Coarse-Grained Modelling of Protein Adsorption
(2020)- Abstract
- The adsorption of proteins is a very common phenomenon, happening almost always when a protein solution comes into contact with a solid. However, it is far from always clear what the results of adsorption will be in terms of adsorbed amount, protein orientation, and protein conformation. In this work, the adsorption of two proteins – histatin 5 and fibrinogen – has been studied using coarse-grained Monte Carlo simulations and, in case of histatin 5, ellipsometry. Histatin 5 is a short (24 residues long), cationic protein present in the saliva of higher primates. Its main function is that it kills the fungus Candida albicans. Fibrinogen is a 340 kDa rod-like protein that is abundant in the blood of vertebrates. It has an important role in... (More)
- The adsorption of proteins is a very common phenomenon, happening almost always when a protein solution comes into contact with a solid. However, it is far from always clear what the results of adsorption will be in terms of adsorbed amount, protein orientation, and protein conformation. In this work, the adsorption of two proteins – histatin 5 and fibrinogen – has been studied using coarse-grained Monte Carlo simulations and, in case of histatin 5, ellipsometry. Histatin 5 is a short (24 residues long), cationic protein present in the saliva of higher primates. Its main function is that it kills the fungus Candida albicans. Fibrinogen is a 340 kDa rod-like protein that is abundant in the blood of vertebrates. It has an important role in blood clotting. While histatin 5 is an intrinsically disordered protein, fibrinogen is mainly ordered with two ~400 amino acid residues long disordered appendages. This difference made us use two different models for the proteins– one for histatin 5 and the disordered fibrinogen fragments, and another for the main body of fibrinogen. Whereas the disordered proteins were modelled as beads on a necklace, the fibrinogen main body was modelled as a completely rigid body based on the crystal structure. The surface that the proteins were adsorbed on was a hydrophilic silica surface – modelled in the simulations as completely flat with (most of the time) a uniform, smeared charge.
The main results for histatin 5 are the following: (i) the adsorbed amount of histatin 5 changes with ionic strength – but the trends are different depending on pH, (ii) the electrostatic interactions between charged groups are not enough to account for the experimentally observed adsorption of histatin 5 to silica surfaces, (iii) the coarse-grained model used in these studies cannot explain the experimentally observed pH-dependence of the adsorbed amount as a function of ionic strength, (iv) a library of only a few structures (with different weights) represent well the conformational ensemble of histatin 5, and (v) simulations suggest that the amount of secondary structure motifs of histatin 5 increases somewhat upon adsorption.
The main results for fibrinogen are the following: (i) the disordered appendages make an important contribution to the adsorption free energy, (ii) the side of the end of the fibrinogen rod adsorbs in a similar manner regardless of surface curvature, meaning that the protein protrudes further into solution the higher the surface curvature, and (iii) we hypothesise that this difference in protrusion can account for the fact that adsorbed fibrinogen increases adhesion of the bacterium S. epidermidis on smooth surfaces while decreasing it on nanostructured surfaces. (Less) - Abstract (Swedish)
- The adsorption of proteins is a very common phenomenon, happening almost always when a protein solution comes into contact with a solid. However, it is far from always clear what the results of adsorption will be in terms of adsorbed amount, protein orientation, and protein conformation. In this work, the adsorption of two proteins – histatin 5 and fibrinogen – has been studied using coarse-grained Monte Carlo simulations and, in case of histatin 5, ellipsometry. Histatin 5 is a short (24 residues long), cationic protein present in the saliva of higher primates. Its main function is that it kills the fungus Candida albicans. Fibrinogen is a 340 kDa rod-like protein that is abundant in the blood of vertebrates. It has an important role in... (More)
- The adsorption of proteins is a very common phenomenon, happening almost always when a protein solution comes into contact with a solid. However, it is far from always clear what the results of adsorption will be in terms of adsorbed amount, protein orientation, and protein conformation. In this work, the adsorption of two proteins – histatin 5 and fibrinogen – has been studied using coarse-grained Monte Carlo simulations and, in case of histatin 5, ellipsometry. Histatin 5 is a short (24 residues long), cationic protein present in the saliva of higher primates. Its main function is that it kills the fungus Candida albicans. Fibrinogen is a 340 kDa rod-like protein that is abundant in the blood of vertebrates. It has an important role in blood clotting. While histatin 5 is an intrinsically disordered protein, fibrinogen is mainly ordered with two ~400 amino acid residues long disordered appendages. This difference made us use two different models for the proteins– one for histatin 5 and the disordered fibrinogen fragments, and another for the main body of fibrinogen. Whereas the disordered proteins were modelled as beads on a necklace, the fibrinogen main body was modelled as a completely rigid body based on the crystal structure. The surface that the proteins were adsorbed on was a hydrophilic silica surface – modelled in the simulations as completely flat with (most of the time) a uniform, smeared charge.
