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Fighting microbial infections with force fields: Evaluating conformational ensembles of intrinsically disordered proteins

Jephthah, Stephanie LU (2021)
Abstract
The main goal of this compilation thesis has been to investigate the conformational ensemble of the intrinsically disordered protein (IDP) histatin 5 by using a mixture of experimental and computational techniques including, but not limited to, small-angle X-ray scattering (SAXS), circular dichroism (CD) spectroscopy, atomistic molecular dynamics (MD) simulations, and coarse-grained Monte Carlo (MC) simulations. Histatin 5 is a peptide of particular interest for two reasons. Firstly, histatin 5 is naturally found in the saliva, where it helps protect the teeth enamel from abrasion and degradation by being part of the dental pellicle. Additionally, it also possesses candidacidal properties and thus acts as a first line of defense against... (More)
The main goal of this compilation thesis has been to investigate the conformational ensemble of the intrinsically disordered protein (IDP) histatin 5 by using a mixture of experimental and computational techniques including, but not limited to, small-angle X-ray scattering (SAXS), circular dichroism (CD) spectroscopy, atomistic molecular dynamics (MD) simulations, and coarse-grained Monte Carlo (MC) simulations. Histatin 5 is a peptide of particular interest for two reasons. Firstly, histatin 5 is naturally found in the saliva, where it helps protect the teeth enamel from abrasion and degradation by being part of the dental pellicle. Additionally, it also possesses candidacidal properties and thus acts as a first line of defense against fungal infections. Therefore, by studying the conformational ensemble histatin 5, we hope to aid in the development of saliva substitutes and new antimicrobial agents. Secondly, histatin 5 acts as a typical IDP that is relatively easy to work with in the lab, which makes it a perfect model IDP for evaluating different MD force fields and other simulation techniques.

In the first study of this thesis, simulations were used to investigate how the conformational ensemble of histatin 5 is affected by protonation of its histidine residues. The study also continues to investigate how this affects the interaction between histatin 5 and a negatively charged surface. This study is followed by an investigation of how histatin 5 is affected by temperature, and of how well modern simulation methods used for simulating IDPs can capture temperature-induced conformational changes. The results of this study led to another project, in which four different force fields were evaluated based on their ability to simulate histatin 5 and four other peptides that are known to possess polyproline II structure. In the final histatin 5 study, a shorter but more potent version of histatin 5 was conjugated to the polyamine spermidine, and was then investigated using a combination of experiments and simulation techniques. The aim of this study was to investigate if the increased candidacidal effect could be connected to the conformational properties of the histatin 5-spermidine conjugate. The final study of this thesis concerned a completely different peptide, namely the intrinsically disordered region of magnesium transporter A (MgtA) found in Escherichia coli. This study was mainly experimental, and the aim was to investigate how this intrinsically disordered region contributes to the function of MgtA, and the knowledge about how bacterial proteins work might help to develop new antibiotics in the future. (Less)
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author
supervisor
opponent
  • Senior Investigator Best, Robert B., National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, USA
organization
publishing date
type
Thesis
publication status
published
subject
keywords
molecular dynamics, force field, Monte Carlo, coarse-grained modeling, simulation, intrinsically disordered protein, histatin 5, small-angle x-ray scattering, circular dichroism, atomistic MD simulations, all-atom protein models
pages
214 pages
publisher
Printed in Sweden by Media-Tryck, Lund University
defense location
Kemicentrum, Sal A, Join via zoom: https://lu-se.zoom.us/j/67554051561
defense date
2021-05-28 13:00:00
ISBN
978-91-7422-806-9
978-91-7422-807-6
language
English
LU publication?
yes
id
b32d46e8-9033-4b67-8169-1a42e50bb25e
date added to LUP
2021-05-02 11:53:35
date last changed
2021-05-25 13:12:14
@phdthesis{b32d46e8-9033-4b67-8169-1a42e50bb25e,
  abstract     = {The main goal of this compilation thesis has been to investigate the conformational ensemble of the intrinsically disordered protein (IDP) histatin 5 by using a mixture of experimental and computational techniques including, but not limited to, small-angle X-ray scattering (SAXS), circular dichroism (CD) spectroscopy, atomistic molecular dynamics (MD) simulations, and coarse-grained Monte Carlo (MC) simulations. Histatin 5 is a peptide of particular interest for two reasons. Firstly, histatin 5 is naturally found in the saliva, where it helps protect the teeth enamel from abrasion and degradation by being part of the dental pellicle. Additionally, it also possesses candidacidal properties and thus acts as a first line of defense against fungal infections. Therefore, by studying the conformational ensemble histatin 5, we hope to aid in the development of saliva substitutes and new antimicrobial agents. Secondly, histatin 5 acts as a typical IDP that is relatively easy to work with in the lab, which makes it a perfect model IDP for evaluating different MD force fields and other simulation techniques. <br/><br/>In the first study of this thesis, simulations were used to investigate how the conformational ensemble of histatin 5 is affected by protonation of its histidine residues. The study also continues to investigate how this affects the interaction between histatin 5 and a negatively charged surface. This study is followed by an investigation of how histatin 5 is affected by temperature, and of how well modern simulation methods used for simulating IDPs can capture temperature-induced conformational changes. The results of this study led to another project, in which four different force fields were evaluated based on their ability to simulate histatin 5 and four other peptides that are known to possess polyproline II structure. In the final histatin 5 study, a shorter but more potent version of histatin 5 was conjugated to the polyamine spermidine, and was then investigated using a combination of experiments and simulation techniques. The aim of this study was to investigate if the increased candidacidal effect could be connected to the conformational properties of the histatin 5-spermidine conjugate. The final study of this thesis concerned a completely different peptide, namely the intrinsically disordered region of magnesium transporter A (MgtA) found in Escherichia coli. This study was mainly experimental, and the aim was to investigate how this intrinsically disordered region contributes to the function of MgtA, and the knowledge about how bacterial proteins work might help to develop new antibiotics in the future.},
  author       = {Jephthah, Stephanie},
  isbn         = {978-91-7422-806-9},
  language     = {eng},
  publisher    = {Printed in Sweden by Media-Tryck, Lund University},
  school       = {Lund University},
  title        = {Fighting microbial infections with force fields: Evaluating conformational ensembles of intrinsically disordered proteins},
  url          = {https://lup.lub.lu.se/search/ws/files/97341660/Stephanie_Jephthah_WEBB.pdf},
  year         = {2021},
}