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Coarse-grained and atomistic modelling of phosphorylated intrinsically disordered proteins

Author

Summary, in English

Intrinsically disordered proteins (IDPs) are involved in many biological processes such as signalling, regulation and recognition. One of the main questions regarding IDPs is how sequence, structure and function are related. Phosphorylation, a type of post-translational modification prevalent in intrinsically disordered proteins and regions, is an example of how modifications at the sequence level can induce changes in structure and thereby influence function. The lack of well-defined tertiary structure in IDPs makes them better described by an ensemble of conformations than a single structure. Furthermore, it causes them to be more difficult to study than conventional proteins, so a combined approach of experimental and simulation techniques are often advantageous. However, simulations rely on appropriate models. In this thesis, the conformational ensembles of IDPs, especially the saliva protein statherin, have been investigated using both simulations with different models and the experimental techniques small-angle X-ray scattering and circular dichroism spectroscopy. The aims have been to contribute to the collection of available tools for studying IDPs, by investigating models, and to explore the link between sequence and structure of IDPs, with special focus on phosphorylation. It was shown that a coarse-grained "one bead per residue model" can be used to describe several different IDPs and provide an understanding of how protein length, charge distribution and salt concentration affects IDPs. Furthermore, by including a hydrophobic interaction the model could qualitatively describe the self-association of statherin and provide insight on the balance of interactions and entropy governing the process. The model was however shown to overestimate the compactness of longer and more phosphorylated IDPs. Turning to atomistic simulations, it was revealed that the conformational ensembles of phosphorylated IDPs are highly influenced by salt bridges forming between phosphorylated residues and arginine/lysine/C-terminus, such that over-stabilised salt bridges cause larger compaction than observed in experiments. Another force field could however detect phosphorylation-induced changes in global compaction and secondary structure and relate them to interactions between specific residues, illustrating the potential ability of simulations to provide insight into phosphorylation.

Publishing year

2021

Language

English

Document type

Dissertation

Publisher

Lund University (Media-Tryck)

Topic

  • Theoretical Chemistry

Keywords

  • intrinsically disordered proteins
  • phosphorylation
  • simulations
  • Monte Carlo
  • molecular dynamics
  • coarse-graining
  • atomistic
  • statherin
  • small-angle X-ray scattering
  • circular dichroism

Status

Published

ISBN/ISSN/Other

  • ISBN: 978-91-7422-828-1
  • ISBN: 978-91-7422-829-8

Defence date

29 October 2021

Defence time

13:00

Defence place

Sal A, Kemicentrum, Lund. Join via zoom: https://lu-se.zoom.us/j/66787839114

Opponent

  • Elena Papaleo (Associate Professor)