The main results for histatin 5 are the following: (i) the adsorbed amount of histatin 5 changes with ionic strength – but the trends are different depending on pH, (ii) the electrostatic interactions between charged groups are not enough to account for the experimentally observed adsorption of histatin 5 to silica surfaces, (iii) the coarse-grained model used in these studies cannot explain the experimentally observed pH-dependence of the adsorbed amount as a function of ionic strength, (iv) a library of only a few structures (with different weights) represent well the conformational ensemble of histatin 5, and (v) simulations suggest that the amount of secondary structure motifs of histatin 5 increases somewhat upon adsorption.
The main results for fibrinogen are the following: (i) the disordered appendages make an important contribution to the adsorption free energy, (ii) the side of the end of the fibrinogen rod adsorbs in a similar manner regardless of surface curvature, meaning that the protein protrudes further into solution the higher the surface curvature, and (iii) we hypothesise that this difference in protrusion can account for the fact that adsorbed fibrinogen increases adhesion of the bacterium S. epidermidis on smooth surfaces while decreasing it on nanostructured surfaces. (Less)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/de0c03f1-c3aa-4f7c-ad73-00a01f573e97
- author
- Hyltegren, Kristin LU
- supervisor
-
- Marie Skepö LU
- Per-Olof Widmark LU
- opponent
-
- Professor Bergenholtz, Johan, Göteborgs universitet, Göteborg
- organization
- publishing date
- 2020
- type
- Thesis
- publication status
- published
- subject
- keywords
- intrinsically disordered proteins, histatin 5, fibrinogen, protein adsorption, nanotopography, ellipsometry, Monte Carlo simulations, Coarse-grained modelling, charge regulation
- pages
- 176 pages
- publisher
- Lund University (Media-Tryck)
- defense location
- Lecture Hall B, Kemicentrum, Naturvetarvägen 14, Lund (Live streaming: https://youtu.be/84FtVyyOAcw)
- defense date
- 2020-04-24 09:15:00
- ISBN
- 978-91-7422-735-2
- 978-91-7422-734-5
- language
- English
- LU publication?
- yes
- id
- de0c03f1-c3aa-4f7c-ad73-00a01f573e97
- date added to LUP
- 2020-03-30 11:55:11
- date last changed
- 2021-04-27 11:06:38
@phdthesis{de0c03f1-c3aa-4f7c-ad73-00a01f573e97,
abstract = {{The adsorption of proteins is a very common phenomenon, happening almost always when a protein solution comes into contact with a solid. However, it is far from always clear what the results of adsorption will be in terms of adsorbed amount, protein orientation, and protein conformation. In this work, the adsorption of two proteins – histatin 5 and fibrinogen – has been studied using coarse-grained Monte Carlo simulations and, in case of histatin 5, ellipsometry. Histatin 5 is a short (24 residues long), cationic protein present in the saliva of higher primates. Its main function is that it kills the fungus Candida albicans. Fibrinogen is a 340 kDa rod-like protein that is abundant in the blood of vertebrates. It has an important role in blood clotting. While histatin 5 is an intrinsically disordered protein, fibrinogen is mainly ordered with two ~400 amino acid residues long disordered appendages. This difference made us use two different models for the proteins– one for histatin 5 and the disordered fibrinogen fragments, and another for the main body of fibrinogen. Whereas the disordered proteins were modelled as beads on a necklace, the fibrinogen main body was modelled as a completely rigid body based on the crystal structure. The surface that the proteins were adsorbed on was a hydrophilic silica surface – modelled in the simulations as completely flat with (most of the time) a uniform, smeared charge.<br/><br/>The main results for histatin 5 are the following: (i) the adsorbed amount of histatin 5 changes with ionic strength – but the trends are different depending on pH, (ii) the electrostatic interactions between charged groups are not enough to account for the experimentally observed adsorption of histatin 5 to silica surfaces, (iii) the coarse-grained model used in these studies cannot explain the experimentally observed pH-dependence of the adsorbed amount as a function of ionic strength, (iv) a library of only a few structures (with different weights) represent well the conformational ensemble of histatin 5, and (v) simulations suggest that the amount of secondary structure motifs of histatin 5 increases somewhat upon adsorption.<br/><br/>The main results for fibrinogen are the following: (i) the disordered appendages make an important contribution to the adsorption free energy, (ii) the side of the end of the fibrinogen rod adsorbs in a similar manner regardless of surface curvature, meaning that the protein protrudes further into solution the higher the surface curvature, and (iii) we hypothesise that this difference in protrusion can account for the fact that adsorbed fibrinogen increases adhesion of the bacterium S. epidermidis on smooth surfaces while decreasing it on nanostructured surfaces.}},
author = {{Hyltegren, Kristin}},
isbn = {{978-91-7422-735-2}},
keywords = {{intrinsically disordered proteins; histatin 5; fibrinogen; protein adsorption; nanotopography; ellipsometry; Monte Carlo simulations; Coarse-grained modelling; charge regulation}},
language = {{eng}},
publisher = {{Lund University (Media-Tryck)}},
school = {{Lund University}},
title = {{Coarse-Grained Modelling of Protein Adsorption}},
url = {{https://lup.lub.lu.se/search/files/77826116/Totalfil_med_omslag_Kristin_H.pdf}},
year = {{2020}},
}