Investigating the structure and evolution of keratin intermediate filaments

Abstract

Intermediate filaments (IFs) are one of the three major types of cytoskeletal filaments present in cells. The monomers of IFs consist of three distinct regions the head, the coiled-coil domain, and the tail. The heads contain serine and glycine repeats and are essential for the formation of the filament. These monomers form coiled-coil dimers, which then form higher-order structures. As IFs form complex filamentous structures, it is hard to experimentally determine their structure. In a previous work, Dr Neelesh Soni used integrative modelling to model the K5K14 filament, but this did not contain any heads or tails. Here, I have used homology modelling using this K5K14 filament as a template. I built a structure of the K8K18 filament, both with and without heads. I carried out molecular dynamics simulations to analysethe stability and flexibility of the proteins. In order to validate this structure, I analysed a datasetof human intermediate filament variants to study the inter and intra-dimer interactions. I discovered that certain types of mutations are more prevalent at specific heptad positions. Volume and charge are two of the key factors that affect dimer assembly, and changes in these due to mutations will lead to keratinopathies. Using this information, we will be able to predict mutations that disrupt the filament and those that do not, and test our findings experimentally. Additionally, by analysing keratin sequences from different organisms, I found that they can be divided into two distinct types. I also discovered that keratins are well-conserved across species. We can build structures of keratin filaments in different organisms, and identify conserved structural regions, and find interacting proteins as well.