TY - BOOK

T1 - Computational modelling in structural biology

T2 - insights from small-angle scattering and molecular dynamics simulations

AU - Barclay, Abigail

PY - 2023

Y1 - 2023

N2 - Proteins play a diverse and crucial role in essential physiological pro-cesses, intricately interacting with other proteins and biomolecules suchas lipids or ligands. Understanding the structures and mechanisms ofthese biomolecular systems is crucial to understanding their specificfunctions. Experimental techniques are constantly improving. It is im-perative to simultaneously develop computational methods to bridgethe gap between raw data and meaningful results. The main focus ofthis thesis is on the development of analytical models and integrativecomputational tools to fully exploit the wealth of structural informationthat can be extracted from small-angle scattering (SAS) data. The thesisalso explores how molecular dynamics (MD) simulations of proteins canenhance the interpretation of experimental data by providing insightswhich are not accessible through experiments alone.Firstly, the thesis focuses on the advancement of size-exclusion chro-matography coupled with small-angle x-ray scattering (SEC-SAXS) andintroduces a novel procedure to investigate underlying structural dis-tributions within a single species. It shows how an analytical modelcan be refined against many frames from the same SEC-SAXS data setssimultaneously to provide more robust fit results. The procedure isapplied to study populations of nanodiscs. This thesis also explores dif-ferent methods for modelling flexible membrane proteins embedded innanodiscs. Flexible particles pose a challenge for SAS analysis, since thescattering signal is averaged over an ensemble of conformations. There-fore, an advanced semi-analytical model accounting for conformationaldiversity was built for the human growth hormone receptor (GHR) in ananodisc and refined against SAXS data. The thesis goes on to discussmethods for ensemble modelling of membrane proteins in nanodiscs.In the case of the GHR, a simulated ensemble of protein structures wasplaced in an analytical nanodisc model with pre-determined parame-ters. The averaged theoretical scattering from the ensemble was in goodagreement with the SAXS data. It is then shown how a novel methodbased on point-cloud models and Fast Debye Sums can be used to refinenanodisc parameters for an entire ensemble of protein structures in amore accurate and computationally efficient manner.Furthermore, this thesis delves into a comprehensive SAS study on theinteraction of α-Synuclein and negatively charged lipid structures. Thedata suggest that the amphipathic properties of the protein can induce abreak down of the lipid structures into smaller disc- or rod-like particles.Detailed model-free analysis as well analytical models were used tocharacterise the structural transformations.Finally, the focus is shifted away from SAS towards all atom simulationsof amyloid fibrils. Experimental Φ-values were employed to guide thesimulations to sample the transition state of amyloid fibril elongation.The crucial interactions sites between the incoming monomer and fibrilend were identified to help shed light on the mechanisms of fibrilformation.

AB - Proteins play a diverse and crucial role in essential physiological pro-cesses, intricately interacting with other proteins and biomolecules suchas lipids or ligands. Understanding the structures and mechanisms ofthese biomolecular systems is crucial to understanding their specificfunctions. Experimental techniques are constantly improving. It is im-perative to simultaneously develop computational methods to bridgethe gap between raw data and meaningful results. The main focus ofthis thesis is on the development of analytical models and integrativecomputational tools to fully exploit the wealth of structural informationthat can be extracted from small-angle scattering (SAS) data. The thesisalso explores how molecular dynamics (MD) simulations of proteins canenhance the interpretation of experimental data by providing insightswhich are not accessible through experiments alone.Firstly, the thesis focuses on the advancement of size-exclusion chro-matography coupled with small-angle x-ray scattering (SEC-SAXS) andintroduces a novel procedure to investigate underlying structural dis-tributions within a single species. It shows how an analytical modelcan be refined against many frames from the same SEC-SAXS data setssimultaneously to provide more robust fit results. The procedure isapplied to study populations of nanodiscs. This thesis also explores dif-ferent methods for modelling flexible membrane proteins embedded innanodiscs. Flexible particles pose a challenge for SAS analysis, since thescattering signal is averaged over an ensemble of conformations. There-fore, an advanced semi-analytical model accounting for conformationaldiversity was built for the human growth hormone receptor (GHR) in ananodisc and refined against SAXS data. The thesis goes on to discussmethods for ensemble modelling of membrane proteins in nanodiscs.In the case of the GHR, a simulated ensemble of protein structures wasplaced in an analytical nanodisc model with pre-determined parame-ters. The averaged theoretical scattering from the ensemble was in goodagreement with the SAXS data. It is then shown how a novel methodbased on point-cloud models and Fast Debye Sums can be used to refinenanodisc parameters for an entire ensemble of protein structures in amore accurate and computationally efficient manner.Furthermore, this thesis delves into a comprehensive SAS study on theinteraction of α-Synuclein and negatively charged lipid structures. Thedata suggest that the amphipathic properties of the protein can induce abreak down of the lipid structures into smaller disc- or rod-like particles.Detailed model-free analysis as well analytical models were used tocharacterise the structural transformations.Finally, the focus is shifted away from SAS towards all atom simulationsof amyloid fibrils. Experimental Φ-values were employed to guide thesimulations to sample the transition state of amyloid fibril elongation.The crucial interactions sites between the incoming monomer and fibrilend were identified to help shed light on the mechanisms of fibrilformation.

M3 - Ph.D. thesis

BT - Computational modelling in structural biology

PB - Niels Bohr Institute, Faculty of Science, University of Copenhagen

ER -