Protein corona composition of poly(ethylene glycol)- and poly(phosphoester)-coated nanoparticles correlates strongly with the amino acid composition of the protein surface
Extensive molecular dynamics simulations reveal that the interactions between proteins and poly(ethylene glycol) (PEG) can be described in terms of the surface composition of the proteins. PEG molecules accumulate around non-polar residues while avoiding the polar ones. A solvent-accessible-surface-area model of protein adsorption accurately fits a large set of data on the composition of the protein corona of poly(ethylene glycol)- and poly(phosphoester)-coated nanoparticles recently obtained by label-free proteomic mass spectrometry.
Blood Proteins and Their Interactions with Nanoparticles Investigated Using Molecular Dynamics Simulations
Blood proteins play a fundamental role in determining the response of the organism to the injection of drugs or, more in general, of therapeutic preparations in the blood stream. Some of these proteins are responsible for mediating immune response and coagulation. Nanoparticles, which are being intensely investigated as possible drug nanocarriers, heavily interact with blood proteins and their ultimate fate is determined by these interactions. Here we report the results of molecular dynamics simulations of several blood proteins aimed to determining their possible behavior at the nanoparticle surface. On one hand we investigated the behavior of fibrinogen, a glycoprotein, which polymerizes …
The Internal Dynamics and Early Adsorption Stages of Fibrinogen Investigated by Molecular Dynamics Simulations
Fibrinogen, a plasma glycoprotein of vertebrates, plays an essential role in blood clotting by polymerizing into fibrin upon activation. It also contributes, upon adsorption on material surfaces, to determine their biocompatibility and has been implicated as a cause of thrombosis and inflammation at medical implants. Here we present the first fully atomistic simulations of the initial stages of the adsorption process of fibrinogen on mica and graphite surfaces. The simulations reveal a weak adsorption on mica that allows frequent desorption and reorientation events. This adsorption is driven by electrostatic interactions between the protein and the silicate surface as well as the counter io…
Data Reweighting in Metadynamics Simulations.
The data collected along a metadynamics simulation can be used to recover information about the underlying unbiased system by means of a reweighting procedure. Here, we analyze the behavior of several reweighting techniques in terms of the quality of the reconstruction of the underlying unbiased free energy landscape in the early stages of the simulation and propose a simple reweighting scheme that we relate to the other techniques. We then show that the free energy landscape reconstructed from reweighted data can be more accurate than the negative bias potential depending on the reweighting technique, the stage of the simulation, and the adoption of well-tempered or standard metadynamics. …
Effects of ligand binding on the mechanical properties of ankyrin repeat protein gankyrin.
Ankyrin repeat proteins are elastic materials that unfold and refold sequentially, repeat by repeat, under force. Herein we use atomistic molecular dynamics to compare the mechanical properties of the 7-ankyrin-repeat oncoprotein Gankyrin in isolation and in complex with its binding partner S6-C. We show that the bound S6-C greatly increases the resistance of Gankyrin to mechanical stress. The effect is specific to those repeats of Gankyrin directly in contact with S6-C, and the mechanical ‘hot spots’ of the interaction map to the same repeats as the thermodynamic hot spots. A consequence of stepwise nature of unfolding and the localized nature of ligand binding is that it impacts on all as…
Molecular Dynamics Simulations of the Initial Adsorption Stages of Fibrinogen on Mica and Graphite Surfaces.
