and cell dynamics.  The pleckstrin homology domain in LL5ß has been highly conserved between species due to it’s vital role in binding with PI(3,4,5)P3.  However the exact mechanistic interaction has not been fully understood and there is a possibility that alternative binding partners also play a crucial role in the function.