Modeling and simulation of intrinsically disordered proteins

Joao Henriques

Research output: ThesisDoctoral Thesis (compilation)

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Abstract

This work is primarily about the development, validation and application of computer simulation models for intrinsically disordered proteins, both in solution and in the presence of uniformly charged, ideal surfaces. The models in question are either coarse-grained or atomistic in nature, and their applications are dependent on the specific purpose of each study. Both, Metropolis Monte Carlo and molecular dynamics simulations were employed to execute them.
In regard to the coarse-grained models, it was found that a simple physical model can be used to mimic the properties of flexible proteins, helping to understand how and why these proteins adsorb to surfaces under certain conditions. The same model later shown that two disordered proteins from different sources (saliva and milk) possess similar structural and thermodynamic properties in solution and when adsorbed to surfaces, thus being hypothesized that it may be possible to use one of them as a substitute for the other under a pharmaceutical context.
After a first indication that the atomistic models used until recently for the simulation of well-folded proteins may not be applicable to their disordered counterparts, it was then confirmed - by evaluating several such models against experimental evidence - that these models do indeed produce overly collapsed IDP conformational ensembles. New models, favoring protein–water over protein–protein interactions, were then shown to effectively produce more extended conformations, which are in much better agreement with each other and with experimental evidence. One of the new atomistic models was then used to perform the structural characterization of a disordered peptide conjugated to a small molecule, which has been shown to possess promising therapeutical applications. The value of computer simulations is well illustrated in this study, as the insight obtainable from experiment was limited and it was only through the analysis of the simulations that a possible link between the average conjugate structure and its increased antifungal activity is established.
Original languageEnglish
QualificationDoctor
Awarding Institution
  • Theoretical Chemistry
Supervisors/Advisors
  • Skepö, Marie, Supervisor
  • Lund, Mikael, Supervisor
Award date2016 Dec 9
Place of PublicationLund
Publisher
Print ISBNs978-91-7422-489-4
Electronic ISBNs978-91-7422-490-0
Publication statusPublished - 2016 Nov

Bibliographical note

Defence details
Date: 2016-12-09
Time: 13:00
Place: Center for chemistry and chemical engineering, lecture hall B, Naturvetarvägen 14, Lund
External reviewer
Name: Best, Robert B.
Title: Ph.D.
Affiliation: National Institutes of Health, Bethesda, MD, USA
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Subject classification (UKÄ)

  • Theoretical Chemistry

Keywords

  • Intrinsically disordered proteins
  • Coarse-grained models
  • Atomistic models
  • Metropolis Monte Carlo simulations
  • Molecular dynamics simulations
  • Sampling
  • Conformational analysis
  • Charge regulation
  • Surface adsorption

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