Fibrinogen, a blood glycoprotein of vertebrates, plays an essential role in blood clotting by polymerizing into fibrin when activated. Upon adsorption on material surfaces, it also contributes to determine their biocompatibility and has been implicated in the onset of thrombosis and inflammation at medical implants. Here we present the first fully atomistic simulations of the initial stages of the adsorption process of fibrinogen on mica and graphite surfaces. The simulations reveal a weak adsorption on mica that allows frequent desorption and reorientation events. This adsorption is driven by electrostatic interactions between the protein and the silicate surface as well as the counterion …
Thermodynamics and Kinetics of the Interactions Between Proteins and Hydrophilic Polymers
Hydrophilic polymers are being investigated as possible coating agents for therapeutic nanoparticles because of their capacity to reduce immune response and increase circulation life time. The mechanism of action of these coatings is not well understood although it is clear that they unspecifically reduce the amount of proteins adsorbing on the nanoparticle surface coming in contact with biological fluids. Here we have investigated, using state-of-the-art atomistic molecular dynamics simulations, the equilibrium and kinetic properties of the interactions forming between human serum albumin, the most abundant protein in the blood stream, and two different and promising polymers poly(ethylene…
Interactions between proteins and poly(ethylene-glycol) investigated using molecular dynamics simulations
Poly(ethylene-glycol) (PEG) is a polymer used to coat therapeutic preparations, like drugs or drug nanocarriers, and improve their efficacy. This effect is probably due to a reduction of the interactions of the coated species with the host organism. Nevertheless, experiments show that PEGylated materials do interact with the surrounding biological milieu, and in particular with blood proteins. Here, we use atomistic molecular dynamics simulations to characterize the interactions between the polymer and several blood proteins. In these simulations, the proteins are immersed in a mixture of PEG and water molecules. We observe how PEG distributes around the protein surface and measure PEG-prot…
Simulations and Experiments in Protein Folding
The interplay between simulations and experiments of protein folding has largely contributed to the elucidation of many important aspects of the phenomenon. In this chapter, I briefly describe the experiments which provide information on the kinetics of the protein folding process, and help to characterize the folding transition state. Then, I show how to probe the kinetics of protein folding using molecular dynamics simulations, how to compare the simulations with the experiments and how to help and rationalize the latter, ultimately offering a molecular picture of the process. After the production of suitable molecular dynamics simulation data in the form of trajectories, the procedure in…
Potassium Triggers a Reversible Specific Stiffness Transition of Polyethylene Glycol
We use plasmon rulers made from two connected gold nanoparticles to monitor the conformation and stiffness of single PEG molecules and their response to cations. By observing equilibrium fluctuations of the interparticle distance, we obtain the spring constants or stiffness of the connecting single-molecule tether with pico-Newton sensitivity. We observe a transition of the PEG molecules’ extension and stiffness above about 1.2 mM K+ ion concentration which is specific to potassium ions. Molecular dynamics simulations reveal the formation of crown-like structures as the most likely molecular mechanism responsible for this specific effect.
Interactions Between Blood Proteins and Nanoparticles Investigated Using Molecular Dynamics Simulations
In the development of new therapeutic agents based on nanoparticles it is of fundamental importance understanding how these substances interact with the underlying biological milieu. Our research is focussed on simulating in silico these interactions using accurate atomistic models, and gather from these information general pictures and simplified models of the underlying phenomena. Here we report results about the interactions of blood proteins with promising hydrophilic polymers used for the coating of therapeutic nanoparticles, about the salt dependent behavior of one of these polymers (poly-(ethylene glycol)) and about the interactions of blood proteins with silica, one of the most used…
Targeting Cavity-Creating p53 Cancer Mutations with Small-Molecule Stabilizers: the Y220X Paradigm
We have previously shown that the thermolabile, cavity-creating p53 cancer mutant Y220C can be reactivated by small-molecule stabilizers. In our ongoing efforts to unearth druggable variants of the p53 mutome, we have now analyzed the effects of other cancer-associated mutations at codon 220 on the structure, stability, and dynamics of the p53 DNA-binding domain (DBD). We found that the oncogenic Y220H, Y220N, and Y220S mutations are also highly destabilizing, suggesting that they are largely unfolded under physiological conditions. A high-resolution crystal structure of the Y220S mutant DBD revealed a mutation-induced surface crevice similar to that of Y220C, whereas the corresponding pock…
Poly-sarcosine and poly(ethylene-glycol) interactions with proteins investigated using molecular dynamics simulations
Nanoparticles coated with hydrophilic polymers often show a reduction in unspecific interactions with the biological environment, which improves their biocompatibility. The molecular determinants of this reduction are not very well understood yet, and their knowledge may help improving nanoparticle design. Here we address, using molecular dynamics simulations, the interactions of human serum albumin, the most abundant serum protein, with two promising hydrophilic polymers used for the coating of therapeutic nanoparticles, poly(ethylene-glycol) and poly-sarcosine. By simulating the protein immersed in a polymer-water mixture, we show that the two polymers have a very similar affinity for the…
The Internal Dynamics of Fibrinogen and Its Implications for Coagulation and Adsorption
Fibrinogen is a serum multi-chain protein which, when activated, aggregates to form fibrin, one of the main components of a blood clot. Fibrinolysis controls blood clot dissolution through the action of the enzyme plasmin, which cleaves fibrin at specific locations. Although the main biochemical factors involved in fibrin formation and lysis have been identified, a clear mechanistic picture of how these processes take place is not available yet. This picture would be instrumental, for example, for the design of improved thrombolytic or anti-haemorrhagic strategies, as well as, materials with improved biocompatibility. Here, we present extensive molecular dynamics simulations of fibrinogen w…