Molecular dynamics simulations of β2-microglobulin interaction with hydrophobic surfaces

2017 ◽  
Vol 13 (12) ◽  
pp. 2625-2637 ◽  
Author(s):  
Cedrix J. Dongmo Foumthuim ◽  
Alessandra Corazza ◽  
Gennaro Esposito ◽  
Federico Fogolari
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Hydrophobic Surfaces ◽  
Β2 Microglobulin ◽  
Partial Unfolding ◽  
Dynamics Simulations

27 copies of β2-microglobulin interacting with a cubic hydrophobic box (not shown for the sake of clarity). The proteins readily adsorb and undergo partial unfolding.

scholarly journals Asymmetric Behavior of Thymidylate Synthase Dimer Subunits in Denaturating Solvent Observed with Molecular Dynamics

2015 ◽  
Vol 2015 ◽  
pp. 1-9
Author(s):  
Filip Leonarski ◽  
Monika Świniarska ◽  
Andrzej Leś
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Thymidylate Synthase ◽  
Guanidinium Chloride ◽  
Guanidinium Hydrochloride ◽  
Asymmetric Behavior ◽  
Partial Unfolding ◽  
Dynamics Simulations

A molecular dynamics simulations of the thymidylate synthase denaturation in chaotrope solvents (urea, guanidinium hydrochloride) were performed on 600 ns timescale. It appeared that this dimeric enzyme undergoes partial unfolding asymmetrically. It was shown also that urea is a better denaturant in the MD condition, as compared to guanidinium chloride. The unfolding occurs first at the external helices (AA 88-118) and follows by the AA 188-200 region. The present results correspond to the suggested in the literature activity of thymidylate synthase through a half-the-site mechanism.

scholarly journals Low-Resolution Models for the Interaction Dynamics of Coated Gold Nanoparticles with β2-microglobulin

2019 ◽  
Vol 20 (16) ◽  
pp. 3866 ◽  
Author(s):  
Giorgia Brancolini ◽  
Hender Lopez ◽  
Stefano Corni ◽  
Valentina Tozzini
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Computational Cost ◽  
Coarse Grained ◽  
Implicit Solvent ◽  
Low Resolution ◽  
Β2 Microglobulin ◽  
Coating Roughness ◽  
Gold Nps ◽  
Dynamics Simulations

A large number of low-resolution models have been proposed in the last decades to reduce the computational cost of molecular dynamics simulations for bio-nano systems, such as those involving the interactions of proteins with functionalized nanoparticles (NPs). For the proteins, “minimalist” models at the one-bead-per residue (Cα-based) level and with implicit solvent are well established. For the gold NPs, widely explored for biotechnological applications, mesoscale (MS) models treating the NP core with a single spheroidal object are commonly proposed. In this representation, the surface details (coating, roughness, etc.) are lost. These, however, and the specificity of the functionalization, have been shown to have fundamental roles for the interaction with proteins. We presented a mixed-resolution coarse-grained (CG) model for gold NPs in which the surface chemistry is reintroduced as superficial smaller beads. We compared molecular dynamics simulations of the amyloid β2-microglobulin represented at the minimalist level interacting with NPs represented with this model or at the MS level. Our finding highlights the importance of describing the surface of the NP at a finer level as the chemical-physical properties of the surface of the NP are crucial to correctly understand the protein-nanoparticle association.

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