Coarse-grained and atomistic modelling of phosphorylated intrinsically disordered proteins
(2021)- Abstract
- 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... (More)
- 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. (Less)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/a5446882-38bc-4045-ae24-c5f08236f110
- author
- Rieloff, Ellen LU
- supervisor
-
- Marie Skepö LU
- Jan Forsman LU
- opponent
-
- Associate Professor Papaleo, Elena, Technical University of Denmark
- organization
- publishing date
- 2021
- type
- Thesis
- publication status
- published
- subject
- keywords
- intrinsically disordered proteins, phosphorylation, simulations, Monte Carlo, molecular dynamics, coarse-graining, atomistic, statherin, small-angle X-ray scattering, circular dichroism
- pages
- 274 pages
- publisher
- Lund University (Media-Tryck)
- defense location
- Sal A, Kemicentrum, Lund. Join via zoom: https://lu-se.zoom.us/j/66787839114
- defense date
- 2021-10-29 13:00:00
- ISBN
- 978-91-7422-829-8
- 978-91-7422-828-1
- language
- English
- LU publication?
- yes
- id
- a5446882-38bc-4045-ae24-c5f08236f110
- date added to LUP
- 2021-09-27 13:39:05
- date last changed
- 2022-06-27 13:34:03
@phdthesis{a5446882-38bc-4045-ae24-c5f08236f110,
abstract = {{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.}},
author = {{Rieloff, Ellen}},
isbn = {{978-91-7422-829-8}},
keywords = {{intrinsically disordered proteins; phosphorylation; simulations; Monte Carlo; molecular dynamics; coarse-graining; atomistic; statherin; small-angle X-ray scattering; circular dichroism}},
language = {{eng}},
publisher = {{Lund University (Media-Tryck)}},
school = {{Lund University}},
title = {{Coarse-grained and atomistic modelling of phosphorylated intrinsically disordered proteins}},
url = {{https://lup.lub.lu.se/search/files/103018645/opponent_ex_ellen.pdf}},
year = {{2021}},
}