Molecular Dynamics Simulation of Protein Adsorption at Fluid Interfaces: A Comparison of All-Atom and Coarse-Grained Models

Euston, Stephen R.

doi:10.1021/bm100857k

Cited by 27 publications

(26 citation statements)

References 41 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…where k B is the Boltzmann constant, R is the chosen molecular descriptor which in our case is the end-to-end distance distribution (the radius of gyration could also been used 27 …”

Section: B Calculated Desorption Free Energymentioning

confidence: 99%

Thermodynamics of linear and star polymers at fluid interfaces

2015

View full text Add to dashboard Cite

Performing molecular dynamics simulations on model systems we study the structural changes and thermodynamic stability of polymers of varying topology (linear and starshaped) at interface between two liquids. We find that homopolymers are attracted to the interface in both good and poor solvent conditions showing that they are surface active molecules even though not amphiphilic. In most cases changing polymer topology had only a minor effect on the desorption free energy. A noticeable dependence on polymer topology is only seen for relatively high molecular weight polymers at interface between two good solvents. Examining separately the enthalpic and entropic components of the desorption free energy suggests that its largest contribution is the decrease in the interfacial free energy caused by the adsorption of the polymer at the interface. Finally we propose a simple method to qualitatively predict the trend of the interfacial free energy as a function of the polymer molecular weight.2

show abstract

“…where k B is the Boltzmann constant, R is the chosen molecular descriptor which in our case is the end-to-end distance distribution (the radius of gyration could also been used 27 …”

Section: B Calculated Desorption Free Energymentioning

confidence: 99%

Thermodynamics of linear and star polymers at fluid interfaces

2015

View full text Add to dashboard Cite

show abstract

“…The purpose this annealing process is to simulate the experimental heat treatment process in finally reaching the static state of the system under investigation. It is widely used in predicting protein adhesion affinities [26,36]. The starting temperatures in the annealing processes in the present study were set to 300 K and the mid-cycle temperature was set to 320 K. This is the temperature range that has been found appropriate to use for the physiological functionality of biomolecules.…”

Section: Methodsmentioning

confidence: 99%

Effect by Diamond Surface Modification on Biomolecular Adhesion

Tian

Larsson

2019

Materials

View full text Add to dashboard Cite

Diamond, as material, show very attractive properties. They include superior electronic properties (when doped), chemical inertness, controllable surface termination, and biocompatibility. It is thus clear that surface termination is very important for those applications where the implant material is based on diamond. The present theoretical work has focused on the effect of diamond surface termination, in combination with type of surface plane, on the adhesion of important biomolecules for vascularization and bone regeneration. These biomolecules include Arginine-Glycine-Aspartic acid (RGD), Chitosan, Heparin, Bone Morphogenetic Protein 2 (BMP2), Angiopoietin 1 (AGP1), Fibronectin and Vascular Endothelial Growth Factor (VEGF). The various surface planes are diamond diamond (100)-2x1 and (111). The theoretical results show that the non-covalent binding of these biomolecules is in proportion with their molecular weights. Moreover, three groups of biomolecules were observed for both types of surface planes. The most strongly binding biomolecule was the BMP2 molecule. The smaller polypeptides (RGD, Chitosan and Heparin) formed a less strongly binding group. Finally, the biomolecules VEGF, Fibronectin and Angiopoietin showed bond strengths numerically in between the other two groups (thereby forming a third group). Moreover, the (111) surface was generally observed to display a stronger bonding of the biomolecules, as compared with the (100)-2x1 surface.

show abstract

“…Due to its ability to model larger systems and its inclusion in the commonly used Gromacs package, the Martini model has been extensively applied to proteins, in particular to membrane-protein systems [51]. Direct comparison between CG and atomistic models shows that these can give qualitatively similar results for proteins at interfaces and surfaces, but, due to the loss of resolution, they can differ in fine detail, such as the position of proteins relative to an oil-water interface [52]. A similar model, the Shinoda-DeVane-Klein model [53,54], has also been developed and extended to investigate proteins.…”

Section: Molecular Simulationmentioning

confidence: 99%

Molecular Dynamics Simulation of Protein Biosurfactants

Cheung

Samantray

2018

Colloids and Interfaces

View full text Add to dashboard Cite

Surfaces and interfaces are ubiquitous in nature and are involved in many biological processes. Due to this, natural organisms have evolved a number of methods to control interfacial and surface properties. Many of these methods involve the use of specialised protein biosurfactants, which due to the competing demands of high surface activity, biocompatibility, and low solution aggregation may take structures that differ from the traditional head–tail structure of small molecule surfactants. As well as their biological functions, these proteins have also attracted interest for industrial applications, in areas including food technology, surface modification, and drug delivery. To understand the biological functions and technological applications of protein biosurfactants, it is necessary to have a molecular level description of their behaviour, in particular at surfaces and interfaces, for which molecular simulation is well suited to investigate. In this review, we will give an overview of simulation studies of a number of examples of protein biosurfactants (hydrophobins, surfactin, and ranaspumin). We will also outline some of the key challenges and future directions for molecular simulation in the investigation of protein biosurfactants and how this can help guide future developments.

show abstract

Molecular Dynamics Simulation of Protein Adsorption at Fluid Interfaces: A Comparison of All-Atom and Coarse-Grained Models

Cited by 27 publications

References 41 publications

Thermodynamics of linear and star polymers at fluid interfaces

Thermodynamics of linear and star polymers at fluid interfaces

Effect by Diamond Surface Modification on Biomolecular Adhesion

Molecular Dynamics Simulation of Protein Biosurfactants

Contact Info

Product

Resources

About