Opis stanowiska
Design of new protein structures with precisely defined features using parametric models
Post-Doctoral Research Assistant in Structural Bioinformatics
The aim of the project is to set up a bioinformatics pipeline for designing new protein structures with the use of parameterization, a procedure that allows representing protein backbones with mathematical equations. The best-known protein structure class that has been fully parameterized is α-helical coiled coils, encompassing very regular structures in which canonical α helices are wound around each other to form bundles. There are a vast number of studies in which parameterization has been used to support analysis of the sequence-structure-function relationship in α-helical coiled-coil domains of various proteins (e.g., involved in bacterial signal transduction). We propose that other protein structures could be also parameterized, and thus manipulated and studied in a similar fashion to α-helical coiled coils. To investigate this hypothesis, we will study two protein classes: π-helical coiled coils, hypothetical structures that have never been observed in nature, and β-helices, widespread regular structural motifs that occur in many functionally unrelated proteins. The key aspect of the project will be experimental validation (crystallography/NMR) of novel structures designed with the aid of the parametric models. The successful candidate will work on development of parametric models for one of the two aforementioned protein classes, in silico design simulations, and deciphering structure-sequence relationships. Individual ideas and side-projects are also welcomed.