Abstract:The crowded environment of biological systems such as
the interior
of living cells is occupied by macromolecules with a broad size distribution.
This situation of polydispersity might influence the dependence of
the diffusive dynamics of a given tracer macromolecule in a monodisperse
solution on its hydrodynamic size and on the volume fraction. The
resulting size dependence of diffusive transport crucially influences
the function of a living cell. Here, we investigate a simplified model
system consisting of tw… Show more
“…It was shown experimentally and by modelling that the diffusion of large proteins at interfaces is reduced compared to small ones. This mechanism could account for a longer time of residence and hence a higher number of protein complexes at the A/L interface, where they are subject to compression and elongation forces favouring further destabilization and aggregation 44 .…”
Protein aggregation in biotherapeutics can reduce their activity and effectiveness. It may also promote immune reactions responsible for severe adverse effects. The impact of plastic materials on protein destabilization is not totally understood. Here, we propose to deconvolve the effects of material surface, air/liquid interface, and agitation to decipher their respective role in protein destabilization and aggregation. We analyzed the effect of polypropylene, TEFLON, glass and LOBIND surfaces on the stability of purified proteins (bovine serum albumin, hemoglobin and α-synuclein) and on a cell extract composed of 6000 soluble proteins during agitation (P = 0.1–1.2 W/kg). Proteomic analysis revealed that chaperonins, intrinsically disordered proteins and ribosomes were more sensitive to the combined effects of material surfaces and agitation while small metabolic oligomers could be protected in the same conditions. Protein loss observations coupled to Raman microscopy, dynamic light scattering and proteomic allowed us to propose a mechanistic model of protein destabilization by plastics. Our results suggest that protein loss is not primarily due to the nucleation of small aggregates in solution, but to the destabilization of proteins exposed to material surfaces and their subsequent aggregation at the sheared air/liquid interface, an effect that cannot be prevented by using LOBIND tubes. A guidance can be established on how to minimize these adverse effects. Remove one of the components of this combined stress - material, air (even partially), or agitation - and proteins will be preserved.
“…It was shown experimentally and by modelling that the diffusion of large proteins at interfaces is reduced compared to small ones. This mechanism could account for a longer time of residence and hence a higher number of protein complexes at the A/L interface, where they are subject to compression and elongation forces favouring further destabilization and aggregation 44 .…”
Protein aggregation in biotherapeutics can reduce their activity and effectiveness. It may also promote immune reactions responsible for severe adverse effects. The impact of plastic materials on protein destabilization is not totally understood. Here, we propose to deconvolve the effects of material surface, air/liquid interface, and agitation to decipher their respective role in protein destabilization and aggregation. We analyzed the effect of polypropylene, TEFLON, glass and LOBIND surfaces on the stability of purified proteins (bovine serum albumin, hemoglobin and α-synuclein) and on a cell extract composed of 6000 soluble proteins during agitation (P = 0.1–1.2 W/kg). Proteomic analysis revealed that chaperonins, intrinsically disordered proteins and ribosomes were more sensitive to the combined effects of material surfaces and agitation while small metabolic oligomers could be protected in the same conditions. Protein loss observations coupled to Raman microscopy, dynamic light scattering and proteomic allowed us to propose a mechanistic model of protein destabilization by plastics. Our results suggest that protein loss is not primarily due to the nucleation of small aggregates in solution, but to the destabilization of proteins exposed to material surfaces and their subsequent aggregation at the sheared air/liquid interface, an effect that cannot be prevented by using LOBIND tubes. A guidance can be established on how to minimize these adverse effects. Remove one of the components of this combined stress - material, air (even partially), or agitation - and proteins will be preserved.
“…Recent work has investigated diffusion in a binary mixture of BSA and IgG, with an interpretation in terms of a binary hard sphere system being quite sensible. 86 An explicit investigation using the coarse-grained models could provide us with more insight into these findings. In addition, our CG model for BSA together with the established CG model for IGG opens opportunities for more realistic simulations of dynamical processes in solutions modeling blood as BSA can be used as substitute for human serum albumin (HSA), which is the most abundant protein in blood.…”
We construct a coarse-grained, structure-based, low-resolution, 6-bead flexible model of bovine serum albumin (BSA, PDB: 4F5S), which is a popular example of a globular protein in biophysical research. The model is obtained via direct Boltzmann inversion using all-atom simulations of a single molecule, and its particular form is selected from a large pool of 6-bead coarse-grained models using two suitable metrics that quantify the agreement in the distribution of collective coordinates between all-atom and coarse-grained Brownian dynamics simulations of solutions in the dilute limit. For immunoglobulin G (IgG), a similar structure-based 12-bead model has been introduced in the literature [Chaudhri et al., J. Phys. Chem. B 116, 8045 (2012)] and is employed here to compare findings for the compact BSA molecule and the more anisotropic IgG molecule. We define several modified coarse-grained models of BSA and IgG, which differ in their internal constraints and thus account for a variation of flexibility. We study denser solutions of the coarse-grained models with purely repulsive molecules (achievable by suitable salt conditions) and address the effect of packing and flexibility on dynamic and static behavior. Translational and rotational self-diffusivity is enhanced for more elastic models. Finally, we discuss a number of effective sphere sizes for the BSA molecule, which can be defined from its static and dynamic properties. Here, it is found that the effective sphere diameters lie between 4.9 and 6.1 nm, corresponding to a relative spread of about ±10% around a mean of 5.5 nm.
“…Since the signal is typically dominated by incoherent scattering, the q-dependence mainly influences the different dynamic features. While this approach includes the separation of the (apparent) global diffusion from internal diffusive processes [8], the same procedure can be applied to separate the scattering signal of the crowders from the one of the protein of interest [23], the contributions of monomers and crystals [30], the contributions of two different proteins [31], or to distinguish the scattering signal of proteins from the one coming from the detergent used for purification [32].…”
With continuously improving signal-to-noise ratios, a statistically sound analysis of quasi-elastic neutron scattering (QENS) spectra requires to fit increasingly complex models which poses several challenges. Simultaneous fits of the spectra for all recorded values of the momentum transfer become a standard approach. Spectrometers at spallation sources can have a complicated non-Gaussian resolution function which has to be described most accurately. At the same time, to speed up the fitting, an analytical convolution with this resolution function is of interest. Here, we discuss basic concepts to efficient approaches for fits of QENS spectra based on standard MATLAB and Python fit algorithms. We illustrate the fits with example data from IN16B, BASIS, and BATS.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.